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Torabi M, Yasami-Khiabani S, Sardari S, Golkar M, Pérez-Sánchez H, Ghasemi F. Identification of new potential candidates to inhibit EGF via machine learning algorithm. Eur J Pharmacol 2024; 963:176176. [PMID: 38000720 DOI: 10.1016/j.ejphar.2023.176176] [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: 06/19/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
One of the cost-effective alternative methods to find new inhibitors has been the repositioning approach of existing drugs. The advantage of computational drug repositioning method is saving time and cost to remove the pre-clinical step and accelerate the drug discovery process. Hence, an ensemble computational-experimental approach, consisting of three steps, a machine learning model, simulation of drug-target interaction and experimental characterization, was developed. The machine learning type used here was a different tree classification method, which is one of the best randomize machine learning model to identify potential inhibitors from weak inhibitors. This model was trained more than one-hundred times, and forty top trained models were extracted for the drug repositioning step. The machine learning step aimed to discover the approved drugs with the highest possible success rate in the experimental step. Therefore, among all the identified molecules with more than 0.9 probability in more than 70% of the models, nine compounds, were selected. Besides, out of the nine chosen drugs, seven compounds have been confirmed to inhibit EGF in the published articles since 2019. Hence, two identified compounds, in addition to gefitinib, as a positive control, five weak-inhibitors and one neutral, were considered via molecular docking study. Finally, the eight proposed drugs, including gefitinib, were investigated using MTT assay and In-Cell ELISA to characterize the drugs' effect on A431 cell growth and EGF-signaling. From our experiments, we could conclude that salicylic acid and piperazine could play an EGF-inhibitor role like gefitinib.
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Affiliation(s)
- Mohammadreza Torabi
- Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Iran
| | | | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Golkar
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Reseach Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Murcia, E30107, Spain
| | - Fahimeh Ghasemi
- Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Iran; Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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2
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [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: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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3
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Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, Wyczalkowski MA, Lu RJH, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo CK, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 2023; 623:432-441. [PMID: 37914932 PMCID: PMC10632147 DOI: 10.1038/s41586-023-06682-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1-4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial-mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Alla Karpova
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | | | - Siqi Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yize Li
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Austin N Southard-Smith
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael D Iglesia
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Michael C Wendl
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Jingxian Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Song Cao
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Xiuting Liu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Andrew Shinkle
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - John M Herndon
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Kazuhito Sato
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Omar M Ibrahim
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Sara E Chasnoff
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Jason M Held
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Russell Pachynski
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Julie K Schwarz
- Department of Radiation Oncology, Washington University in St Louis, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Albert H Kim
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- Department of Neurological Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Ravi Vij
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - John F DiPersio
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Sidharth V Puram
- Department of Otolaryngology-Head & Neck Surgery, Washington University in St Louis, St Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Katherine C Fuh
- Department of Obstetrics and Gynecology, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics and Gynecology, Washington University in St Louis, St Louis, MO, USA
| | - David G DeNardo
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
| | - Ryan C Fields
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Feng Chen
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Li Ding
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University in St Louis, St Louis, MO, USA.
