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Zhang Z, Huang J, Zhang Z, Shen H, Tang X, Wu D, Bao X, Xu G, Chen S. Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia. Biomark Res 2024; 12:60. [PMID: 38858750 PMCID: PMC11165883 DOI: 10.1186/s40364-024-00600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Acute myeloid leukemia (AML) is the most frequent leukemia in adults with a high mortality rate. Current diagnostic criteria and selections of therapeutic strategies are generally based on gene mutations and cytogenetic abnormalities. Chemotherapy, targeted therapies, and hematopoietic stem cell transplantation (HSCT) are the major therapeutic strategies for AML. Two dilemmas in the clinical management of AML are related to its poor prognosis. One is the inaccurate risk stratification at diagnosis, leading to incorrect treatment selections. The other is the frequent resistance to chemotherapy and/or targeted therapies. Genomic features have been the focus of AML studies. However, the DNA-level aberrations do not always predict the expression levels of genes and proteins and the latter is more closely linked to disease phenotypes. With the development of high-throughput sequencing and mass spectrometry technologies, studying downstream effectors including RNA, proteins, and metabolites becomes possible. Transcriptomics can reveal gene expression and regulatory networks, proteomics can discover protein expression and signaling pathways intimately associated with the disease, and metabolomics can reflect precise changes in metabolites during disease progression. Moreover, omics profiling at the single-cell level enables studying cellular components and hierarchies of the AML microenvironment. The abundance of data from different omics layers enables the better risk stratification of AML by identifying prognosis-related biomarkers, and has the prospective application in identifying drug targets, therefore potentially discovering solutions to the two dilemmas. In this review, we summarize the existing AML studies using omics methods, both separately and combined, covering research fields of disease diagnosis, risk stratification, prognosis prediction, chemotherapy, as well as targeted therapy. Finally, we discuss the directions and challenges in the application of multi-omics in precision medicine of AML. Our review may inspire both omics researchers and clinical physicians to study AML from a different angle.
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Affiliation(s)
- Zhiyu Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jiayi Huang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhibo Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hongjie Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaowen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
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Ostojić M, Đurić A, Živić K, Grahovac J. Analysis of the nischarin expression across human tumor types reveals its context-dependent role and a potential as a target for drug repurposing in oncology. PLoS One 2024; 19:e0299685. [PMID: 38781180 PMCID: PMC11115306 DOI: 10.1371/journal.pone.0299685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Nischarin was reported to be a tumor suppressor that plays a critical role in breast cancer initiation and progression, and a positive prognostic marker in breast, ovarian and lung cancers. Our group has found that nischarin had positive prognostic value in female melanoma patients, but negative in males. This opened up a question whether nischarin has tumor type-specific and sex-dependent roles in cancer progression. In this study, we systematically examined in the public databases the prognostic value of nischarin in solid tumors, regulation of its expression and associated signaling pathways. We also tested the effects of a nischarin agonist rilmenidine on cancer cell viability in vitro. Nischarin expression was decreased in tumors compared to the respective healthy tissues, most commonly due to the deletions of the nischarin gene and promoter methylation. Unlike in healthy tissues where it was located in the cytoplasm and at the membrane, in tumor tissues nischarin could also be observed in the nuclei, implying that nuclear translocation may also account for its cancer-specific role. Surprisingly, in several cancer types high nischarin expression was a negative prognostic marker. Gene set enrichment analysis showed that in tumors in which high nischarin expression was a negative prognostic marker, signaling pathways that regulate stemness were enriched. In concordance with the findings that nischarin expression was negatively associated with pathways that control cancer growth and progression, nischarin agonist rilmenidine decreased the viability of cancer cells in vitro. Taken together, our study lays a ground for functional studies of nischarin in a context-dependent manner and, given that nischarin has several clinically approved agonists, provides rationale for their repurposing, at least in tumors in which nischarin is predicted to be a positive prognostic marker.
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Affiliation(s)
- Marija Ostojić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Ana Đurić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Kristina Živić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Jelena Grahovac
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
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Wiphakphongpakorn P, Juengsomjit R, Poomsawat S, Meesakul O, Bhattarai BP, Klongnoi B, Buajeeb W, Khovidhunkit SOP. Expression of CLLD7 and CHC1L Proteins in Oral Epithelial Dysplasia in a Group of Thai Patients. Asian Pac J Cancer Prev 2024; 25:1257-1264. [PMID: 38679985 PMCID: PMC11162717 DOI: 10.31557/apjcp.2024.25.4.1257] [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: 10/02/2023] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
OBJECTIVES Previous study showed aberrant CLLD7 and CHC1L protein expression in oral squamous cell carcinoma (OSCC) compared to normal oral mucosa (NOM). This study aimed to evaluate the expression of these proteins in oral epithelial dysplasia (OED). MATERIALS AND METHODS Forty specimens of OED and 11 NOM were used. The expression of CLLD7 and CHC1L was determined by immunohistochemistry. In each case, at least 1000 cells were counted. Presence of nuclear, cytoplasmic, and/or membrane staining of CLLD7 and CHC1L were considered positive. Percentages of total positive cells and positive cells at different locations were recorded. SPSS version 18 was used to compare variation between groups with statistical significance at p<0.05. RESULTS No significant differences in the percentages of total positive cells of CLLD7 and CHC1L were found between NOM and all grades of OED. Nevertheless, there were significant differences in subcellular staining of these two proteins. In CLLD7, the nuclear staining of the moderate and the severe OED groups was significantly lower than that of the NOM group (p<0.05). The percentages of membrane staining of CHC1L in moderate and severe OED were significantly higher than that of NOM (p<0.001). In addition, the nuclear staining of CHC1L in each grade of OED was significantly lower than that of NOM (p<0.05). CONCLUSION The subcellular mislocalization of CLLD7 and CHC1L in OED suggests that the expression of these potential tumor suppressor proteins might be dysregulated during the dysplastic process. The distinct membrane staining of CHC1L observed in OED but not in NOM is a useful characteristic that can be used to separate OED from NOM. Thus, CHC1L may be a good marker to assist in the diagnosis of OED.
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Affiliation(s)
| | - Rachai Juengsomjit
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
| | - Sopee Poomsawat
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
| | - Ounruean Meesakul
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
| | | | - Boworn Klongnoi
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
| | - Waranun Buajeeb
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
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Xiao H, Zou Y, Wang J, Wan S. A Review for Artificial Intelligence Based Protein Subcellular Localization. Biomolecules 2024; 14:409. [PMID: 38672426 PMCID: PMC11048326 DOI: 10.3390/biom14040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer's disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcellular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.
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Affiliation(s)
- Hanyu Xiao
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Yijin Zou
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Jieqiong Wang
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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Shaw TI, Wagner J, Tian L, Wickman E, Poudel S, Wang J, Paul R, Koo SC, Lu M, Sheppard H, Fan Y, O’Neil F, Lau CC, Zhou X, Zhang J, Gottschalk S. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression. RESEARCH SQUARE 2024:rs.3.rs-3821632. [PMID: 38260279 PMCID: PMC10802740 DOI: 10.21203/rs.3.rs-3821632/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Immunotherapy with CAR T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons (CSE) present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify CSE targets, we analyzed 1,532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We found 2,933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n=148) or the alternatively spliced (AS) isoform (n=9) level. Expression of selected AS targets, including the EDB domain of FN1 (EDB), and gene targets, such as COL11A1, were validated in pediatric PDX tumors. We generated CAR T cells specific to EDB or COL11A1 and demonstrated that COL11A1-CAR T-cells have potent antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
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Affiliation(s)
- Timothy I Shaw
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jessica Wagner
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Wickman
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robin Paul
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Selene C. Koo
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Meifen Lu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francis O’Neil
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Ching C. Lau
- The Jackson Laboratory Cancer Center, Farmington, CT, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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6
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Vieira LS, Zhang Y, López Quiñones AJ, Hu T, Singh DK, Stevens J, Prasad B, Park JR, Wang J. The Plasma Membrane Monoamine Transporter is Highly Expressed in Neuroblastoma and Functions as an mIBG Transporter. J Pharmacol Exp Ther 2023; 387:239-248. [PMID: 37541765 PMCID: PMC10658915 DOI: 10.1124/jpet.123.001672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 08/06/2023] Open
Abstract
Neuroblastoma (NB) is a pediatric cancer with low survival rates in high-risk patients. 131I-mIBG has emerged as a promising therapy for high-risk NB and kills tumor cells by radiation. Consequently, 131I-mIBG tumor uptake and retention are major determinants for its therapeutic efficacy. mIBG enters NB cells through the norepinephrine transporter (NET), and accumulates in mitochondria through unknown mechanisms. Here we evaluated the expression of monoamine and organic cation transporters in high-risk NB tumors and explored their relationship with MYCN amplification and patient survival. We found that NB mainly expresses NET, the plasma membrane monoamine transporter (PMAT), and the vesicular membrane monoamine transporter 1/2 (VMAT1/2), and that the expression of these transporters is significantly reduced in MYCN-amplified tumor samples. PMAT expression is the highest and correlates with overall survival in high-risk NB patients without MYCN amplification. Immunostaining showed that PMAT resides intracellularly in NB cells and co-localizes with mitochondria. Using cells expressing PMAT, mIBG was identified as a PMAT substrate. In mitochondria isolated from NB cell lines, mIBG uptake was reduced by ∼50% by a PMAT inhibitor. Together, our data suggest that PMAT is a previously unrecognized transporter highly expressed in NB and could impact intracellular transport and therapeutic response to 131I-mIBG. SIGNIFICANCE STATEMENT: This study identified that plasma membrane monoamine transporter (PMAT) is a novel transporter highly expressed in neuroblastoma and its expression level is associated with overall survival rate in high-risk patients without MYCN amplification. PMAT is expressed intracellularly in neuroblastoma cells, transports meta-iodobenzylguanidine (mIBG) and thus could impact tumor retention and response to 131I-mIBG therapy. These findings have important clinical implications as PMAT could represent a novel molecular marker to help inform disease prognosis and predict response to 131I-mIBG therapy.
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Affiliation(s)
- Letícia Salvador Vieira
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Yuchen Zhang
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Antonio J López Quiñones
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Tao Hu
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Dilip Kumar Singh
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Jeffrey Stevens
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Julie R Park
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
| | - Joanne Wang
- Department of Pharmaceutics, University of Washington, Seattle, Washington (L.S.V., Y.Z., A.J.L.Q., T.H., J.W.); Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington (D.K.S., B.P.); and Seattle Children's Hospital, Seattle, Washington (J.S., J.R.P.)
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7
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Zhang Z, Chen X, Tang R, Zhu Y, Guo H, Qu Y, Xie P, Lian IY, Wang Y, Lo YH. Interpretable unsupervised learning enables accurate clustering with high-throughput imaging flow cytometry. Sci Rep 2023; 13:20533. [PMID: 37996496 PMCID: PMC10667244 DOI: 10.1038/s41598-023-46782-w] [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: 01/26/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023] Open
Abstract
A primary challenge of high-throughput imaging flow cytometry (IFC) is to analyze the vast amount of imaging data, especially in applications where ground truth labels are unavailable or hard to obtain. We present an unsupervised deep embedding algorithm, the Deep Convolutional Autoencoder-based Clustering (DCAEC) model, to cluster label-free IFC images without any prior knowledge of input labels. The DCAEC model first encodes the input images into the latent representations and then clusters based on the latent representations. Using the DCAEC model, we achieve a balanced accuracy of 91.9% for human white blood cell (WBC) clustering and 97.9% for WBC/leukemia clustering using the 3D IFC images and 3D DCAEC model. Above all, although no human recognizable features can separate the clusters of cells with protein localization, we demonstrate the fused DCAEC model can achieve a cluster balanced accuracy of 85.3% from the label-free 2D transmission and 3D side scattering images. To reveal how the neural network recognizes features beyond human ability, we use the gradient-weighted class activation mapping method to discover the cluster-specific visual patterns automatically. Evaluation results show that the automatically identified salient image regions have strong cluster-specific visual patterns for different clusters, which we believe is a stride for the interpretable neural network for cell analysis with high-throughput IFCs.
