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Lin C, Sniezek C, Giglio RM, Karki R, McGann C, Garcia BA, McFaline-Figeroa JL, Schweppe DK. Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.592075. [PMID: 38853901 PMCID: PMC11160595 DOI: 10.1101/2024.05.23.592075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule compounds. The molecular study of the extent of this heterogeneity often measures changes in a single cell line or using a small number of compounds. To more comprehensively profile the effects of small-molecule perturbations and their influence on these heterogeneous cellular responses, we present a molecular resource based on the quantification of chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitors (HDACi) in non-isogenic cell lines. Through quantitative molecular profiling of 10,621 proteins, these data reveal coordinated molecular remodeling of HDACi treated cancer cells. HDACi-regulated proteins differ greatly across cell lines with consistent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) cell-state effectors. Together these data provide valuable insight into cell-type driven and heterogeneous responses that must be taken into consideration when monitoring molecular perturbations in culture models.
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Affiliation(s)
- Chuwei Lin
- University of Washington, Seattle, WA 98105, USA
| | | | | | - Rashmi Karki
- Washington University School of Medicine, St. Louis, MO 63110, USA
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He K, Xie MY, Gao XJ, Wang H, Li JD. The Correlation of Centromere Protein Q with Diagnosis and Prognosis in Hepatocellular Carcinoma. Pharmgenomics Pers Med 2024; 17:271-288. [PMID: 38827182 PMCID: PMC11141762 DOI: 10.2147/pgpm.s456965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/18/2024] [Indexed: 06/04/2024] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is one of the major types of liver cancer. Previous studies have shown that the centromere protein family is associated with malignant biological behaviors such as HCC proliferation. As a member of the centromere protein family, centromere protein Q (CENPQ) is closely associated with immunotherapy and immune cell infiltration in various tumors. However, the role and mechanism of CENPQ in HCC remain unclear. Methods Multiple public databases and RT-qPCR were used to study the expression of CENPQ in HCC. Based on TCGA data, the correlation between CENPQ and clinicopathological characteristics and prognosis of HCC patients was analyzed, and its diagnostic value was evaluated. The potential biological functions of CENPQ in HCC were explored by functional enrichment analysis of differentially expressed genes. The distribution of tumor-infiltrating immune cell types was assessed using single-sample GSEA, and immune checkpoint gene expression was analyzed using Spearman correlation. Subsequently, loss-of-function experiments were performed to determine the function of CENPQ on the cell cycle and proliferation of HCC cells in vitro. Results CENPQ was found highly expressed in HCC and correlated with weight, BMI, age, AFP, T stage, pathologic stage, histologic grade, and prothrombin time (all p < 0.05). ROC and Kaplan-Meier analyses indicated that CENPQ may be potentially used as a diagnostic marker for HCC (AUC = 0.881), and its upregulation is associated with decreased OS (p = 0.002), DSS (p < 0.001), and PFI (p = 0.002). Functional enrichment analysis revealed an association of CENPQ with biological processes such as immune cell infiltration, cell cycle, and hippo-merlin signaling deregulation in HCC. Furthermore, knockdown of CENPQ manifested in HCC cells with G0/1 phase cycle arrest and decreased proliferative capacity. Conclusion CENPQ expression was higher in HCC tissues than in normal liver tissues. It was significantly associated with poor prognosis, immune cell infiltration, cell cycle, and proliferation. Therefore, CENPQ may become a promising prognostic biomarker for HCC patients.
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Affiliation(s)
- Kun He
- Institute of Hepatobiliary, Pancreatic and Intestinal Diseases, North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
| | - Meng-yi Xie
- Institute of Hepatobiliary, Pancreatic and Intestinal Diseases, North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
| | - Xiao-jin Gao
- Institute of Hepatobiliary, Pancreatic and Intestinal Diseases, North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
| | - Hao Wang
- Institute of Hepatobiliary, Pancreatic and Intestinal Diseases, North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
| | - Jing-dong Li
- Institute of Hepatobiliary, Pancreatic and Intestinal Diseases, North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
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Tang J, Lam GT, Brooks RD, Miles M, Useckaite Z, Johnson IR, Ung BSY, Martini C, Karageorgos L, Hickey SM, Selemidis S, Hopkins AM, Rowland A, Vather R, O'Leary JJ, Brooks DA, Caruso MC, Logan JM. Exploring the role of sporadic BRAF and KRAS mutations during colorectal cancer pathogenesis: A spotlight on the contribution of the endosome-lysosome system. Cancer Lett 2024; 585:216639. [PMID: 38290660 DOI: 10.1016/j.canlet.2024.216639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 02/01/2024]
Abstract
The highly heterogenous nature of colorectal cancer can significantly hinder its early and accurate diagnosis, eventually contributing to high mortality rates. The adenoma-carcinoma sequence and serrated polyp-carcinoma sequence are the two most common sequences in sporadic colorectal cancer. Genetic alterations in adenomatous polyposis coli (APC), v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and tumour protein 53 (TP53) genes are critical in adenoma-carcinoma sequence, whereas v-Raf murine sarcoma viral oncogene homolog B (BRAF) and MutL Homolog1 (MLH1) are driving oncogenes in the serrated polyp-carcinoma sequence. Sporadic mutations in these genes contribute differently to colorectal cancer pathogenesis by introducing distinct alterations in several signalling pathways that rely on the endosome-lysosome system. Unsurprisingly, the endosome-lysosome system plays a pivotal role in the hallmarks of cancer and contributes to specialised colon function. Thus, the endosome-lysosome system might be distinctively influenced by different mutations and these alterations may contribute to the heterogenous nature of sporadic colorectal cancer. This review highlights potential connections between major sporadic colorectal cancer mutations and the diverse pathogenic mechanisms driven by the endosome-lysosome system in colorectal carcinogenesis.