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Ma XL, Nie YY, Xie SH, Zheng H, Tong Y, Wang YC, Yan TQ, Meng X, Cao JZ, Tang WG, Guo L, Lu RQ. ASAP2 interrupts c-MET-CIN85 interaction to sustain HGF/c-MET-induced malignant potentials in hepatocellular carcinoma. Exp Hematol Oncol 2023; 12:38. [PMID: 37061723 PMCID: PMC10105420 DOI: 10.1186/s40164-023-00393-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/27/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Sustained activation of hepatocyte growth factor (HGF)/c-MET signaling is a major driver of hepatocellular carcinoma (HCC) progression, but underlying mechanism is unclear. ArfGAP With SH3 Domain, Ankyrin Repeat And PH Domain 2 (ASAP2) can reportedly activate GTPases and promote receptor tyrosine kinase signaling. However, the exact role of ASAP2 in HCC, especially for c-MET activation, also remains elusive. METHODS ASAP2 expression levels in HCC tissues and cells were quantified using qRT-PCR, western blot (WB) analysis, and immunohistochemistry staining. Cell counting kit-8 (CCK-8) and colony formation assays were performed to evaluate cell proliferation rates. Flow cytometry assays were conducted to assess apoptosis rates. Wound healing and Transwell assays were performed to determine cell migration and invasion capacities. Epithelial-mesenchymal transition (EMT)-related marker expression levels were also examined. Subcutaneous implantation and tail vein injection models were applied for in vivo growth and metastasis evaluations, respectively. Bioinformatics analyses of The Cancer Genome Atlas and STRING datasets were performed to explore ASAP2 downstream signaling. Co-immunoprecipitation and Cycloheximide chasing experiments were performed to assess protein-protein interactions and protein half-life, respectively. RESULTS ASAP2 had higher expression levels in HCC tissues than in normal liver, and also predicted poor prognosis. Knocking down ASAP2 significantly impaired cell proliferation, migration, and invasion capacities, but promoted apoptosis in HCC cells in vitro. However, overexpression of ASAP2 achieved the opposite effects. In vivo experiments confirmed that ASAP2 could promote HCC cell growth and facilitate lung metastasis. Interestingly, ASAP2 was essential for triggering EMT. Gene Set Enrichment Analysis demonstrated that c-MET signaling was greatly enriched in ASAP2-high HCC cases. Additionally, c-MET signaling activity was significantly decreased following ASAP knockdown, evidenced by reduced c-MET, p-AKT, and p-ERK1/2 protein levels. Importantly, ASAP2 knockdown effectively attenuated HGF/c-MET signaling-induced malignant phenotypes. c-MET and ASAP2 expression levels were positively correlated in our cohort. Mechanistically, ASAP2 can directly bind to CIN85, thereby disrupting its interaction with c-MET, and can thus antagonize CIN85-induced c-MET internalization and lysosome-mediated degradation. Notably, knocking down CIN85 can rescue the observed inhibitory effects caused by ASAP2 knockdown. CONCLUSIONS This study highlights the importance of ASAP2 in sustaining c-MET signaling, which can facilitate HCC progression.
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Affiliation(s)
- Xiao-Lu Ma
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Yan-Yan Nie
- Shanghai Lab. Animal Research Center, Shanghai, 201203, China
| | - Su-Hong Xie
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Hui Zheng
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Ying Tong
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Yan-Chun Wang
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Tian-Qing Yan
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Xin Meng
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Jia-Zhen Cao
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China
| | - Wei-Guo Tang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Department of Hepatobiliary and Pancreatic Surgery, Minhang Hospital, Fudan University, Shanghai, 201100, China
| | - Lin Guo
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China.
| | - Ren-Quan Lu
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 200032, China.
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Xu Z, Wang Y, Xu J, Ang X, Ge N, Xu M, Pei C. Identify AGAP2 as prognostic biomarker in clear cell renal cell carcinoma based on bioinformatics and IHC staining. Heliyon 2023; 9:e13543. [PMID: 36846683 PMCID: PMC9947311 DOI: 10.1016/j.heliyon.2023.e13543] [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: 07/02/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Background Arf GTPase-activating proteins are aberrantly expressed in a variety of tumors, but their role in clear cell renal cell carcinoma (ccRCC) was unclear. Exploring the biological role of Arf GAP with GTP binding protein like domain, Ankyrin repeat and PH domain 2 (AGAP2) in ccRCC could improve our understanding on the aggressiveness and immune relevance of ccRCC. Methods The expression of AGAP2 was analyzed based on the Cancer Genome Atlas (TCGA) database and verified in ccRCC samples using immunohistochemistry. The association between AGAP2 and clinical cancer stages was explored by TCGA dataset and UALCAN. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to analyze the biological functions of AGAP2-related genes. Moreover, the relationship between AGAP2 and immune cell infiltration was investigated with TIME and TCGA dataset. Results Compared to normal tissues, AGAP2 was upregulated in ccRCC tissues. Higher expression of AGAP2 was associated with clinical cancer stages, TNM stages, pathologic stages, and status. Prognostic analysis on AGAP2 showed that AGAP2 overexpression was associated with KIRC overall survival (OS) reduction (P = 0.019). However, higher expression of AGAP2 may improve the OS of CESC (P = 0.002), THYM (P = 0.006) and UCEC (P = 0.049). GO and KEGG analysis showed that AGAP2-related genes was related to T cell activation, immune activity and PD-L1 expression and PD-1 checkpoint pathway. Furthermore, our study showed that AGAP2 were significantly associated with T cells, Cytotoxic cells, Treg, Th1 cells, CD8 T cells, T helper cells. And AGAP2 expression level affected the abundance of immune cells infiltration. The infiltrating level of immune cells was different between the AGAP2 high-expression and low-expression groups. Conclusion The expression of AGAP2 in ccRCC was higher than that in normal kidney tissues. It was significantly associated with clinical stage, poor prognosis, and immune cell infiltration. Therefore, AGAP2 may become an important component for ccRCC patients who receive precision cancer therapy and may be a promising prognostic biomarker.