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Affiliation(s)
- Zunming Zhang
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Xinyu Chen
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rui Tang
- NanoCellect Biomedical, Inc., San Diego, CA, 92121, USA
| | - Yuxuan Zhu
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Han Guo
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yunjia Qu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0435, USA
| | - Pengtao Xie
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ian Y Lian
- Department of Biology, Lamar University, Beaumont, TX, 77710, USA
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0435, USA
| | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
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8
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Ayama-Canden S, Tondo R, Pineros Leyton ML, Ninane N, Demazy C, Dieu M, Fattaccioli A, Sauvage A, Tabarrant T, Lucas S, Bonifazi D, Michiels C. Indacaterol inhibits collective cell migration and IGDQ-mediated single cell migration in metastatic breast cancer MDA-MB-231 cells. Cell Commun Signal 2023; 21:301. [PMID: 37904233 PMCID: PMC10614342 DOI: 10.1186/s12964-023-01340-9] [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: 08/22/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023] Open
Abstract
Metastasis is the main cause of deaths related to breast cancer. This is particular the case for triple negative breast cancer. No targeted therapies are reported as efficient until now. The extracellular matrix, in particular the fibronectin type I motif IGDQ, plays a major role in regulating cell migration prior metastasis formation. This motif interacts with specific integrins inducing their activation and the migratory signal transduction.Here, we characterized the migratory phenotype of MDA-MB-231 cells, using functionalized IGDQ-exposing surfaces, and compared it to integrin A5 and integrin B3 knock-down cells. A multiomic analysis was developed that highlighted the splicing factor SRSF6 as a putative master regulator of cell migration and of integrin intracellular trafficking. Indacaterol-induced inhibition of SRSF6 provoked: i) the inhibition of collective and IGDQ-mediated cell migration and ii) ITGA5 sequestration into endosomes and lysosomes. Upon further studies, indacaterol may be a potential therapy to prevent cell migration and reduce metastasis formation in breast cancer. Video Abstract.
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Affiliation(s)
- Sophie Ayama-Canden
- URBC - NARILIS, University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Rodolfo Tondo
- Cardiff University, Park Place, Main Building, Wales, CF10 3AT, UK
| | | | - Noëlle Ninane
- URBC - NARILIS, University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Catherine Demazy
- URBC - NARILIS, University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
- MaSUN, Mass Spectrometry Facility, University of Namur, 61, Rue de Bruxelles, 5000, Namur, Belgium
| | - Marc Dieu
- MaSUN, Mass Spectrometry Facility, University of Namur, 61, Rue de Bruxelles, 5000, Namur, Belgium
| | - Antoine Fattaccioli
- URBC - NARILIS, University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Aude Sauvage
- URBC - NARILIS, University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Tijani Tabarrant
- LARN - NARILIS, University of Namur, Rue de Bruxelles 61, Namur, 5000, Belgium
| | - Stéphane Lucas
- LARN - NARILIS, University of Namur, Rue de Bruxelles 61, Namur, 5000, Belgium
| | - Davide Bonifazi
- Cardiff University, Park Place, Main Building, Wales, CF10 3AT, UK
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Carine Michiels
- URBC - NARILIS, University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium.
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Arthur NB, Christensen KA, Mannino K, Ruzinova MB, Kumar A, Gruszczynska A, Day RB, Erdmann-Gilmore P, Mi Y, Sprung R, York CR, Reid Townsend R, Spencer DH, Sykes SM, Ferraro F. Missense mutations in Myc Box I influence MYC cellular localization, mRNA partitioning and turnover to promote leukemogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563493. [PMID: 37961226 PMCID: PMC10634725 DOI: 10.1101/2023.10.22.563493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Somatic missense mutations in the phosphodegron domain of the MYC gene ( M YC Box I) are detected in the dominant clones of a subset of acute myeloid leukemia (AML) patients, but the mechanisms by which they contribute to AML are unknown. To unveil unique proprieties of MBI MYC mutant proteins, we systematically compared the cellular and molecular consequences of expressing similar oncogenic levels of wild type and MBI mutant MYC. We found that MBI MYC mutants can accelerate leukemia by driving unique transcriptional signatures in highly selected, myeloid progenitor subpopulations. Although these mutations increase MYC stability, they overall dampen MYC chromatin localization and lead to a cytoplasmic accumulation of the mutant proteins. This phenotype is coupled with increased translation of RNA binding proteins and nuclear export machinery, which results in altered RNA partitioning and accelerated decay of select transcripts encoding proapoptotic and proinflammatory genes. Heterozygous knockin mice harboring the germline MBI mutation Myc p.T73N exhibit cytoplasmic MYC localization, myeloid progenitors' expansion with similar transcriptional signatures to the overexpression model, and eventually develop hematological malignancies. This study uncovers that MBI MYC mutations alter MYC localization and disrupt mRNA subcellular distribution and turnover of select transcripts to accelerate tumor initiation and growth.
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10
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Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. A general method for quantitative fractionation of mammalian cells. J Cell Biol 2023; 222:213941. [PMID: 36920247 PMCID: PMC10040634 DOI: 10.1083/jcb.202209062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
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Affiliation(s)
- Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University , New York, NY, USA
| | - Hilda A Pasolli
- Electron Microscopy Resource Center, The Rockefeller University , New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
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11
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Wang RH, Luo T, Zhang HL, Du PF. PLA-GNN: Computational inference of protein subcellular location alterations under drug treatments with deep graph neural networks. Comput Biol Med 2023; 157:106775. [PMID: 36921458 DOI: 10.1016/j.compbiomed.2023.106775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
The aberrant protein sorting has been observed in many conditions, including complex diseases, drug treatments, and environmental stresses. It is important to systematically identify protein mis-localization events in a given condition. Experimental methods for finding mis-localized proteins are always costly and time consuming. Predicting protein subcellular localizations has been studied for many years. However, only a handful of existing works considered protein subcellular location alterations. We proposed a computational method for identifying alterations of protein subcellular locations under drug treatments. We took three drugs, including TSA (trichostain A), bortezomib and tacrolimus, as instances for this study. By introducing dynamic protein-protein interaction networks, graph neural network algorithms were applied to aggregate topological information under different conditions. We systematically reported potential protein mis-localization events under drug treatments. As far as we know, this is the first attempt to find protein mis-localization events computationally in drug treatment conditions. Literatures validated that a number of proteins, which are highly related to pharmacological mechanisms of these drugs, may undergo protein localization alterations. We name our method as PLA-GNN (Protein Localization Alteration by Graph Neural Networks). It can be extended to other drugs and other conditions. All datasets and codes of this study has been deposited in a GitHub repository (https://github.com/quinlanW/PLA-GNN).
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Affiliation(s)
- Ren-Hua Wang
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Tao Luo
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Han-Lin Zhang
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
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12
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Zhang X, Gan Y, Zhu H, Liu Z, Yao X, Cheng C, Liu Z, Su C, Zou J. Role of mitochondrial metabolism in immune checkpoint inhibitors-related myocarditis. Front Cardiovasc Med 2023; 10:1112222. [PMID: 36760573 PMCID: PMC9902768 DOI: 10.3389/fcvm.2023.1112222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Background Immune checkpoint inhibitor-related myocarditis is the deadliest complication of immunotherapy. However, the underlying pathophysiological mechanisms of its occurrence and development remain unclear. Due to the long-term lack of effective early diagnosis and treatment options, it is of great significance to understand the pathophysiological mechanism of immune checkpoint inhibitor-related myocarditis. Methods Tissue samples from three patients with immune checkpoint inhibitor-related myocarditis and three control tissue samples were collected for protein analysis. Differentially expressed proteins were screened out using quantitative proteomics technology based on TMT markers. Protein-protein interaction (PPI) and Gene Ontology (GO) functional enrichment analyses of cross-factors were subsequently performed. Combined with the PD-L1 subcellular organelle- level protein interaction network, we searched for hub proteins involved in immune checkpoint inhibitor-related myocarditis and explored potential drug sensitivity and disease correlation. Results A total of 306 differentially expressed proteins were identified in immune checkpoint inhibitor-related myocarditis. Enrichment analysis showed that the differentially expressed proteins were closely related to mitochondrial metabolism. By analyzing mitochondria-related proteins and PD-L1-related proteins, we found four hub proteins, mammalian target of rapamycin (mTOR), Glycogen synthase kinase 3β (GSK3β), Protein tyrosine phosphatase non-receptor type 11 (PTPN11), and Mitofusin 2 (MFN2), indicating that they are closely related to immune checkpoint inhibitor-related myocarditis. Finally, we explored potential drugs for the treatment of immune checkpoint inhibitor-related myocarditis. Conclusion Mitochondrial metabolism is involved in the process of immune checkpoint inhibitor-related myocarditis, and we identified four hub proteins, which may become new biomarkers for the early diagnosis and treatment of immune checkpoint inhibitor-related myocarditis.
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13
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Castro A, Kaabinejadian S, Yari H, Hildebrand W, Zanetti M, Carter H. Subcellular location of source proteins improves prediction of neoantigens for immunotherapy. EMBO J 2022; 41:e111071. [PMID: 36314681 PMCID: PMC9753441 DOI: 10.15252/embj.2022111071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 12/23/2022] Open
Abstract
Antigen presentation via the major histocompatibility complex (MHC) is essential for anti-tumor immunity. However, the rules that determine which tumor-derived peptides will be immunogenic are still incompletely understood. Here, we investigated whether constraints on peptide accessibility to the MHC due to protein subcellular location are associated with peptide immunogenicity potential. Analyzing over 380,000 peptides from studies of MHC presentation and peptide immunogenicity, we find clear spatial biases in both eluted and immunogenic peptides. We find that including parent protein location improves the prediction of peptide immunogenicity in multiple datasets. In human immunotherapy cohorts, the location was associated with a neoantigen vaccination response, and immune checkpoint blockade responders generally had a higher burden of neopeptides from accessible locations. We conclude that protein subcellular location adds important information for optimizing cancer immunotherapies.