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Affiliation(s)
- Jingying Tang
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Giang T Lam
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Robert D Brooks
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Mark Miles
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora, Melbourne, Vic, Australia
| | - Zivile Useckaite
- College of Medicine and Public Health, Flinders University, Flinders Drive, Bedford Park, Adelaide, SA, Australia
| | - Ian Rd Johnson
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Ben S-Y Ung
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Carmela Martini
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Litsa Karageorgos
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Shane M Hickey
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Stavros Selemidis
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora, Melbourne, Vic, Australia
| | - Ashley M Hopkins
- College of Medicine and Public Health, Flinders University, Flinders Drive, Bedford Park, Adelaide, SA, Australia
| | - Andrew Rowland
- College of Medicine and Public Health, Flinders University, Flinders Drive, Bedford Park, Adelaide, SA, Australia
| | - Ryash Vather
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia; Centre for Cancer Biology, University of South Australia, Adelaide, South Australia, Australia
| | - John J O'Leary
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Douglas A Brooks
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Maria C Caruso
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia
| | - Jessica M Logan
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, Australia.
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Zheng N, Liu S, Chen J, Xu Y, Cao W, Lin J, Lu G, Zhang G. SARS-CoV-2 NSP2 as a Potential Delivery Vehicle for Proteins. Mol Pharm 2024; 21:1149-1159. [PMID: 38288708 DOI: 10.1021/acs.molpharmaceut.3c00680] [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] [Indexed: 03/05/2024]
Abstract
The development of biomolecule delivery systems is essential for the treatment of various diseases such as cancer, immunological diseases, and metabolic disorders. For the first time, we found that SARS-CoV-2-encoded nonstructural protein 2 (NSP2) can be secreted from the cells, where it is synthesized. Brefeldin A and H89, inhibitors of ER/Golgi secretion pathways, did not inhibit NSP2 secretion. NSP2 is likely secreted via an unconventional secretory pathway. Moreover, both secreted and purified NSP2 proteins were able to traverse the plasma membrane barrier and enter both immortalized human umbilical vein endothelial cells and tumor cell lines. After entry, the NSP2 protein was localized in only the cytoplasm. Cytochalasin D, a potent inhibitor of actin polymerization, inhibited the entry of NSP2. NSP2 can carry other molecules into cells. Burkholderia lethal factor 1, a monomeric toxin from the intracellular pathogen Burkholderia pseudomallei, has demonstrated antitumor activity by targeting host eukaryotic initiation translation factor 4A. An NSP2-BLF1 fusion protein was translocated across the cellular membranes of Huh7 cells and mediated cell killing. By using different approaches, including protein purification, chemical inhibition, and cell imaging, we confirm that NSP2 is able to deliver heterologous proteins into cells. NSP2 can act as a potential delivery vehicle for proteins.
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Affiliation(s)
- Ningze Zheng
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Shurui Liu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jianheng Chen
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yue Xu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wenyin Cao
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jinyi Lin
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Guang Lu
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Guigen Zhang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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Soriani A, Vulpis E, Cuollo L, Santoni A, Zingoni A. Cancer extracellular vesicles as novel regulators of NK cell response. Cytokine Growth Factor Rev 2020; 51:19-26. [DOI: 10.1016/j.cytogfr.2019.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/21/2022]
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Li SS, Zhao XB, Tian JM, Wang HR, Wei TH. Prediction of seed gene function in progressive diabetic neuropathy by a network-based inference method. Exp Ther Med 2019; 17:4176-4182. [PMID: 31007748 PMCID: PMC6468912 DOI: 10.3892/etm.2019.7441] [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: 07/06/2018] [Accepted: 03/07/2019] [Indexed: 11/07/2022] Open
Abstract
Guilt by association (GBA) algorithm has been widely used to statistically predict gene functions, and network-based approach increases the confidence and veracity of identifying molecular signatures for diseases. This work proposed a network-based GBA method by integrating the GBA algorithm and network, to identify seed gene functions for progressive diabetic neuropathy (PDN). The inference of predicting seed gene functions comprised of three steps: i) Preparing gene lists and sets; ii) constructing a co-expression matrix (CEM) on gene lists by Spearman correlation coefficient (SCC) method and iii) predicting gene functions by GBA algorithm. Ultimately, seed gene functions were selected according to the area under the receiver operating characteristics curve (AUC) index. A total of 79 differentially expressed genes (DEGs) and 40 background gene ontology (GO) terms were regarded as gene lists and sets for the subsequent analyses, respectively. The predicted results obtained from the network-based GBA approach showed that 27.5% of all gene sets had a good classified performance with AUC >0.5. Most significantly, 3 gene sets with AUC >0.6 were denoted as seed gene functions for PDN, including binding, molecular function and regulation of the metabolic process. In summary, we predicted 3 seed gene functions for PDN compared with non-progressors utilizing network-based GBA algorithm. The findings provide insights to reveal pathological and molecular mechanism underlying PDN.