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Affiliation(s)
- Zekun Xu
- Department of Urology Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | | | - Jiangnan Xu
- Department of Urology Surgery, The First People's Hospital of Yancheng, China
| | - Xiaojie Ang
- Department of Urology Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Nianxin Ge
- Department of Urology Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Min Xu
- Department of Urology Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China,Corresponding author.
| | - Changsong Pei
- Department of Urology Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China,Corresponding author.
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How I Treat TP53-Mutated Acute Myeloid Leukemia and Myelodysplastic Syndromes. Cancers (Basel) 2022; 14:cancers14184519. [PMID: 36139679 PMCID: PMC9496940 DOI: 10.3390/cancers14184519] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 12/19/2022] Open
Abstract
TP53-mutated acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are among the myeloid malignancies with the poorest prognosis. In this review, we analyze the prognosis of these two diseases, focussing particularly on the extent of the mono or biallelic mutation status of TP53 mutation, which is largely correlated with cytogenetic complexity. We discuss the possible/potential improvement in outcome based on recent results obtained with new drugs (especially eprenetapopt and magrolimab). We also focus on the impact of allogeneic hematopoietic stem cell transplantation (aHSCT) including post aHSCT treatment.
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Zhang D, Lindstrom A, Kim EJ, Hwang CI, Hall ML, Lin TY, Li Y. SEMA3C Supports Pancreatic Cancer Progression by Regulating the Autophagy Process and Tumor Immune Microenvironment. Front Oncol 2022; 12:890154. [PMID: 35785187 PMCID: PMC9243227 DOI: 10.3389/fonc.2022.890154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/16/2022] [Indexed: 01/26/2023] Open
Abstract
To date, driver genes for pancreatic cancer treatment are difficult to pursue therapeutically. Targeting mutated KRAS, the most renowned driver gene in pancreatic cancer, is an active area of study. We discovered a gene named SEMA3C was highly expressed in pancreatic cancer cell lines and patients with a G12D mutation in KRAS. High expression of SEMA3C in patients was significantly associated with the decreased survival of pancreatic cancer patients based on the TCGA database. In pancreatic cancer cells, SEMA3C knockdown or inhibition exhibited growth/colony inhibition and cell cycle arrest. In addition, SEMA3C inhibition sensitized KRAS or MEK1/2 inhibition in pancreatic cancer cells. Overexpression of SEMA3C resulted in the induction of autophagy, whereas depletion of SEMA3C compromised induction of autophagy. SEMA3C modified the PD-L1 expression in tumor and immune cells and is correlated with the M2-like macrophage marker ARG1/CD163 expression, which could reshape the tumor microenvironment. Inhibition of SEMA3C decreased tumor formation in the xenograft model in vivo. Taken together, our data suggest that SEMA3C plays a substantial role in promoting cancer cell survival by regulating the autophagy process and impacting the tumor environment immune response. SEMA3C can be used as a novel target or marker with therapeutic or diagnostic potential in pancreatic cancer especially in tumors harboring the specific KRAS G12D mutation.