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Affiliation(s)
- Andrea Castro
- Bioinformatics and Systems Biology ProgramUniversity of California San DiegoLa JollaCAUSA
| | - Saghar Kaabinejadian
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOKUSA
- Pure MHC LLCOklahoma CityOKUSA
| | - Hooman Yari
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOKUSA
| | - William Hildebrand
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOKUSA
| | - Maurizio Zanetti
- The Laboratory of Immunology and Department of MedicineUniversity of California San DiegoLa JollaCAUSA
- Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | - Hannah Carter
- Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
- Department of Medicine, Division of Medical GeneticsUniversity of California San DiegoLa JollaCAUSA
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14
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Deb Roy A, Gross EG, Pillai GS, Seetharaman S, Etienne-Manneville S, Inoue T. Non-catalytic allostery in α-TAT1 by a phospho-switch drives dynamic microtubule acetylation. J Cell Biol 2022; 221:213540. [PMID: 36222836 PMCID: PMC9565784 DOI: 10.1083/jcb.202202100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/03/2022] [Accepted: 07/20/2022] [Indexed: 11/22/2022] Open
Abstract
Spatiotemporally dynamic microtubule acetylation underlies diverse physiological and pathological events. Despite its ubiquity, the molecular mechanisms that regulate the sole microtubule acetylating agent, α-tubulin-N-acetyltransferase-1 (α-TAT1), remain obscure. Here, we report that dynamic intracellular localization of α-TAT1 along with its catalytic activity determines efficiency of microtubule acetylation. Specifically, we newly identified a conserved signal motif in the intrinsically disordered C-terminus of α-TAT1, consisting of three competing regulatory elements-nuclear export, nuclear import, and cytosolic retention. Their balance is tuned via phosphorylation by CDK1, PKA, and CK2, and dephosphorylation by PP2A. While the unphosphorylated form binds to importins and resides both in cytosol and nucleus, the phosphorylated form binds to specific 14-3-3 adapters and accumulates in the cytosol for maximal substrate access. Unlike other molecules with a similar phospho-regulated signal motif, α-TAT1 uniquely uses the nucleus as a hideout. This allosteric spatial regulation of α-TAT1 function may help uncover a spatiotemporal code of microtubule acetylation in normal and aberrant cell behavior.
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Affiliation(s)
- Abhijit Deb Roy
- Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - Shailaja Seetharaman
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691, Université Paris Cité, Centre national de la recherche scientifique, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691, Université Paris Cité, Centre national de la recherche scientifique, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Takanari Inoue
- Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD
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15
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Solís-Fernández G, Montero-Calle A, Martínez-Useros J, López-Janeiro Á, de los Ríos V, Sanz R, Dziakova J, Milagrosa E, Fernández-Aceñero MJ, Peláez-García A, Casal JI, Hofkens J, Rocha S, Barderas R. Spatial Proteomic Analysis of Isogenic Metastatic Colorectal Cancer Cells Reveals Key Dysregulated Proteins Associated with Lymph Node, Liver, and Lung Metastasis. Cells 2022; 11:cells11030447. [PMID: 35159257 PMCID: PMC8834500 DOI: 10.3390/cells11030447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
Metastasis is the primary cause of colorectal cancer (CRC) death. The liver and lung, besides adjacent lymph nodes, are the most common sites of metastasis. Here, we aimed to study the lymph nodes, liver, and lung CRC metastasis by quantitative spatial proteomics analysis using CRC cell-based models that recapitulate these metastases. The isogenic KM12 cell system composed of the non-metastatic KM12C cells, liver metastatic KM12SM cells, and liver and lung metastatic KM12L4a cells, and the isogenic non-metastatic SW480 and lymph nodes metastatic SW620 cells, were used. Cells were fractionated to study by proteomics five subcellular fractions corresponding to cytoplasm, membrane, nucleus, chromatin-bound proteins, and cytoskeletal proteins, and the secretome. Trypsin digested extracts were labeled with TMT 11-plex and fractionated prior to proteomics analysis on a Q Exactive. We provide data on protein abundance and localization of 4710 proteins in their different subcellular fractions, depicting dysregulation of proteins in abundance and/or localization in the most common sites of CRC metastasis. After bioinformatics, alterations in abundance and localization for selected proteins from diverse subcellular localizations were validated via WB, IF, IHC, and ELISA using CRC cells, patient tissues, and plasma samples. Results supported the relevance of the proteomics results in an actual CRC scenario. It was particularly relevant that the measurement of GLG1 in plasma showed diagnostic ability of advanced stages of the disease, and that the mislocalization of MUC5AC and BAIAP2 in the nucleus and membrane, respectively, was significantly associated with poor prognosis of CRC patients. Our results demonstrate that the analysis of cell extracts dilutes protein alterations in abundance in specific localizations that might only be observed studying specific subcellular fractions, as here observed for BAIAP2, GLG1, PHYHIPL, TNFRSF10A, or CDKN2AIP, which are interesting proteins that should be further analyzed in CRC metastasis.
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Affiliation(s)
- Guillermo Solís-Fernández
- Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium; (G.S.-F.); (J.H.); (S.R.)
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Madrid, Spain;
| | - Ana Montero-Calle
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Madrid, Spain;
| | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Health Research Institute—Fundacion Jimenez Diaz University Hospital, 28040 Madrid, Spain;
| | - Álvaro López-Janeiro
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain; (Á.L.-J.); (A.P.-G.)
| | - Vivian de los Ríos
- Proteomics Facility, Centro de Investigaciones Biológicas (CIB-CSIC), 28039 Madrid, Spain;
| | - Rodrigo Sanz
- Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain; (R.S.); (J.D.); (E.M.); (M.J.F.-A.)
| | - Jana Dziakova
- Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain; (R.S.); (J.D.); (E.M.); (M.J.F.-A.)
| | - Elena Milagrosa
- Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain; (R.S.); (J.D.); (E.M.); (M.J.F.-A.)
| | | | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain; (Á.L.-J.); (A.P.-G.)
| | - José Ignacio Casal
- Centro de Investigaciones Biológicas (CIB-CSIC), Department of Molecular Biomedicine, 28039 Madrid, Spain;
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium; (G.S.-F.); (J.H.); (S.R.)
| | - Susana Rocha
- Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium; (G.S.-F.); (J.H.); (S.R.)
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Madrid, Spain;
- Correspondence: ; Tel.: +34-918223231
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16
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CYCLON and NPM1 Cooperate within an Oncogenic Network Predictive of R-CHOP Response in DLBCL. Cancers (Basel) 2021; 13:cancers13235900. [PMID: 34885010 PMCID: PMC8656558 DOI: 10.3390/cancers13235900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/05/2021] [Accepted: 11/17/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary CYCLON is a nuclear protein, which has been associated with disease progression and treatment resistance in DLBCL, the most common form of aggressive B-cell lymphoma, but also represents a predictive factor of refractory disease and relapse for immuno-chemotherapy-treated DLBCL patients. The molecular mechanisms related to this unstructured protein remain largely uncharacterized. Here, we performed a mass-spectrometry-based identification of the CYCLON protein interactome that suggested it could exert nucleolar functions related to cell proliferation. Among the CYCLON oncogenic network, we performed an immunohistochemical evaluation of the multi-functional nucleolar protein NPM1 in a DLBCL cohort and showed that CYCLON/NPM1 concomitant expression delineates a poor prognosis subgroup of patients. Multivariate survival analyses demonstrated that specific sub-cellular localizations of CYCLON and NPM1 represent independent novel predictors specifically associated with refractory DLBCL. Abstract R-CHOP immuno-chemotherapy significantly improved clinical management of diffuse large B-cell lymphoma (DLBCL). However, 30–40% of DLBCL patients still present a refractory disease or relapse. Most of the prognostic markers identified to date fail to accurately stratify high-risk DLBCL patients. We have previously shown that the nuclear protein CYCLON is associated with DLBCL disease progression and resistance to anti-CD20 immunotherapy in preclinical models. We also recently reported that it also represents a potent predictor of refractory disease and relapse in a retrospective DLBCL cohort. However, only sparse data are available to predict the potential biological role of CYCLON and how it might exert its adverse effects on lymphoma cells. Here, we characterized the protein interaction network of CYCLON, connecting this protein to the nucleolus, RNA processing, MYC signaling and cell cycle progression. Among this network, NPM1, a nucleolar multi-functional protein frequently deregulated in cancer, emerged as another potential target related to treatment resistance in DLBCL. Immunohistochemistry evaluation of CYCLON and NPM1 revealed that their co-expression is strongly related to inferior prognosis in DLBCL. More specifically, alternative sub-cellular localizations of the proteins (extra-nucleolar CYCLON and pan-cellular NPM1) represent independent predictive factors specifically associated to R-CHOP refractory DLBCL patients, which could allow them to be orientated towards risk-adapted or novel targeted therapies.
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Nair J, Syed SB, Mahaddalkar T, Ketkar M, Thorat R, Sastri Goda J, Dutt S. DUSP6 regulates radio-sensitivity in glioblastoma by modulating the recruitment of p-DNAPKcs at DNA double-strand breaks. J Cell Sci 2021; 134:273732. [PMID: 34792128 DOI: 10.1242/jcs.259520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Glioblastoma (GBM) has poor median survival due to its resistance to chemo-radiotherapy regimen, resulting in tumor recurrence. Recurrent GBMs currently lack effective treatments. DUSP6 is known to be pro-tumorigenic and is up-regulated in GBM. We show that DUSP6 expression is significantly higher in recurrent GBM patient biopsies (n=11) compared to primary biopsies (n=11). Importantly, although reported as cytoplasmic protein, we found nuclear localization of DUSP6 in primary and recurrent patient samples and in parent and relapse population of GBM cell lines generated from in vitro radiation survival model. DUSP6 inhibition using BCI resulted in decreased proliferation and clonogenic survival of parent and relapse cells. Pharmacological or genetic inhibition of DUSP6 catalytic activity radio-sensitized primary and importantly, relapse GBM cells by inhibiting the recruitment of p-DNAPKcs, subsequently down-regulating the recruitment of γH2AX and 53BP1. This resulted in decreased cell survival and prolonged growth arrest upon irradiation in vitro and significantly increased the progression-free survival in orthotopic mouse models of GBM. Our study highlights a non-canonical function of DUSP6, emphasizing the potential application of DUSP6 inhibitors in the treatment of recurrent GBM.
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Affiliation(s)
- Jyothi Nair
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Safiulla Basha Syed
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India
| | - Tejashree Mahaddalkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Madhura Ketkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India
| | - Jayant Sastri Goda
- Department of Radiation Oncology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai - 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, India
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18
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Rose M, Cardon T, Aboulouard S, Hajjaji N, Kobeissy F, Duhamel M, Fournier I, Salzet M. Surfaceome Proteomic of Glioblastoma Revealed Potential Targets for Immunotherapy. Front Immunol 2021; 12:746168. [PMID: 34646273 PMCID: PMC8503648 DOI: 10.3389/fimmu.2021.746168] [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: 07/23/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma (GBM) is the most common and devastating malignant brain tumor in adults. The mortality rate is very high despite different treatments. New therapeutic targets are therefore highly needed. Cell-surface proteins represent attractive targets due to their accessibility, their involvement in essential signaling pathways, and their dysregulated expression in cancer. Moreover, they are potential targets for CAR-based immunotherapy or mRNA vaccine strategies. In this context, we investigated the GBM-associated surfaceome by comparing it to astrocytes cell line surfaceome to identify new specific targets for GBM. For this purpose, biotinylation of cell surface proteins has been carried out in GBM and astrocytes cell lines. Biotinylated proteins were purified on streptavidin beads and analyzed by shotgun proteomics. Cell surface proteins were identified with Cell Surface Proteins Atlas (CSPA) and Gene Ontology enrichment. Among all the surface proteins identified in the different cell lines we have confirmed the expression of 66 of these in patient’s glioblastoma using spatial proteomic guided by MALDI-mass spectrometry. Moreover, 87 surface proteins overexpressed or exclusive in GBM cell lines have been identified. Among these, we found 11 specific potential targets for GBM including 5 mutated proteins such as RELL1, CYBA, EGFR, and MHC I proteins. Matching with drugs and clinical trials databases revealed that 7 proteins were druggable and under evaluation, 3 proteins have no known drug interaction yet and none of them are the mutated form of the identified proteins. Taken together, we discovered potential targets for immune therapy strategies in GBM.
