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Megino-Luque C, Bravo-Cordero JJ. Metastasis suppressor genes and their role in the tumor microenvironment. Cancer Metastasis Rev 2023; 42:1147-1154. [PMID: 37982987 PMCID: PMC10842895 DOI: 10.1007/s10555-023-10155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
The metastatic cascade is a complex process with multiple factors contributing to the seeding and growth of cancer cells at metastatic sites. Within this complex process, several genes have been identified as metastasis suppressors, playing a role in the inhibition of metastasis. Interestingly, some of these genes have been shown to also play a role in regulating the tumor microenvironment. In this review, we comment on the recent developments in the biology of metastasis suppressor genes and their crosstalk with the microenvironment.
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Affiliation(s)
- Cristina Megino-Luque
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose Javier Bravo-Cordero
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Walters SH, Castillo AJ, Develin AM, Labrecque CL, Qu Y, Fuglestad B. Investigating protein-membrane interactions using native reverse micelles constructed from naturally sourced lipids. Protein Sci 2023; 32:e4786. [PMID: 37746759 PMCID: PMC10578115 DOI: 10.1002/pro.4786] [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: 07/11/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Advancing the study of membrane associated proteins and their interactions is dependent on accurate membrane models. While a variety of membrane models for high-resolution membrane protein study exist, most do not reflect the diversity of lipids found within biological membranes. In this work, we have developed native reverse micelles (nRMs) formulated with lipids from multiple eukaryotic sources, which encapsulate proteins and enable them to interact as they would with a biological membrane. Diverse formulations of nRMs using soy lecithin, porcine brain lipids, or bovine heart lipids combined with n-dodecylphosphocholine were developed and characterized by dynamic light scattering and 31 P-NMR. To optimize protein encapsulation, ubiquitin was used as a standard and protein NMR verified minimal changes to its structure. Peripheral membrane proteins, which bind reversibly to membranes, were encapsulated and include glutathione peroxidase 4 (GPx4), phosphatidylethanolamine-binding protein 1 (PEBP1), and fatty acid binding protein 4 (FABP4). All three proteins showed anticipated interactions with the membrane-like inner surface of the nRMs as assessed by protein NMR. The nRM formulations developed here allow for efficient, high-resolution study of membrane interacting proteins up to and beyond ~21 kDa, in a more biologically relevant context compared to other non-native membrane models. The approach outlined here may be applied to a wide range of lipid extracts, allowing study of a variety of membrane associated proteins in their specific biological context.
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Affiliation(s)
- Sara H. Walters
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Abdul J. Castillo
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Angela M. Develin
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | - Yun Qu
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Brian Fuglestad
- Department of ChemistryVirginia Commonwealth UniversityRichmondVirginiaUSA
- Institute for Structural Biology, Drug Discovery and DevelopmentVirginia Commonwealth UniversityRichmondVirginiaUSA
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Nilsson J, Cousins KAQ, Gobom J, Portelius E, Chen-Plotkin A, Shaw LM, Grossman M, Irwin DJ, Trojanowski JQ, Zetterberg H, Blennow K, Brinkmalm A. Cerebrospinal fluid biomarker panel of synaptic dysfunction in Alzheimer's disease and other neurodegenerative disorders. Alzheimers Dement 2023; 19:1775-1784. [PMID: 36239248 PMCID: PMC10102247 DOI: 10.1002/alz.12809] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/21/2022] [Accepted: 09/02/2022] [Indexed: 11/11/2022]
Abstract
INTRODUCTION Synaptic degeneration is a key part of the pathophysiology of neurodegenerative diseases, and biomarkers reflecting the pathological alterations are greatly needed. METHOD Seventeen synaptic proteins were quantified in a pathology-confirmed cerebrospinal fluid cohort of patients with Alzheimer's disease (AD; n = 63), frontotemporal lobar degeneration (FTLD; n = 53), and Lewy body spectrum of disorders (LBD; n = 21), as well as healthy controls (HC; n = 48). RESULTS Comparisons revealed four distinct patterns: markers decreased across all neurodegenerative conditions compared to HC (the neuronal pentraxins), markers increased across all neurodegenerative conditions (14-3-3 zeta/delta), markers selectively increased in AD compared to other neurodegenerative conditions (neurogranin and beta-synuclein), and markers selectively decreased in LBD and FTLD compared to HC and AD (AP2B1 and syntaxin-1B). DISCUSSION Several of the synaptic proteins may serve as biomarkers for synaptic dysfunction in AD, LBD, and FTLD. Additionally, differential patterns of synaptic protein alterations seem to be present across neurodegenerative diseases. HIGHLIGHTS A panel of synaptic proteins were quantified in the cerebrospinal fluid using mass spectrometry. We compared Alzheimer's disease, frontotemporal degeneration, and Lewy body spectrum of disorders. Pathology was confirmed by autopsy or familial mutations. We discovered synaptic biomarkers for synaptic degeneration and cognitive decline. We found differential patterns of synaptic proteins across neurodegenerative diseases.