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Affiliation(s)
- Dalin Zhang
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, United States
| | - Aaron Lindstrom
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, United States
| | - Edward J Kim
- Division of Hematology and Oncology, Department of Internal Medicine, University of California, Davis, Sacramento, CA, United States
| | - Chang-il Hwang
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Madison Lee Hall
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Tzu-Yin Lin
- Division of Hematology and Oncology, Department of Internal Medicine, University of California, Davis, Sacramento, CA, United States
| | - Yuanpei Li
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, United States,*Correspondence: Yuanpei Li,
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Nephrotoxicity evaluation and proteomic analysis in kidneys of rats exposed to thioacetamide. Sci Rep 2022; 12:6837. [PMID: 35477741 PMCID: PMC9046159 DOI: 10.1038/s41598-022-11011-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
Abstract
Thioacetamide (TAA) was administered orally at 0, 10, and 30 mg/kg body weight (BW) daily to Sprague–Dawley rats aged 6–7 weeks for 28 consecutive days. Nephrotoxicity and proteomics were evaluated in the kidneys of rats exposed to TAA. The BW decreased, however, the relative kidneys weight increased. No significant histopathologic abnormalities were found in the kidneys. The numbers of monocytes and platelets were significantly increased. However, the mean corpuscular volume and hematocrit values were decreased significantly in rats exposed to 30 mg/kg BW TAA. The expression levels of Kim-1 and NGAL were increased 4 to 5-fold in the kidneys, resulting in significant nephrotoxicity. Proteomic analysis was conducted and a total of 5221 proteins spots were resolved. Of these, 3 and 21 protein spots were up- and downregulated, respectively. The validation of seven proteins was performed by Western blot analysis. The expression level of ASAP2 was significantly upregulated, whereas RGS14, MAP7Dl, IL-3Rα, Tmod1, NQO2, and MUP were reduced. Sixteen isoforms of MUP were found by the 2DE immunoblot assay and were significantly downregulated with increasing exposure to TAA. MUP isoforms were compared in the liver, kidneys, and urine of untreated rats and a total of 43 isoforms were found.
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9
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Pham TH, Qiu Y, Liu J, Zimmer S, O’Neill E, Xie L, Zhang P. Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. PATTERNS 2022; 3:100441. [PMID: 35465231 PMCID: PMC9023899 DOI: 10.1016/j.patter.2022.100441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 01/12/2022] [Indexed: 12/18/2022]
Abstract
Chemical-induced gene expression profiles provide critical information of chemicals in a biological system, thus offering new opportunities for drug discovery. Despite their success, large-scale analysis leveraging gene expressions is limited by time and cost. Although several methods for predicting gene expressions were proposed, they only focused on imputation and classification settings, which have limited applications to real-world scenarios of drug discovery. Therefore, a chemical-induced gene expression ranking (CIGER) framework is proposed to target a more realistic but more challenging setting in which overall rankings in gene expression profiles induced by de novo chemicals are predicted. The experimental results show that CIGER significantly outperforms existing methods in both ranking and classification metrics. Furthermore, a drug screening pipeline based on CIGER is proposed to identify potential treatments of drug-resistant pancreatic cancer. Our predictions have been validated by experiments, thereby showing the effectiveness of CIGER for phenotypic compound screening of precision medicine. A new deep-learning method (CIGER) for chemical-induced gene expression ranking CIGER can predict gene expression for de novo chemicals from chemical structures We discovered drugs for the treatment of drug-resistant pancreatic cancer
In recent years, a phenotype-based drug discovery approach using chemical-induced gene expressions has shown to be effective in drug discovery and precision medicine. However, it is not feasible to experimentally determine chemical-induced gene expressions for all available chemicals of interest, thereby hindering the application of gene expression-based compound screening on a large scale. Thus, it is crucial to design a computational approach that can generate gene expression information for any chemicals. We proposed a new, deep-learning framework named chemical-induced gene expression ranking (CIGER) to predict a landmark gene expression profile (i.e., gene ranking) induced by de novo chemicals based on their chemical structures. Leveraging CIGER, we predicted and experimentally validated that several existing drugs can increase the therapeutic response on drug-resistant pancreatic cancer. Our results demonstrated the effectiveness of CIGER for precision drug discovery in practice.