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Affiliation(s)
- Mélanie Rose
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Soulaimane Aboulouard
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Nawale Hajjaji
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Marie Duhamel
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Isabelle Fournier
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut Universitaire de France, Paris, France
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Kynurenine Monooxygenase Expression and Activity in Human Astrocytomas. Cells 2021; 10:cells10082028. [PMID: 34440798 PMCID: PMC8393384 DOI: 10.3390/cells10082028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/24/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor. The enzyme indoleamine-2,3-dioxygenase (IDO), which participates in the rate-limiting step of tryptophan catabolism through the kynurenine pathway (KP), is associated with poor prognosis in patients with GBM. The metabolites produced after tryptophan oxidation have immunomodulatory properties that can support the immunosuppressor environment. In this study, mRNA expression, protein expression, and activity of the enzyme kynurenine monooxygenase (KMO) were analyzed in GBM cell lines (A172, LN-18, U87, U373) and patient-derived astrocytoma samples. KMO mRNA expression was assessed by real-time RT-qPCR, KMO protein expression was evaluated by flow cytometry and immunofluorescence, and KMO activity was determined by quantifying 3-hydroxykynurenine by HPLC. Heterogenous patterns of both KMO expression and activity were observed among the GBM cell lines, with the A172 cell line showing the highest KMO expression and activity. Higher KMO mRNA expression was observed in glioma samples than in patients diagnosed with only a neurological disease; high KMO mRNA expression was also observed when using samples from patients with GBM in the TCGA program. The KMO protein expression was localized in GFAP+ cells in tumor tissue. These results suggest that KMO is a relevant target to be explored in glioma since it might play a role in supporting tumor metabolism and immune suppression.
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20
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Sugár S, Tóth G, Bugyi F, Vékey K, Karászi K, Drahos L, Turiák L. Alterations in protein expression and site-specific N-glycosylation of prostate cancer tissues. Sci Rep 2021; 11:15886. [PMID: 34354152 PMCID: PMC8342536 DOI: 10.1038/s41598-021-95417-5] [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: 05/05/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023] Open
Abstract
Identifying molecular alterations occurring during cancer progression is essential for a deeper understanding of the underlying biological processes. Here we have analyzed cancerous and healthy prostate biopsies using nanoLC-MS(MS) to detect proteins with altered expression and N-glycosylation. We have identified 75 proteins with significantly changing expression during disease progression. The biological processes involved were assigned based on protein-protein interaction networks. These include cellular component organization, metabolic and localization processes. Multiple glycoproteins were identified with aberrant glycosylation in prostate cancer, where differences in glycosite-specific sialylation, fucosylation, and galactosylation were the most substantial. Many of the glycoproteins with altered N-glycosylation were extracellular matrix constituents, and are heavily involved in the establishment of the tumor microenvironment.
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Affiliation(s)
- Simon Sugár
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.11804.3c0000 0001 0942 9821Semmelweis University, Ph.D. School of Pharmaceutical Sciences, Üllői út 26, 1085 Budapest, Hungary
| | - Gábor Tóth
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.6759.d0000 0001 2180 0451Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rakpart 3, 1111 Budapest, Hungary
| | - Fanni Bugyi
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.5591.80000 0001 2294 6276Eötvös Loránd University, Hevesy György Ph.D. School of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Károly Vékey
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Katalin Karászi
- grid.11804.3c0000 0001 0942 98211St Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary
| | - László Drahos
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Lilla Turiák
- grid.425578.90000 0004 0512 3755MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok körútja 2, 1117 Budapest, Hungary ,grid.11804.3c0000 0001 0942 9821Semmelweis University, Ph.D. School of Pharmaceutical Sciences, Üllői út 26, 1085 Budapest, Hungary
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21
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Lang YD, Jou YS. PSPC1 is a new contextual determinant of aberrant subcellular translocation of oncogenes in tumor progression. J Biomed Sci 2021; 28:57. [PMID: 34340703 PMCID: PMC8327449 DOI: 10.1186/s12929-021-00753-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/24/2021] [Indexed: 12/30/2022] Open
Abstract
Dysregulation of nucleocytoplasmic shuttling is commonly observed in cancers and emerging as a cancer hallmark for the development of anticancer therapeutic strategies. Despite its severe adverse effects, selinexor, a selective first-in-class inhibitor of the common nuclear export receptor XPO1, was developed to target nucleocytoplasmic protein shuttling and received accelerated FDA approval in 2019 in combination with dexamethasone as a fifth-line therapeutic option for adults with relapsed refractory multiple myeloma (RRMM). To explore innovative targets in nucleocytoplasmic shuttling, we propose that the aberrant contextual determinants of nucleocytoplasmic shuttling, such as PSPC1 (Paraspeckle component 1), TGIF1 (TGF-β Induced Factor Homeobox 1), NPM1 (Nucleophosmin), Mortalin and EBP50, that modulate shuttling (or cargo) proteins with opposite tumorigenic functions in different subcellular locations could be theranostic targets for developing anticancer strategies. For instance, PSPC1 was recently shown to be the contextual determinant of the TGF-β prometastatic switch and PTK6/β-catenin reciprocal oncogenic nucleocytoplasmic shuttling during hepatocellular carcinoma (HCC) progression. The innovative nucleocytoplasmic shuttling inhibitor PSPC1 C-terminal 131 polypeptide (PSPC1-CT131), which was developed to target both the shuttling determinant PSPC1 and the shuttling protein PTK6, maintained their tumor-suppressive characteristics and exhibited synergistic effects on tumor suppression in HCC cells and mouse models. In summary, targeting the contextual determinants of nucleocytoplasmic shuttling with cargo proteins having opposite tumorigenic functions in different subcellular locations could be an innovative strategy for developing new therapeutic biomarkers and agents to improve cancer therapy.
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Affiliation(s)
- Yaw-Dong Lang
- Institute of Biomedical Sciences, Academia Sinica, 11529, Taipei, Taiwan
| | - Yuh-Shan Jou
- Institute of Biomedical Sciences, Academia Sinica, 11529, Taipei, Taiwan.
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22
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Loss of the MAF Transcription Factor in Laryngeal Squamous Cell Carcinoma. Biomolecules 2021; 11:biom11071035. [PMID: 34356658 PMCID: PMC8301809 DOI: 10.3390/biom11071035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022] Open
Abstract
MAF is a transcription factor that may act either as a tumor suppressor or as an oncogene, depending on cell type. We have shown previously that the overexpressed miR-1290 influences MAF protein levels in LSCC (laryngeal squamous cell carcinoma) cell lines. In this study, we shed further light on the interaction between miR-1290 and MAF, as well as on cellular MAF protein localization in LSCC. We confirmed the direct interaction between miR-1290 and MAF 3′UTR by a dual-luciferase reporter assay. In addition, we used immunohistochemistry staining to analyze MAF protein distribution and observed loss of MAF nuclear expression in 58% LSCC samples, of which 10% showed complete absence of MAF, compared to nuclear and cytoplasmatic expression in 100% normal mucosa. Using TCGA data, bisulfite pyrosequencing and CNV analysis, we excluded the possibility that loss-of-function mutations, promoter region DNA methylation or CNV are responsible for MAF loss in LSCC. Finally, we identified genes involved in the regulation of apoptosis harboring the MAF binding motif in their promoter region by applied FIMO and DAVID GO analysis. Our results highlight the role of miR-1290 in suppressing MAF expression in LSCC. Furthermore, MAF loss or mislocalization in FFPE LSCC tumor samples might suggest that MAF acts as a LSCC tumor suppressor by regulating apoptosis.
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23
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Yang J, Lee J, Land MA, Lai S, Igoshin OA, St-Pierre F. A synthetic circuit for buffering gene dosage variation between individual mammalian cells. Nat Commun 2021; 12:4132. [PMID: 34226556 PMCID: PMC8257781 DOI: 10.1038/s41467-021-23889-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits - Equalizers - that buffer copy-number variation at the single-cell level. Equalizers couple a transcriptional negative feedback loop with post-transcriptional incoherent feedforward control. Computational modeling suggests that the combination of these two topologies enables Equalizers to operate over a wide range of plasmid copy numbers. We demonstrate experimentally that Equalizers outperform other gene dosage compensation topologies and produce as low cell-to-cell variation as chromosomally integrated genes. We also show that episome-encoded Equalizers enable the rapid generation of extrachromosomal cell lines with stable and uniform expression. Overall, Equalizers are simple and versatile devices for homogeneous gene expression and can facilitate the engineering of synthetic circuits that function reliably in every cell.
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Affiliation(s)
- Jin Yang
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Michelle A Land
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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24
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The G-Protein-Coupled Membrane Estrogen Receptor Is Present in Horse Cryptorchid Testes and Mediates Downstream Pathways. Int J Mol Sci 2021; 22:ijms22137131. [PMID: 34281183 PMCID: PMC8269005 DOI: 10.3390/ijms22137131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/18/2022] Open
Abstract
Cryptorchidism in horses is a commonly occurring malformation. The molecular basis of this pathology is not fully known. In addition, the origins of high intratesticular estrogen levels in horses remain obscure. In order to investigate the role of the G-protein-coupled membrane estrogen receptor (GPER) and establish histological and biochemical cryptorchid testis status, healthy and cryptorchid horse testes were subjected to scanning electron microscopy analysis, histochemical staining for total protein (with naphthol blue black; NBB), acid content (with toluidine blue O; TBO), and polysaccharide content (with periodic acid-Schiff; PAS). The expression of GPER was analyzed by immunohistochemistry and Western blot. GPER-mediated intracellular cAMP and calcium (Ca2+) signaling were measured immunoenzymatically or colorimetrically. Our data revealed changes in the distribution of polysaccharide content but not the protein and acid content in the cryptorchid testis. Polysaccharides seemed to be partially translocated from the interstitial compartment to the seminiferous tubule compartment. Moreover, the markedly decreased expression of GPER and GPER downstream molecules, cAMP and Ca2+, suggests their potential role in testis pathology. Increased estrogen levels in cryptorchid conditions may be linked to disturbed GPER signaling. We postulate that GPER is a prominent key player in testis development and function and may be used as a new biomarker of horse testis in health and disease.
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25
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NR4A1 Regulates Tamoxifen Resistance by Suppressing ERK Signaling in ER-Positive Breast Cancer. Cells 2021; 10:cells10071633. [PMID: 34209871 PMCID: PMC8307977 DOI: 10.3390/cells10071633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Endocrine therapy is used to treat estrogen receptor (ER)-positive breast cancer. Tamoxifen is effective against this cancer subtype. Nonetheless, approximately 30% of patients treated with tamoxifen acquire resistance, resulting in therapeutic challenges. NR4A1 plays key roles in processes associated with carcinogenesis, apoptosis, DNA repair, proliferation, and inflammation. However, the role of NR4A1 in tamoxifen-resistant ER-positive breast cancer has not yet been elucidated. Here, we propose that NR4A1 is a promising target to overcome tamoxifen resistance. NR4A1 gene expression was downregulated in tamoxifen-resistant MCF7 (TamR) cells compared to that in MCF7 cells. Kaplan-Meier plots were used to identify high NR4A1 expression correlated with increased survival rates in patients with ER-positive breast cancer following tamoxifen treatment. Gain and loss of function experiments showed that NR4A1 restores sensitivity to tamoxifen by regulating cell proliferation, migration, invasion, and apoptosis. NR4A1 localized to the cytoplasm enhanced the expression of apoptotic factors. In silico and in vitro analyses revealed that NR4A1 enhanced responsiveness to tamoxifen by suppressing ERK signaling in ER-positive breast cancer, suggesting that the NR4A1/ERK signaling axis modulates tamoxifen resistance. These results indicate that NR4A1 could be a potential therapeutic target to overcome tamoxifen resistance in ER-positive breast cancer.