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Affiliation(s)
- Shan-Shan Li
- Department of Endocrinology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Xin-Bo Zhao
- Department of Endocrinology, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Jia-Mei Tian
- Department of Pediatrics, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Hao-Ren Wang
- Department of Medicine, Linyi Luozhuang Central Hospital, Linyi, Shandong 276000, P.R. China
| | - Tong-Huan Wei
- Department of Medicine, People's Hospital of Linyi High-Tech Industrial Development Zone, Linyi, Shandong 276000, P.R. China
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Liu YY, Tanikawa C, Ueda K, Matsuda K. INKA2, a novel p53 target that interacts with the serine/threonine kinase PAK4. Int J Oncol 2019; 54:1907-1920. [PMID: 31081062 PMCID: PMC6521941 DOI: 10.3892/ijo.2019.4786] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/21/2019] [Indexed: 12/17/2022] Open
Abstract
The p53 protein is a tumour suppressor and transcription factor that regulates the expression of target genes involved in numerous stress responses systems. In this study, we designed a screening strategy using DNA damage-induced mouse and human transcriptome data to identify novel downstream targets of p53. Our method selected genes with an induced expression in multiple organs of X-ray-irradiated p53 wild-type mice. The expression of inka box actin regulator 2 gene, known as Inka2, was upregulated in 12 organs when p53 expression was induced. Similarly, INKA2 was induced in a p53-dependent manner at both the mRNA and protein level in human cells treated with adriamycin. Reporter assays confirmed that p53 directly regulated INKA2 through an intronic binding site. The overexpression of INKA2 produced a slight decrease in cancer cell growth in the colony formation assay. Moreover, the analysis of The Cancer Genome Atlas (TCGA) data revealed a decreased INKA2 expression in tumour samples carrying p53 mutations compared with p53 wild-type samples. In addition, significantly higher levels of DNA methylation were observed in the INKA2 promoter in tumour samples, concordant with the reduced INKA2 expression in tumour tissues. These results demonstrate the potential of INKA2 as a cancer cell growth inhibitor. Furthermore, INKA2 protein interacts with the serine/threonine-protein kinase, p21 (RAC1) activated kinase (PAK)4, which phosphorylates β-catenin to prevent ubiquitin-proteasomal degradation. As β-catenin was downregulated in a stable INKA2-expressing cell line, the findings of this study suggest that INKA2 is a novel, direct downstream target of p53 that potentially decreases cell growth by inhibiting the PAK4-β-catenin pathway.
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Affiliation(s)
- Yu-Yu Liu
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo 108‑8639, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo 108‑8639, Tokyo, Japan
| | - Koji Ueda
- Project for Realization of Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135‑8550, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo 108‑8639, Tokyo, Japan
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Shaughnessy R, Echard A. Rab35 GTPase and cancer: Linking membrane trafficking to tumorigenesis. Traffic 2018; 19:247-252. [PMID: 29314576 DOI: 10.1111/tra.12546] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022]
Abstract
Rab35 is a small GTPase that is involved in many cellular processes, including membrane trafficking, cell polarity, lipid homeostasis, immunity, phagocytosis and cytokinesis. Recent studies showed that activating mutations confer Rab35 with oncogenic properties. Conversely, downregulation of Rab35 inverts apico-basal cell polarity and promotes cell migration. Here we review Rab35's known functions in membrane trafficking and signaling, cell division and cell migration in cancer cells and discuss the importance of Rab35-dependent membrane trafficking in cancer progression.
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Affiliation(s)
- Ronan Shaughnessy
- Membrane Traffic and Cell Division Lab, Cell Biology and Infection Department, Institut Pasteur, Paris, France
| | - Arnaud Echard
- Membrane Traffic and Cell Division Lab, Cell Biology and Infection Department, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique UMR3691, Paris, France
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