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Affiliation(s)
- Thai-Hoang Pham
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yue Qiu
- Ph.D. Program in Biology, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Jiahui Liu
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Eric O’Neill
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
- EpiCombi.AI Therapeutics, Oxford OX7 3SB, UK
| | - Lei Xie
- Ph.D. Program in Biology, The Graduate Center, The City University of New York, New York, NY 10016, USA
- Department of Computer Science, Hunter College, The City University of New York, New York, NY 10065, USA
- Ph.D. Program in Computer Science and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Ping Zhang
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
- Corresponding author
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10
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Naruse M, Ishigamori R, Imai T. The Unique Genetic and Histological Characteristics of DMBA-Induced Mammary Tumors in an Organoid-Based Carcinogenesis Model. Front Genet 2021; 12:765131. [PMID: 34912374 PMCID: PMC8666664 DOI: 10.3389/fgene.2021.765131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/29/2021] [Indexed: 01/23/2023] Open
Abstract
Here, we report a model system using in vitro 7,12-dimethylbenz[a]anthracene (DMBA; 0.6 μM)-treated mammary tissue-derived organoids generated from heterozygous BALB/c-Trp53 knockout mice to induce tumors after injection into the nude mouse subcutis. In parallel, a single oral dose of DMBA (50 mg/kg bodyweight) to the same murine strain induced mammary adenocarcinomas, characterized by biphasic structures differentiated into luminal and myoepithelial lineages and frequent Hras mutations at codon 61. In the present study, the genetic and histological characteristics of DMBA-induced tumors in the organoid-based model were evaluated to validate its similarities to the in vivo study. The organoid-derived tumors were low-grade adenocarcinomas composed of luminal and basal/myoepithelial cells. When the organoid-derived carcinomas were passaged to other nude mice, they partly progressed to squamous cell carcinomas (SCCs). Whole exome sequencing revealed no mutations at Hras codon 61 in the organoid-derived tumors. However, various mutations were detected in other genes such as Tusc3 and Tgfbr2, which have been reported as cancer-associated or homeostatic squamous cell genes. The most common mutational pattern observed in these genes were the G:C to T:A transversions and G:C to A:T transitions, which are not typical of the mutations caused by DMBA treatment. In conclusion, DMBA exhibited carcinogenicity in the both the ex vivo and in vivo mammary carcinogenesis models, albeit with distinct histological and genetical alterations. Further studies are needed to clarify whether organoid-based carcinogenesis models generated following chemical treatment in vitro could be applied to the clarification of the novel mode of action of chemical carcinogenesis.
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Affiliation(s)
- Mie Naruse
- Central Animal Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Rikako Ishigamori
- Central Animal Division, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshio Imai
- Central Animal Division, National Cancer Center Research Institute, Tokyo, Japan
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11
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Tebani A, Jotanovic J, Hekmati N, Sivertsson Å, Gudjonsson O, Edén Engström B, Wikström J, Uhlèn M, Casar-Borota O, Pontén F. Annotation of pituitary neuroendocrine tumors with genome-wide expression analysis. Acta Neuropathol Commun 2021; 9:181. [PMID: 34758873 PMCID: PMC8579660 DOI: 10.1186/s40478-021-01284-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Pituitary neuroendocrine tumors (PitNETs) are common, generally benign tumors with complex clinical characteristics related to hormone hypersecretion and/or growing sellar tumor mass. PitNETs can be classified based on the expression pattern of anterior pituitary hormones and three main transcriptions factors (TF), SF1, PIT1 and TPIT that regulate differentiation of adenohypophysial cells. Here, we have extended this classification based on the global transcriptomics landscape using tumor tissue from a well-defined cohort comprising 51 PitNETs of different clinical and histological types. The molecular profiles were compared with current classification schemes based on immunohistochemistry. Our results identified three main clusters of PitNETs that were aligned with the main pituitary TFs expression patterns. Our analyses enabled further identification of specific genes and expression patterns, including both known and unknown genes, that could distinguish the three different classes of PitNETs. We conclude that the current classification of PitNETs based on the expression of SF1, PIT1 and TPIT reflects three distinct subtypes of PitNETs with different underlying biology and partly independent from the expression of corresponding hormones. The transcriptomic analysis reveals several potentially targetable tumor-driving genes with previously unknown role in pituitary tumorigenesis.