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26
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NR4A1 Regulates Tamoxifen Resistance by Suppressing ERK Signaling in ER-Positive Breast Cancer. Cells 2021. [PMID: 34209871 DOI: 10.3390/cells10071633/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Endocrine therapy is used to treat estrogen receptor (ER)-positive breast cancer. Tamoxifen is effective against this cancer subtype. Nonetheless, approximately 30% of patients treated with tamoxifen acquire resistance, resulting in therapeutic challenges. NR4A1 plays key roles in processes associated with carcinogenesis, apoptosis, DNA repair, proliferation, and inflammation. However, the role of NR4A1 in tamoxifen-resistant ER-positive breast cancer has not yet been elucidated. Here, we propose that NR4A1 is a promising target to overcome tamoxifen resistance. NR4A1 gene expression was downregulated in tamoxifen-resistant MCF7 (TamR) cells compared to that in MCF7 cells. Kaplan-Meier plots were used to identify high NR4A1 expression correlated with increased survival rates in patients with ER-positive breast cancer following tamoxifen treatment. Gain and loss of function experiments showed that NR4A1 restores sensitivity to tamoxifen by regulating cell proliferation, migration, invasion, and apoptosis. NR4A1 localized to the cytoplasm enhanced the expression of apoptotic factors. In silico and in vitro analyses revealed that NR4A1 enhanced responsiveness to tamoxifen by suppressing ERK signaling in ER-positive breast cancer, suggesting that the NR4A1/ERK signaling axis modulates tamoxifen resistance. These results indicate that NR4A1 could be a potential therapeutic target to overcome tamoxifen resistance in ER-positive breast cancer.
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27
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Badar S, Azarkan M, Mekkawy AH, Akhter J, Pillai K, El Mahyaoui R, Ke K, Cavanaugh L, Morris DL. Comparison of proteolytic, cytotoxic and anticoagulant properties of chromatographically fractionated bromelain to un-fractionated bromelain. Am J Transl Res 2021; 13:4309-4321. [PMID: 34150016 PMCID: PMC8205729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Bromelain consisting of a number of proteolytic enzymes possess anticancer and thrombotic properties. Hence, four chromatically separated fractions were examined for their proteolytic, anticancer and antithrombotic activity. Bromelain fractions were separated using ion-exchange column chromatography. Proteolytic properties were assessed using standard azocasein assay. Anticancer properties were first assessed using four different cell lines PANC-1, HEP 2B, HEP 3G and OVCAR-3 on cells grown in 96 well plates. Subsequently, fraction 2 and fraction 3 combined with gemcitabine were tested in ASPC-1 cells. Then cytotoxicity of fraction 3 was compared to bromelain in combination with doxorubicin and N-acetylcysteine on HEP G2 and HEP 3B cells. Finally, the anticoagulation effect of fraction 3 or bromelain combined with N-acetylcysteine was evaluated using human blood. Fraction 3 showed the highest proteolytic activity (5% greater than standard bromelain) whilst others were less active. Cytotoxicity as assessed by IC50 indicated fraction 3 to be the most potent whilst the others did not follow their proteolytic potency order. OVCAR-3 was the most sensitive amongst the cell lines. Fraction 3 showed higher potency in combination with gemcitabine in ASPC-1 cells compared to fraction 2. Similarly, fraction 3 in combination with doxorubicin showed higher toxicity when compared to bromelain. Fraction 3 or bromelain only showed thrombolytic activity in combination with N-acetylcysteine. Fraction 3 may be developed for clinical use since it showed better cytotoxicity compared to bromelain.
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Affiliation(s)
- Samina Badar
- Department of Surgery, University of New South Wales, St. George HospitalKogarah, NSW, Australia
| | - Mohamed Azarkan
- Service de Chimie Générale I (CP 609), Protein Chemistry Unit, Faculty of Medicine, Université Libre de Bruxelles (ULB)Brussels, Belgium
| | - Ahmed H Mekkawy
- Department of Surgery, University of New South Wales, St. George HospitalKogarah, NSW, Australia
- Mucpharm Pty LtdAustralia
| | - Javed Akhter
- Department of Surgery, University of New South Wales, St. George HospitalKogarah, NSW, Australia
- Mucpharm Pty LtdAustralia
| | - Krishna Pillai
- Department of Surgery, University of New South Wales, St. George HospitalKogarah, NSW, Australia
- Mucpharm Pty LtdAustralia
| | - Rachida El Mahyaoui
- Service de Chimie Générale I (CP 609), Protein Chemistry Unit, Faculty of Medicine, Université Libre de Bruxelles (ULB)Brussels, Belgium
| | - Kevin Ke
- Department of Surgery, University of New South Wales, St. George HospitalKogarah, NSW, Australia
| | - Lauren Cavanaugh
- Haematology Department, St. George HospitalKogarah, NSW, Australia
| | - David L Morris
- Department of Surgery, University of New South Wales, St. George HospitalKogarah, NSW, Australia
- Mucpharm Pty LtdAustralia
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28
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Kong KYE, Coelho JPL, Feige MJ, Khmelinskii A. Quality control of mislocalized and orphan proteins. Exp Cell Res 2021; 403:112617. [PMID: 33930402 DOI: 10.1016/j.yexcr.2021.112617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Abstract
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structure and function, thereby disrupting proteome homeostasis. Among a variety of potential mistakes, proteins can be targeted to incorrect compartments or subunits of protein complexes may fail to assemble properly with their partners, resulting in the formation of mislocalized and orphan proteins, respectively. Quality control systems are in place to handle these aberrant proteins, and to minimize their detrimental impact on cellular functions. Here, we discuss recent findings on quality control mechanisms handling mislocalized and orphan proteins. We highlight common principles involved in their recognition and summarize how accumulation of these aberrant molecules is associated with aging and disease.
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Affiliation(s)
| | - João P L Coelho
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Matthias J Feige
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
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29
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Lai MH, Liao CH, Tsai NM, Chang KF, Liu CC, Chiu YH, Huang KC, Lin CS. Surface Expression of Kynurenine 3-Monooxygenase Promotes Proliferation and Metastasis in Triple-Negative Breast Cancers. Cancer Control 2021; 28:10732748211009245. [PMID: 33887987 PMCID: PMC8204454 DOI: 10.1177/10732748211009245] [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] [Indexed: 12/24/2022] Open
Abstract
Kynurenine 3-monooxygenase (KMO) is the pivotal enzyme in the kynurenine pathway and is located on the mitochondrial outer membrane. The dysregulation of KMO leads to various neurodegenerative diseases; however, it is rarely mentioned in cancer progression. Our previous study showed that KMO overexpression in canine mammary gland tumors (cMGT) is associated with poor prognosis in cMGT patients. Surprisingly, it was also found that KMO can be located on the cell membranes of cMGT cells, unlike its location in normal cells, where KMO is expressed only within the cytosol. Since cMGT and human breast cancer share similar morphologies and pathogenesis, this study investigated the possibility of detecting surface KMO in human breast cancers and the role of surface KMO in tumorigenesis. Using immunohistochemistry (IHC), flow cytometry (FC), immunofluorescence assay (IFA), and transmission electron microscopy (TEM), we demonstrated that KMO can be aberrantly and highly expressed on the cell membranes of breast cancer tissues and in an array of cell lines. Masking surface KMO with anti-KMO antibody reduced the cell viability and inhibited the migration and invasion of the triple-negative breast cancer cell line, MDA-MB-231. These results indicated that aberrant surface expression of KMO may be a potential therapeutic target for human breast cancers.
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Affiliation(s)
- Min-Hua Lai
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei
| | - Chi-Hsun Liao
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei
| | - Nu-Man Tsai
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung.,Department of Pathology and Clinical Laboratory, Chung Shan Medical University Hospital, Taichung
| | - Kai-Fu Chang
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung.,Institute of Medicine of Chung Shun Medical University, Taichung
| | - Cheng-Chi Liu
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei
| | - Yi-Han Chiu
- Department of Nursing, St. Mary's Junior College of Medicine, Nursing and Management, Yilan
| | - Kuo-Ching Huang
- Holistic Education Center, Mackay Medical College, New Taipei City. Chiu is now with Department of Microbiology, Soochow University, Taipei
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei
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30
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Chao JT, Roskelley CD, Loewen CJR. MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy. BMC Bioinformatics 2021; 22:202. [PMID: 33879063 PMCID: PMC8056608 DOI: 10.1186/s12859-021-04117-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/02/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic testing is widely used in evaluating a patient's predisposition to hereditary diseases. In the case of cancer, when a functionally impactful mutation (i.e. genetic variant) is identified in a disease-relevant gene, the patient is at elevated risk of developing a lesion in their lifetime. Unfortunately, as the rate and coverage of genetic testing has accelerated, our ability to assess the functional status of new variants has fallen behind. Therefore, there is an urgent need for more practical, streamlined and cost-effective methods for classifying variants. RESULTS To directly address this issue, we designed a new approach that uses alterations in protein subcellular localization as a key indicator of loss of function. Thus, new variants can be rapidly functionalized using high-content microscopy (HCM). To facilitate the analysis of the large amounts of imaging data, we developed a new software toolkit, named MAPS for machine-assisted phenotype scoring, that utilizes deep learning to extract and classify cell-level features. MAPS helps users leverage cloud-based deep learning services that are easy to train and deploy to fit their specific experimental conditions. Model training is code-free and can be done with limited training images. Thus, MAPS allows cell biologists to easily incorporate deep learning into their image analysis pipeline. We demonstrated an effective variant functionalization workflow that integrates HCM and MAPS to assess missense variants of PTEN, a tumor suppressor that is frequently mutated in hereditary and somatic cancers. CONCLUSIONS This paper presents a new way to rapidly assess variant function using cloud deep learning. Since most tumor suppressors have well-defined subcellular localizations, our approach could be widely applied to functionalize variants of uncertain significance and help improve the utility of genetic testing.
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Affiliation(s)
- Jesse T Chao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, V6T1Z3, Canada.
| | - Calvin D Roskelley
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, V6T1Z3, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, V6T1Z3, Canada
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31
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Jayanthi B, Bachhav B, Wan Z, Martinez Legaspi S, Segatori L. A platform for post-translational spatiotemporal control of cellular proteins. Synth Biol (Oxf) 2021; 6:ysab002. [PMID: 33763602 PMCID: PMC7976946 DOI: 10.1093/synbio/ysab002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Mammalian cells process information through coordinated spatiotemporal regulation of proteins. Engineering cellular networks thus relies on efficient tools for regulating protein levels in specific subcellular compartments. To address the need to manipulate the extent and dynamics of protein localization, we developed a platform technology for the target-specific control of protein destination. This platform is based on bifunctional molecules comprising a target-specific nanobody and universal sequences determining target subcellular localization or degradation rate. We demonstrate that nanobody-mediated localization depends on the expression level of the target and the nanobody, and the extent of target subcellular localization can be regulated by combining multiple target-specific nanobodies with distinct localization or degradation sequences. We also show that this platform for nanobody-mediated target localization and degradation can be regulated transcriptionally and integrated within orthogonal genetic circuits to achieve the desired temporal control over spatial regulation of target proteins. The platform reported in this study provides an innovative tool to control protein subcellular localization, which will be useful to investigate protein function and regulate large synthetic gene circuits.
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Affiliation(s)
- Brianna Jayanthi
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Bhagyashree Bachhav
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Zengyi Wan
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Laura Segatori
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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32
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Yeh CW, Huang WC, Hsu PH, Yeh KH, Wang LC, Hsu PWC, Lin HC, Chen YN, Chen SC, Yeang CH, Yen HCS. The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes. EMBO J 2021; 40:e105846. [PMID: 33469951 PMCID: PMC8013793 DOI: 10.15252/embj.2020105846] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 01/22/2023] Open
Abstract
Protein termini are determinants of protein stability. Proteins bearing degradation signals, or degrons, at their amino‐ or carboxyl‐termini are eliminated by the N‐ or C‐degron pathways, respectively. We aimed to elucidate the function of C‐degron pathways and to unveil how normal proteomes are exempt from C‐degron pathway‐mediated destruction. Our data reveal that C‐degron pathways remove mislocalized cellular proteins and cleavage products of deubiquitinating enzymes. Furthermore, the C‐degron and N‐degron pathways cooperate in protein removal. Proteome analysis revealed a shortfall in normal proteins targeted by C‐degron pathways, but not of defective proteins, suggesting proteolysis‐based immunity as a constraint for protein evolution/selection. Our work highlights the importance of protein termini for protein quality surveillance, and the relationship between the functional proteome and protein degradation pathways.
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Affiliation(s)
- Chi-Wei Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wei-Chieh Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Life Science, Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Kun-Hai Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Li-Chin Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | | | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yi-Ning Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Chuan Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.,Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
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Li GP, Du PF, Shen ZA, Liu HY, Luo T. DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks. Front Genet 2020; 11:600454. [PMID: 33193746 PMCID: PMC7644922 DOI: 10.3389/fgene.2020.600454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/07/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells contain numerous components, which are known as subcellular compartments or subcellular organelles. Proteins must be sorted to proper subcellular compartments to carry out their molecular functions. Mis-localized proteins are related to various cancers. Identifying mis-localized proteins is important in understanding the pathology of cancers and in developing therapies. However, experimental methods, which are used to determine protein subcellular locations, are always costly and time-consuming. We tried to identify cancer-related mis-localized proteins in three different cancers using computational approaches. By integrating gene expression profiles and dynamic protein-protein interaction networks, we established DPPN-SVM (Dynamic Protein-Protein Network with Support Vector Machine), a predictive model using the SVM classifier with diffusion kernels. With this predictive model, we identified a number of mis-localized proteins. Since we introduced the dynamic protein-protein network, which has never been considered in existing works, our model is capable of identifying more mis-localized proteins than existing studies. As far as we know, this is the first study to incorporate dynamic protein-protein interaction network in identifying mis-localized proteins in cancers.
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Affiliation(s)
- Guang-Ping Li
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Zi-Ang Shen
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Hang-Yu Liu
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Tao Luo
- College of Intelligence and Computing, Tianjin University, Tianjin, China
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34
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Tan M, Schaffalitzky de Muckadell OB, Jøergensen MT. Gene Expression Network Analysis of Precursor Lesions in Familial Pancreatic Cancer. J Pancreat Cancer 2020; 6:73-84. [PMID: 32783019 PMCID: PMC7415888 DOI: 10.1089/pancan.2020.0007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose: High-grade pancreatic intraepithelial neoplasia (PanIN) are aggressive premalignant lesions, associated with risk of progression to pancreatic ductal adenocarcinoma (PDAC). A depiction of co-dysregulated gene activity in high-grade familial pancreatic cancer (FPC)-related PanIN lesions may characterize the molecular events during the progression from familial PanIN to PDAC. Materials and Methods: We performed weighted gene coexpression network analysis (WGCNA) to identify clusters of coexpressed genes associated with FPC-related PanIN lesions in 13 samples with PanIN-2/3 from FPC predisposed individuals, 6 samples with PDAC from sporadic pancreatic cancer (SPC) patients, and 4 samples of normal donor pancreatic tissue. Results: WGCNA identified seven differentially expressed gene (DEG) modules and two commonly expressed gene (CEG) modules with significant enrichment for Gene Ontology (GO) terms in FPC and SPC, including three upregulated (p < 5e-05) and four downregulated (p < 6e-04) gene modules in FPC compared to SPC. Among the DEG modules, the upregulated modules include 14 significant genes (p < 1e-06): ALOX12-AS1, BCL2L11, EHD4, C4B, BTN3A3, NDUFA11, RBM4B, MYOC, ZBTB47, TTTY15, NAPRT, LOC102606465, LOC100505711, and PTK2. The downregulated modules include 170 genes (p < 1e-06), among them 13 highly significant genes (p < 1e-10): COL10A1, SAMD9, PLPP4, COMP, POSTN, IGHV4-31, THBS2, MMP9, FNDC1, HOPX, TMEM200A, INHBA, and SULF1. The DEG modules are enriched for GO terms related to mitochondrial structure and adenosine triphosphate metabolic processes, extracellular structure and binding properties, humoral and complement mediated immune response, ligand-gated ion channel activity, and transmembrane receptor activity. Among the CEG modules, IL22RA1, DPEP1, and BCAT1 were found as highly connective hub genes associated with both FPC and SPC. Conclusion: FPC-related PanIN lesions exhibit a common molecular basis with SPC as shown by gene network activities and commonly expressed high-connectivity hub genes. The differential molecular pathology of FPC and SPC involves multiple coexpressed gene clusters enriched for GO terms including extracellular activities and mitochondrion function.
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Affiliation(s)
- Ming Tan
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Ove B. Schaffalitzky de Muckadell
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Maiken Thyregod Jøergensen
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
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35
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Bouziane H, Chouarfia A. Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment. J Integr Bioinform 2020; 18:51-79. [PMID: 32598314 PMCID: PMC8035964 DOI: 10.1515/jib-2019-0091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
To date, many proteins generated by large-scale genome sequencing projects are still uncharacterized and subject to intensive investigations by both experimental and computational means. Knowledge of protein subcellular localization (SCL) is of key importance for protein function elucidation. However, it remains a challenging task, especially for multiple sites proteins known to shuttle between cell compartments to perform their proper biological functions and proteins which do not have significant homology to proteins of known subcellular locations. Due to their low-cost and reasonable accuracy, machine learning-based methods have gained much attention in this context with the availability of a plethora of biological databases and annotated proteins for analysis and benchmarking. Various predictive models have been proposed to tackle the SCL problem, using different protein sequence features pertaining to the subcellular localization, however, the overwhelming majority of them focuses on single localization and cover very limited cellular locations. The prediction was basically established on sorting signals, amino acids compositions, and homology. To improve the prediction quality, focus is actually on knowledge information extracted from annotation databases, such as protein-protein interactions and Gene Ontology (GO) functional domains annotation which has been recently a widely adopted and essential information for learning systems. To deal with such problem, in the present study, we considered SCL prediction task as a multi-label learning problem and tried to label both single site and multiple sites unannotated bacterial protein sequences by mining proteins homology relationships using both GO terms of protein homologs and PSI-BLAST profiles. The experiments using 5-fold cross-validation tests on the benchmark datasets showed a significant improvement on the results obtained by the proposed consensus multi-label prediction model which discriminates six compartments for Gram-negative and five compartments for Gram-positive bacterial proteins.
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Affiliation(s)
- Hafida Bouziane
- Département d’Informatique, Université des Sciences et de la Technologie d’Oran Mohamed Boudiaf, USTO-MB BP 1505, El M’Naouer, 31000, Oran, Algeria
| | - Abdallah Chouarfia
- Département d’Informatique, Université des Sciences et de la Technologie d’Oran Mohamed Boudiaf, USTO-MB BP 1505, El M’Naouer, 31000, Oran, Algeria
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36
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He H, Guo J, Lin X, Xu B. Enzyme-Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells. Angew Chem Int Ed Engl 2020; 59:9330-9334. [PMID: 32119754 PMCID: PMC7269854 DOI: 10.1002/anie.202000983] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Indexed: 01/11/2023]
Abstract
Presently, little is known of how the inter-organelle crosstalk impacts cancer cells owing to the lack of approaches that can manipulate inter-organelle communication in cancer cells. We found that a negatively charged, enzyme cleavable peptide (MitoFlag) enables the trafficking of histone protein H2B, a nuclear protein, to the mitochondria in cancer cells. MitoFlag interacts with the nuclear location sequence of H2B to block it from entering the nucleus. A protease on the mitochondria cleaves the Flag from the MitoFlag/H2B complex to form assemblies that retain H2B on the mitochondria and facilitate H2B entering the mitochondria. Adding NLS, replacing aspartic acid by glutamic acid residues, or changing the l- to d-aspartic acid residue on MitoFlag abolishes the trafficking of H2B into mitochondria of HeLa cells. As the first example of the enzyme-instructed self-assembly of a synthetic peptide for trafficking endogenous proteins, this work provides insights for understanding and manipulating inter-organelle communication in cells.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Xingyi Lin
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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37
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Badve SS, Gökmen-Polar Y. TP53 Status and Estrogen Receptor-Beta in Triple-Negative Breast Cancer: Company Matters. J Natl Cancer Inst 2020; 111:1118-1119. [PMID: 30989234 DOI: 10.1093/jnci/djz052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/05/2019] [Indexed: 01/21/2023] Open
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Clark DJ, Schnaubelt M, Hoti N, Hu Y, Zhou Y, Gooya M, Zhang H. Impact of Increased FUT8 Expression on the Extracellular Vesicle Proteome in Prostate Cancer Cells. J Proteome Res 2020; 19:2195-2205. [PMID: 32378902 DOI: 10.1021/acs.jproteome.9b00578] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Extracellular vesicles (EVs) are involved in intercellular communication, transporting proteins and nucleic acids to proximal and distal regions. There is evidence of glycosylation influencing protein routing into EVs; however, the impact of aberrant cellular glycotransferase expression on EV protein profiles has yet to be evaluated. In this study, we paired extracellular vesicle characterization and quantitative proteomics to determine the systemic impact of altered α(1,6)fucosyltranferase (FUT8) expression on prostate cancer-derived EVs. Our results showed that increased cellular expression of FUT8 could reduce the number of vesicles secreted by prostate cancer cells as well as increase the abundance of proteins associated with cell motility and prostate cancer metastasis. In addition, overexpression of FUT8 resulted in altered glycans on select EV-derived glycoproteins. This study presents the first evidence of altered cellular glycosylation impacting EV protein profiles and provides further rationale for exploring the functional role of glycosylation in EV biogenesis and biology.