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12
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Koike K, Masuda T, Sato K, Fujii A, Wakiyama H, Tobo T, Takahashi J, Motomura Y, Nakano T, Saito H, Matsumoto Y, Otsu H, Takeishi K, Yonemura Y, Mimori K, Nakagawa T. GET4 is a novel driver gene in colorectal cancer that regulates the localization of BAG6, a nucleocytoplasmic shuttling protein. Cancer Sci 2021; 113:156-169. [PMID: 34704338 PMCID: PMC8748226 DOI: 10.1111/cas.15174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer and a significant cause of cancer mortality worldwide. Further improvements of CRC therapeutic approaches are needed. BCL2‐associated athanogene 6 (BAG6), a multifunctional scaffold protein, plays an important role in tumor progression. However, regulation of BAG6 in malignancies remains unclear. This study showed that guided entry of tail‐anchored proteins factor 4 (GET4), a component of the BAG6 complex, regulates the intercellular localization of BAG6 in CRC. Furthermore, GET4 was identified as a candidate driver gene on the short arm of chromosome 7, which is often amplified in CRC, by our bioinformatics approach using the CRC dataset from The Cancer Genome Atlas. Clinicopathologic and prognostic analyses using CRC datasets showed that GET4 was overexpressed in tumor cells due to an increased DNA copy number. High GET4 expression was an independent poor prognostic factor in CRC, whereas BAG6 was mainly overexpressed in the cytoplasm of tumor cells without gene alteration. The biological significance of GET4 was examined using GET4 KO CRC cells generated with CRISPR‐Cas9 technology or transfected CRC cells. In vitro and in vivo analyses showed that GET4 promoted tumor growth. It appears to facilitate cell cycle progression by cytoplasmic enrichment of BAG6‐mediated p53 acetylation followed by reduced p21 expression. In conclusion, we showed that GET4 is a novel driver gene and a prognostic biomarker that promotes CRC progression by inducing the cytoplasmic transport of BAG6. GET4 could be a promising therapeutic molecular target in CRC.
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Affiliation(s)
- Kensuke Koike
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan.,Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Kuniaki Sato
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Atsushi Fujii
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hiroaki Wakiyama
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, Japan
| | - Junichi Takahashi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yushi Motomura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takafumi Nakano
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hideyuki Saito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | | | - Hajime Otsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Kazuki Takeishi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takashi Nakagawa
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
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Kaitoh K, Yamanishi Y. TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning. J Chem Inf Model 2021; 61:4303-4320. [PMID: 34528432 DOI: 10.1021/acs.jcim.1c00967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One of the most challenging tasks in the drug-discovery process is the efficient identification of small molecules with desired phenotypes. In this study, we propose a novel computational method for omics-based de novo drug design, which we call TRIOMPHE (transcriptome-based inference and generation of molecules with desired phenotypes). We investigated the correlation between chemically induced transcriptome profiles (reflecting cellular responses to compound treatment) and genetically perturbed transcriptome profiles (reflecting cellular responses to gene knock-down or gene overexpression of target proteins) in terms of ligand-target interactions. Subsequently, we developed novel machine learning methods to generate the chemical structures of new molecules with desired transcriptome profiles in the framework of a variational autoencoder. The use of desired transcriptome profiles enables the automatic design of molecules that are likely to have bioactivities for target proteins of interest. We showed that our methods can generate chemically valid molecules that are likely to have biological activities on 10 target proteins; moreover, they can outperform previous methods that had the same objective. Our omics-based structure generator is expected to be useful for the de novo design of drugs for a variety of target proteins.