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Affiliation(s)
- David J Clark
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Michael Schnaubelt
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Naseruddin Hoti
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Yingwei Hu
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Yangying Zhou
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Mahta Gooya
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
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Fernandes E, Freitas R, Ferreira D, Soares J, Azevedo R, Gaiteiro C, Peixoto A, Oliveira S, Cotton S, Relvas-Santos M, Afonso LP, Palmeira C, Oliveira MJ, Ferreira R, Silva AMN, Lara Santos L, Ferreira JA. Nucleolin-Sle A Glycoforms as E-Selectin Ligands and Potentially Targetable Biomarkers at the Cell Surface of Gastric Cancer Cells. Cancers (Basel) 2020; 12:cancers12040861. [PMID: 32252346 PMCID: PMC7226152 DOI: 10.3390/cancers12040861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/24/2020] [Accepted: 03/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gastric cancer (GC) is a major health burden worldwide, with half of patients developing metastases within 5 years after treatment, urging novel biomarkers for diagnosis and efficient therapeutic targeting. Sialyl-Lewis A (SLeA), a terminal glycoepitope of glycoproteins and glycolipids, offers tremendous potential towards this objective. It is rarely expressed in healthy tissues and blood cells, while it is present in highly metastatic cell lines and metastases. SLeA is also involved in E-selectin mediated metastasis, making it an ideal target to control disease dissemination. METHODS AND RESULTS To improve cancer specificity, we have explored the SLeA-glycoproteome of six GC cell models, with emphasis on glycoproteins showing affinity for E-selectin. A novel bioinformatics-assisted algorithm identified nucleolin (NCL), a nuclear protein, as a potential targetable biomarker potentially involved in metastasis. Several immunoassays, including Western blot and in situ proximity ligation reinforced the existence of cell surface NCL-SLeA glycoforms in GC. The NCL-SLeA glycophenotype was associated with decreased survival and was not reflected in relevant healthy tissues. CONCLUSIONS NCL-SLeA is a biomarker of poor prognosis in GC holding potential for precise cancer targeting. This is the first report describing SLeA in preferentially nuclear protein, setting a new paradigm for cancer biomarkers discovery and targeted therapies.
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Affiliation(s)
- Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
- Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Rui Freitas
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
- Digestive Cancer Research Group, 1495-161 Algés, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
| | - Sara Oliveira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal;
| | - Luis Pedro Afonso
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Pathology Department, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Immunology Department, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
- Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
| | - Maria José Oliveira
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal;
- Institute for Biomedical Engineering (INEB), Porto, Portugal, 4200-135 Porto, Portugal
| | - Rita Ferreira
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - André M. N. Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal;
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Digestive Cancer Research Group, 1495-161 Algés, Portugal
- Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology of Porto, 4200-162 Porto, Portugal
- Department, Porto Comprehensive Cancer Centre (P.ccc), 4200-162 Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, 4200-162 Porto, Portugal; (E.F.); (R.F.); (D.F.); (J.S.); (R.A.); (C.G.); (A.P.); (S.O.); (S.C.); (M.R.-S.); (L.P.A.); (C.P.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-013 Porto, Portugal
- Department, Porto Comprehensive Cancer Centre (P.ccc), 4200-162 Porto, Portugal
- Correspondence: ; Tel.: +351-225084000 (ext. 5111)
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He H, Guo J, Lin X, Xu B. Enzyme‐Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hongjian He
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Jiaqi Guo
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Xinyi Lin
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Bing Xu
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
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Paz MFCJ, de Alencar MVOB, de Lima RMP, Sobral ALP, do Nascimento GTM, dos Reis CA, Coêlho MDPSDS, do Nascimento MLLB, Gomes Júnior AL, Machado KDC, de Menezes AAPM, de Lima RMT, de Oliveira Filho JWG, Dias ACS, dos Reis AC, da Mata AMOF, Machado SA, Sousa CDDC, da Silva FCC, Islam MT, de Castro e Sousa JM, Melo Cavalcante AADC. Pharmacological Effects and Toxicogenetic Impacts of Omeprazole: Genomic Instability and Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3457890. [PMID: 32308801 PMCID: PMC7146093 DOI: 10.1155/2020/3457890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/19/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022]
Abstract
Omeprazole (OME) is commonly used to treat gastrointestinal disorders. However, long-term use of OME can increase the risk of gastric cancer. We aimed to characterize the pharmacological effects of OME and to correlate its adverse effects and toxicogenetic risks to the genomic instability mechanisms and cancer-based on database reports. Thus, a search (till Aug 2019) was made in the PubMed, Scopus, and ScienceDirect with relevant keywords. Based on the study objective, we included 80 clinical reports, forty-six in vitro, and 76 in vivo studies. While controversial, the findings suggest that long-term use of OME (5 to 40 mg/kg) can induce genomic instability. On the other hand, OME-mediated protective effects are well reported and related to proton pump blockade and anti-inflammatory activity through an increase in gastric flow, anti-inflammatory markers (COX-2 and interleukins) and antiapoptotic markers (caspases and BCL-2), glycoprotein expression, and neutrophil infiltration reduction. The reported adverse and toxic effects, especially in clinical studies, were atrophic gastritis, cobalamin deficiencies, homeostasis disorders, polyp development, hepatotoxicity, cytotoxicity, and genotoxicity. This study highlights that OME may induce genomic instability and increase the risk of certain types of cancer. Therefore, adequate precautions should be taken, especially in its long-term therapeutic strategies and self-medication practices.
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Affiliation(s)
- Márcia Fernanda Correia Jardim Paz
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, PI, Brazil
- Laboratory of Genetic Toxicity, Postgraduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina, PI, Brazil
| | | | | | - André Luiz Pinho Sobral
- Laboratory of Genetic Toxicity, Postgraduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina, PI, Brazil
- University Hospital, Teresina, PI, Brazil
| | | | | | | | | | - Antonio Luiz Gomes Júnior
- Laboratory of Genetic Toxicity, Postgraduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina, PI, Brazil
- University Centre UNINOVAFAPI, Teresina, PI, Brazil
| | | | | | - Rosália Maria Torres de Lima
- Laboratory of Genetic Toxicity, Postgraduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina, PI, Brazil
| | | | - Ana Carolina Soares Dias
- Laboratory of Genetics and Molecular Biology, Federal University of Maranhão, São Luís, MA, Brazil
| | - Antonielly Campinho dos Reis
- Laboratory of Genetic Toxicity, Postgraduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina, PI, Brazil
| | | | | | | | - Felipe Cavalcanti Carneiro da Silva
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, PI, Brazil
- Department of Biological Sciences, Federal University of Piauí, Picos, PI, Brazil
| | - Muhammad Torequl Islam
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | | | - Ana Amélia de Carvalho Melo Cavalcante
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, PI, Brazil
- Laboratory of Genetic Toxicity, Postgraduate Program in Pharmaceutical Sciences, Federal University of Piauí, Teresina, PI, Brazil
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Alanazi B, Munje CR, Rastogi N, Williamson AJK, Taylor S, Hole PS, Hodges M, Doyle M, Baker S, Gilkes AF, Knapper S, Pierce A, Whetton AD, Darley RL, Tonks A. Integrated nuclear proteomics and transcriptomics identifies S100A4 as a therapeutic target in acute myeloid leukemia. Leukemia 2020; 34:427-440. [PMID: 31611628 PMCID: PMC6995695 DOI: 10.1038/s41375-019-0596-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/18/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022]
Abstract
Inappropriate localization of proteins can interfere with normal cellular function and drive tumor development. To understand how this contributes to the development of acute myeloid leukemia (AML), we compared the nuclear proteome and transcriptome of AML blasts with normal human CD34+ cells. Analysis of the proteome identified networks and processes that significantly affected transcription regulation including misexpression of 11 transcription factors with seven proteins not previously implicated in AML. Transcriptome analysis identified changes in 40 transcription factors but none of these were predictive of changes at the protein level. The highest differentially expressed protein in AML nuclei compared with normal CD34+ nuclei (not previously implicated in AML) was S100A4. In an extended cohort, we found that over-expression of nuclear S100A4 was highly prevalent in AML (83%; 20/24 AML patients). Knock down of S100A4 in AML cell lines strongly impacted their survival whilst normal hemopoietic stem progenitor cells were unaffected. These data are the first analysis of the nuclear proteome in AML and have identified changes in transcription factor expression or regulation of transcription that would not have been seen at the mRNA level. These data also suggest that S100A4 is essential for AML survival and could be a therapeutic target in AML.
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Affiliation(s)
- Bader Alanazi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Chinmay R Munje
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Paul O'Gorman Leukaemia Research Centre, University of Glasgow, Glasgow, G12 0ZD, UK
| | - Namrata Rastogi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Andrew J K Williamson
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Samuel Taylor
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Paul S Hole
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Marie Hodges
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Michelle Doyle
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Sarah Baker
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Amanda F Gilkes
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Steven Knapper
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Andrew Pierce
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Anthony D Whetton
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, M20 3LJ, UK
| | - Richard L Darley
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Alex Tonks
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK.
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Salomon MS, Malapati SH, O' Dwyer J, Silva CL, Williams CC, Barbeau MC, Yip D, Punzalan P, Nagle VL, Hinton SD, Roggero VR, Allison LA. Mislocalization of Cancer-associated Thyroid Hormone Receptor Mutants. NUCLEAR RECEPTOR RESEARCH 2020; 2020:https://web.archive.org/web/20210227193123/https://www.kenzpub.com/journals/nurr/inpress/2020/101453/. [PMID: 35280700 PMCID: PMC8909557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
The thyroid hormone receptor (TR) is essential for the proper regulation of metabolism and development, as it regulates gene expression in response to thyroid hormone. Nuclear localization signals (NLSs) and nuclear export signals (NESs) allow for TR transport into and out of the nucleus, respectively. Previous research suggests that nuclear import, nuclear retention, and nuclear export of TR are associated with modulation of gene expression, the alteration of which can contribute to various diseases. Here, we examined the impact of cancer-associated mutations on TR localization patterns as a way of analyzing key structural components of TR and to further explore the correlation between TR trafficking, misfolding, and disease. Through mammalian cell transfection of expression plasmids for green fluorescent protein (GFP) and mCherry-tagged TRα1 and quantitative fluorescence microscopy, we examined particular groups of TRα1 mutations that were observed in patients with hepatocellular carcinoma, renal cell carcinoma, and thyroid cancer, and are associated with NLSs and NESs of TRα1. We also investigated structural alterations of the mutants by in silico modeling. Our results show striking shifts towards a more cytoplasmic localization for many of the mutants and an increased tendency to form cytosolic and nuclear aggregates.
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Affiliation(s)
- Michael S Salomon
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - S Harshini Malapati
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Jerry O' Dwyer
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Carolina Lopez Silva
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Cheyenne C Williams
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Michelle C Barbeau
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Delbert Yip
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Paige Punzalan
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Veronica L Nagle
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Shantá D Hinton
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Vincent R Roggero
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
| | - Lizabeth A Allison
- Department of Biology, William & Mary, 540 Landrum Drive, ISC 3035, Williamsburg, VA, 23185, USA
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Ghaemimanesh F. The Protein Subcellular Mislocalization in Human Cancers. Avicenna J Med Biotechnol 2020; 12:1. [PMID: 32153731 PMCID: PMC7035461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Emanuelli A, Manikoth Ayyathan D, Koganti P, Shah PA, Apel-Sarid L, Paolini B, Detroja R, Frenkel-Morgenstern M, Blank M. Altered Expression and Localization of Tumor Suppressive E3 Ubiquitin Ligase SMURF2 in Human Prostate and Breast Cancer. Cancers (Basel) 2019; 11:cancers11040556. [PMID: 31003445 PMCID: PMC6521037 DOI: 10.3390/cancers11040556] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/21/2022] Open
Abstract
SMURF2, an E3 ubiquitin ligase and suggested tumor suppressor, operates in normal cells to prevent genomic instability and carcinogenesis. However, the mechanisms underlying SMURF2 inactivation in human malignancies remain elusive, as SMURF2 is rarely found mutated or deleted in cancers. We hypothesized that SMURF2 might have a distinct molecular biodistribution in cancer versus normal cells and tissues. The expression and localization of SMURF2 were analyzed in 666 human normal and cancer tissues, with primary focus on prostate and breast tumors. These investigations were accompanied by SMURF2 gene expression analyses, subcellular fractionation and biochemical studies, including SMURF2’s interactome analysis. We found that while in normal cells and tissues SMURF2 has a predominantly nuclear localization, in prostate and aggressive breast carcinomas SMURF2 shows a significantly increased cytoplasmic sequestration, associated with the disease progression. Mechanistic studies showed that the nuclear export machinery was not involved in cytoplasmic accumulation of SMURF2, while uncovered that its stability is markedly increased in the cytoplasmic compartment. Subsequent interactome analyses pointed to 14-3-3s as SMURF2 interactors, which could potentially affect its localization. These findings link the distorted expression of SMURF2 to human carcinogenesis and suggest the alterations in SMURF2 localization as a potential mechanism obliterating its tumor suppressor activities.
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Affiliation(s)
- Andrea Emanuelli
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
| | - Dhanoop Manikoth Ayyathan
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
| | - Praveen Koganti
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
| | - Pooja Anil Shah
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
| | - Liat Apel-Sarid
- Department of Pathology, The Galilee Medical Center, 22100 Nahariya, Israel.
| | - Biagio Paolini
- Department of Pathology and Laboratory Medicine, Anatomic Pathology Unit 1, Fondazione IRCCS, Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Rajesh Detroja
- Laboratory of Cancer Genomics and BioComputing of Complex Diseases, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
| | - Milana Frenkel-Morgenstern
- Laboratory of Cancer Genomics and BioComputing of Complex Diseases, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502 Safed, Israel.
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La Manna S, Scognamiglio PL, Roviello V, Borbone F, Florio D, Di Natale C, Bigi A, Cecchi C, Cascella R, Giannini C, Sibillano T, Novellino E, Marasco D. The acute myeloid leukemia-associated Nucleophosmin 1 gene mutations dictate amyloidogenicity of the C-terminal domain. FEBS J 2019; 286:2311-2328. [PMID: 30921500 DOI: 10.1111/febs.14815] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/29/2019] [Accepted: 03/21/2019] [Indexed: 01/04/2023]
Abstract
Nucleophosmin 1 (NPM1) is a nucleus-cytoplasm shuttling protein ubiquitously expressed and highly conserved. It is involved in many cellular processes and its gene is mutated in ~ 50-60% of Acute Myeloid Leukemia (AML) patients. These mutations cause its cytoplasmic mislocation and accumulation (referred to as NPM1c+) and open the door to rational targeted therapy for AML diseases with mutated NPM1. Currently, there is limited knowledge on the mechanism of action of NPM1c+ and on structural determinants of the leukemogenic potential of AML mutations. Numerous previous studies outlined an unexpected amyloid-like aggregation tendency of several regions located in the C-terminal domain that, in wild-type form, fold as a three-helical-bundle. Here, using a combination of different techniques including Thioflavin T fluorescence, congo red absorbance, CD spectroscopy, Scanning Electron Microscopy (SEM) and wide-angle X-ray scattering on a series of peptides bearing mutations, we evidence that the amyloidogenicity of NPM1 mutants is directly linked to AML. Noticeably, AML point mutations strongly affect the amyloid cytotoxic effects in neuroblastoma cells and the morphologies of deriving fibrils. This study paves the way to deepen our understanding of AML-associated NPM1 mutants, and could help to break new ground for the identification of novel drugs targeting NPM1c+ for treatment of AML.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Pasqualina Liana Scognamiglio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and CeSMA (Advanced Metrologic Service Center), University of Naples "Federico II", Italy
| | - Fabio Borbone
- Department of Chemical Sciences, University of Naples "Federico II", Italy
| | - Daniele Florio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Concetta Di Natale
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), National Research Council, Bari, Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), National Research Council, Bari, Italy
| | - Ettore Novellino
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", Italy
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Spits M, Janssen LJ, Voortman LM, Kooij R, Neefjes ACM, Ovaa H, Neefjes J. Homeostasis of soluble proteins and the proteasome post nuclear envelope reformation in mitosis. J Cell Sci 2019; 132:jcs.225524. [DOI: 10.1242/jcs.225524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/08/2019] [Indexed: 12/22/2022] Open
Abstract
Upon Nuclear envelope (NE) fragmentation in the prometaphase the nuclear and cytosolic proteomes blend and must be redefined to reinstate homeostasis. Using a molecular GFP ladder, we show that in early mitosis, condensed chromatin excludes cytosolic proteins. When the NE reforms tightly around condensed chromatin in late mitosis, large GFP multimers are automatically excluded from the nucleus. This can be circumvented by limiting DNA condensation with Q15, a Condensin II inhibitor. Soluble small and other NLS-targeted proteins then swiftly enter the expanding nuclear space. We then examined the proteasome, located in cytoplasm and nucleus. A significant fraction of 20S proteasomes is imported by importin IPO5 within 20 minutes following reformation of the nucleus, after which import comes to an abrupt halt. This suggests that maintaining the nuclear-cytosol distribution after mitosis requires chromatin condensation to exclude cytosolic material from the nuclear space and specialized machineries for nuclear import of large protein complexes such as the proteasome.
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Affiliation(s)
- Menno Spits
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
| | - Lennert J. Janssen
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
| | - Lenard M. Voortman
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
| | - Raymond Kooij
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
| | - Anna C. M. Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden NL, USA
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Expression of calcium pumps is differentially regulated by histone deacetylase inhibitors and estrogen receptor alpha in breast cancer cells. BMC Cancer 2018; 18:1029. [PMID: 30352569 PMCID: PMC6199715 DOI: 10.1186/s12885-018-4945-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Background Remodeling of Ca2+ signaling is an important step in cancer progression, and altered expression of members of the Ca2+ signaling toolkit including the plasma membrane Ca2+ ATPases (PMCA proteins encoded by ATP2B genes) is common in tumors. Methods In this study PMCAs were examined in breast cancer datasets and in a variety of breast cancer cell lines representing different subtypes. We investigated how estrogen receptor alpha (ER-α) and histone deacetylase (HDAC) inhibitors regulate the expression of these pumps. Results Three distinct datasets displayed significantly lower ATP2B4 mRNA expression in invasive breast cancer tissue samples compared to normal breast tissue, whereas the expression of ATP2B1 and ATP2B2 was not altered. Studying the protein expression profiles of Ca2+ pumps in a variety of breast cancer cell lines revealed low PMCA4b expression in the ER-α positive cells, and its marked upregulation upon HDAC inhibitor treatments. PMCA4b expression was also positively regulated by the ER-α pathway in MCF-7 cells that led to enhanced Ca2+ extrusion capacity in response to 17β-estradiol (E2) treatment. E2-induced PMCA4b expression was further augmented by HDAC inhibitors. Surprisingly, E2 did not affect the expression of PMCA4b in other ER-α positive cells ZR-75-1, T-47D and BT-474. These findings were in good accordance with ChIP-seq data analysis that revealed an ER-α binding site in the ATP2B4 gene in MCF-7 cells but not in other ER-α positive tumor cells. In the triple negative cells PMCA4b expression was relatively high, and the effect of HDAC inhibitor treatment was less pronounced as compared to that of the ER-α positive cells. Although, the expression of PMCA4b was relatively high in the triple negative cells, a fraction of the protein was found in intracellular compartments that could interfere with the cellular function of the protein. Conclusions Our results suggest that the expression of Ca2+ pumps is highly regulated in breast cancer cells in a subtype specific manner. Our results suggest that hormonal imbalances, epigenetic modifications and impaired protein trafficking could interfere with the expression and cellular function of PMCA4b in the course of breast cancer progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4945-x) contains supplementary material, which is available to authorized users.
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49
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Anyetei-Anum CS, Roggero VR, Allison LA. Thyroid hormone receptor localization in target tissues. J Endocrinol 2018; 237:R19-R34. [PMID: 29440347 PMCID: PMC5843491 DOI: 10.1530/joe-17-0708] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
Abstract
The thyroid hormone receptors, TRα1, TRβ1 and other subtypes, are members of the nuclear receptor superfamily that mediate the action of thyroid hormone signaling in numerous tissues to regulate important physiological and developmental processes. Their most well-characterized role is as ligand-dependent transcription factors; TRs bind thyroid hormone response elements in the presence or absence of thyroid hormone to facilitate the expression of target genes. Although primarily residing in the nucleus, TRα1 and TRβ1 shuttle rapidly between the nucleus and cytoplasm. We have identified multiple nuclear localization signals and nuclear export signals within TRα1 and TRβ1 that interact with importins and exportins, respectively, to mediate translocation across the nuclear envelope. More recently, enigmatic cytoplasmic functions have been ascribed to other TR subtypes, expanding the diversity of the cellular response to thyroid hormone. By integrating data on localization signal motifs, this review provides an overview of the complex interplay between TR's dynamic transport pathways and thyroid hormone signaling activities. We examine the variation in TR subtype response to thyroid hormone signaling, and what is currently known about regulation of the variety of tissue-specific localization patterns, including targeting to the nucleus, the mitochondria and the inner surface of the plasma membrane.
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Affiliation(s)
| | - Vincent R Roggero
- Department of BiologyCollege of William and Mary, Williamsburg, Virginia, USA
| | - Lizabeth A Allison
- Department of BiologyCollege of William and Mary, Williamsburg, Virginia, USA
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50
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Dianati E, Plante I. Analysis of Protein-protein Interactions and Co-localization Between Components of Gap, Tight, and Adherens Junctions in Murine Mammary Glands. J Vis Exp 2017. [PMID: 28605375 DOI: 10.3791/55772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cell-cell interactions play a pivotal role in preserving tissue integrity and the barrier between the different compartments of the mammary gland. These interactions are provided by junctional proteins that form nexuses between adjacent cells. Junctional protein mislocalization and reduced physical associations with their binding partners can result in the loss of function and, consequently, to organ dysfunction. Thus, identifying protein localization and protein-protein interactions (PPIs) in normal and disease-related tissues is essential to finding new evidences and mechanisms leading to the progression of diseases or alterations in developmental status. This manuscript presents a two-step method to evaluate PPIs in murine mammary glands. In protocol section 1, a method to perform co-immunofluorescence (co-IF) using antibodies raised against the proteins of interest, followed by secondary antibodies labeled with fluorochromes, is described. Although co-IF allows for the demonstration of the proximity of the proteins, it does make it possible to study their physical interactions. Therefore, a detailed protocol for co-immunoprecipitation (co-IP) is provided in protocol section 2. This method is used to determine the physical interactions between proteins, without confirming whether these interactions are direct or indirect. In the last few years, co-IF and co-IP techniques have demonstrated that certain components of intercellular junctions co-localize and interact together, creating stage-dependent junctional nexuses that vary during mammary gland development.
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