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Affiliation(s)
- Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
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14
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Repurposing Niclosamide for Targeting Pancreatic Cancer by Inhibiting Hh/Gli Non-Canonical Axis of Gsk3β. Cancers (Basel) 2021; 13:cancers13133105. [PMID: 34206370 PMCID: PMC8269055 DOI: 10.3390/cancers13133105] [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: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The current obstacles for discovering new drugs for cancer therapy have necessitated the development of the alternative strategy of drug repurposing, the identification of new uses for approved or investigational drugs for new therapeutic purposes. Niclosamide (Nic) is a Food and Drug Administration (FDA)-approved anti-helminthic drug, reported to have anti-cancer effects, and is being assessed in various clinical trials. In the current study, we assessed the therapeutic efficacy of Nic on pancreatic cancer (PC) in vitro. Our results revealed mitochondrial stress and mTORC1-dependent autophagy as the predominant players of Nic-induced PC cell death. This study provided a novel mechanistic insight for anti-cancer efficacy of Nic by increasing p-Gsk3β that modulates molecular signaling(s), including inhibition of hedgehog (Hh) signaling-mediated cellular proliferation and increased apoptosis through mTORC1-dependent autophagy may prove helpful for the development of novel PC therapies. Abstract Niclosamide (Nic), an FDA-approved anthelmintic drug, is reported to have anti-cancer efficacy and is being assessed in clinical trials for various solid tumors. Based on its ability to target multiple signaling pathways, in the present study, we evaluated the therapeutic efficacy of Nic on pancreatic cancer (PC) in vitro. We observed an anti-cancerous effect of this drug as shown by the G0/G1 phase cell cycle arrest, inhibition of PC cell viability, colony formation, and migration. Our results revealed the involvement of mitochondrial stress and mTORC1-dependent autophagy as the predominant players of Nic-induced PC cell death. Significant reduction of Nic-induced reactive oxygen species (ROS) and cell death in the presence of a selective autophagy inhibitor spautin-1 demonstrated autophagy as a major contributor to Nic-mediated cell death. Mechanistically, Nic inhibited the interaction between BCL2 and Beclin-1 that supported the crosstalk of autophagy and apoptosis. Further, Nic treatment resulted in Gsk3β inactivation by phosphorylating its Ser-9 residue leading to upregulation of Sufu and Gli3, thereby negatively impacting hedgehog signaling and cell survival. Nic induced autophagic cell death, and p-Gsk3b mediated Sufu/Gli3 cascade was further confirmed by Gsk3β activator, LY-294002, by rescuing inactivation of Hh signaling upon Nic treatment. These results suggested the involvement of a non-canonical mechanism of Hh signaling, where p-Gsk3β acts as a negative regulator of Hh/Gli1 cascade and a positive regulator of autophagy-mediated cell death. Overall, this study established the therapeutic efficacy of Nic for PC by targeting p-Gsk3β mediated non-canonical Hh signaling and promoting mTORC1-dependent autophagy and cell death.
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15
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Bi G, Bian Y, Liang J, Yin J, Li R, Zhao M, Huang Y, Lu T, Zhan C, Fan H, Wang Q. Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targets. J Transl Med 2021; 19:219. [PMID: 34030708 PMCID: PMC8142489 DOI: 10.1186/s12967-021-02889-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Background Generally, cancer cells undergo metabolic reprogramming to adapt to energetic and biosynthetic requirements that support their uncontrolled proliferation. However, the mutual relationship between two critical metabolic pathways, glycolysis and oxidative phosphorylation (OXPHOS), remains poorly defined. Methods We developed a “double-score” system to quantify glycolysis and OXPHOS in 9668 patients across 33 tumor types from The Cancer Genome Atlas and classified them into four metabolic subtypes. Multi-omics bioinformatical analyses was conducted to detect metabolism-related molecular features. Results Compared with patients with low glycolysis and high OXPHOS (LGHO), those with high glycolysis and low OXPHOS (HGLO) were consistently associated with worse prognosis. We identified common dysregulated molecular features between different metabolic subgroups across multiple cancers, including gene, miRNA, transcription factor, methylation, and somatic alteration, as well as investigated their mutual interfering relationships. Conclusion Overall, this work provides a comprehensive atlas of metabolic heterogeneity on a pan-cancer scale and identified several potential drivers of metabolic rewiring, suggesting corresponding prognostic and therapeutic utility. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02889-0.
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Affiliation(s)
- Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yunyi Bian
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Jiacheng Yin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Runmei Li
- Department of Biostatistics, Public Health, Fudan University, Shanghai, 200000, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Tao Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| | - Hong Fan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
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16
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Fujii A, Masuda T, Iwata M, Tobo T, Wakiyama H, Koike K, Kosai K, Nakano T, Kuramitsu S, Kitagawa A, Sato K, Kouyama Y, Shimizu D, Matsumoto Y, Utsunomiya T, Ohtsuka T, Yamanishi Y, Nakamura M, Mimori K. The novel driver gene ASAP2 is a potential druggable target in pancreatic cancer. Cancer Sci 2021; 112:1655-1668. [PMID: 33605496 PMCID: PMC8019229 DOI: 10.1111/cas.14858] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Targeting mutated oncogenes is an effective approach for treating cancer. The 4 main driver genes of pancreatic ductal adenocarcinoma (PDAC) are KRAS, TP53, CDKN2A, and SMAD4, collectively called the "big 4" of PDAC, however they remain challenging therapeutic targets. In this study, ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 (ASAP2), one of the ArfGAP family, was identified as a novel driver gene in PDAC. Clinical analysis with PDAC datasets showed that ASAP2 was overexpressed in PDAC cells based on increased DNA copy numbers, and high ASAP2 expression contributed to a poor prognosis in PDAC. The biological roles of ASAP2 were investigated using ASAP2-knockout PDAC cells generated with CRISPR-Cas9 technology or transfected PDAC cells. In vitro and in vivo analyses showed that ASAP2 promoted tumor growth by facilitating cell cycle progression through phosphorylation of epidermal growth factor receptor (EGFR). A repositioned drug targeting the ASAP2 pathway was identified using a bioinformatics approach. The gene perturbation correlation method showed that niclosamide, an antiparasitic drug, suppressed PDAC growth by inhibition of ASAP2 expression. These data show that ASAP2 is a novel druggable driver gene that activates the EGFR signaling pathway. Furthermore, niclosamide was identified as a repositioned therapeutic agent for PDAC possibly targeting ASAP2.
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Affiliation(s)
- Atsushi Fujii
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takaaki Masuda
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | - Michio Iwata
- Department of Bioscience and BioinformaticsFaculty of Computer Science and Systems EngineeringKyushu Institute of TechnologyFukuokaJapan
| | - Taro Tobo
- Department of Clinical Laboratory MedicineKyushu University Beppu HospitalOitaJapan
| | | | - Kensuke Koike
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | - Keisuke Kosai
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | - Takafumi Nakano
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | | | | | - Kuniaki Sato
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | - Yuta Kouyama
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | - Dai Shimizu
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
| | | | | | - Takao Ohtsuka
- Department of Digestive Surgery, Breast and Thyroid SurgeryKagoshima UniversityKagoshimaJapan
| | - Yoshihiro Yamanishi
- Department of Bioscience and BioinformaticsFaculty of Computer Science and Systems EngineeringKyushu Institute of TechnologyFukuokaJapan
| | - Masafumi Nakamura
- Department of Surgery and OncologyGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Koshi Mimori
- Department of SurgeryKyushu University Beppu HospitalOitaJapan
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