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Affiliation(s)
- Johanna Nilsson
- Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, SE-43180 Mölndal, Sweden
| | - Katheryn AQ Cousins
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Johan Gobom
- Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, SE-43180 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, SE-43180 Mölndal, Sweden
| | - Erik Portelius
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, SE-43180 Mölndal, Sweden
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Murray Grossman
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - David J. Irwin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, SE-43180 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, SE-43180 Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, United Kingdom
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, SE-43180 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, SE-43180 Mölndal, Sweden
| | - Ann Brinkmalm
- Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, SE-43180 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, SE-43180 Mölndal, Sweden
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Papale M, Netti GS, Stallone G, Ranieri E. Understanding Mechanisms of RKIP Regulation to Improve the Development of New Diagnostic Tools. Cancers (Basel) 2022; 14:cancers14205070. [PMID: 36291854 PMCID: PMC9600137 DOI: 10.3390/cancers14205070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Raf Kinase Inhibitor protein is a protein that governs multiple intracellular signalling involved primarily in the progression of tumours and the development of metastases. In this review, we discussed the main mechanisms that regulate the expression and activity of RKIP with the aim of identifying the link between the transcriptional, post-transcriptional and post-translational events in different tumour settings. We also tried to analyse the studies that have measured the levels of RKIP in biological fluids in order to highlight the possible advantages and potential of RKIP assessment to obtain an accurate diagnosis and prognosis of various tumours. Abstract One of the most dangerous aspects of cancer cell biology is their ability to grow, spread and form metastases in the main vital organs. The identification of dysregulated markers that drive intracellular signalling involved in the malignant transformation of neoplastic cells and the understanding of the mechanisms that regulate these processes is undoubtedly a key objective for the development of new and more targeted therapies. RAF-kinase inhibitor protein (RKIP) is an endogenous tumour suppressor protein that affects tumour cell survival, proliferation, and metastasis. RKIP might serve as an early tumour biomarker since it exhibits significantly different expression levels in various cancer histologies and it is often lost during metastatic progression. In this review, we discuss the specific impact of transcriptional, post-transcriptional and post-translational regulation of expression and activation/inhibition of RKIP and focus on those tumours for which experimental data on all these factors are available. In this way, we could select how these processes cooperate with RKIP expression in (1) Lung cancer; (2) Colon cancer, (3) Breast cancer; (4) myeloid neoplasm and Multiple Myeloma, (5) Melanoma and (6) clear cell Renal Cell Carcinoma. Furthermore, since RKIP seems to be a key marker of the development of several tumours and it may be assessed easily in various biological fluids, here we discuss the potential role of RKIP dosing in more accessible biological matrices other than tissues. Moreover, this objective may intercept the still unmet need to identify new and more accurate markers for the early diagnosis and prognosis of many tumours.
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Affiliation(s)
- Massimo Papale
- Unit of Clinical Pathology, Department of Laboratory Diagnostics, University Hospital “Policlinico Foggia”, 71122 Foggia, Italy
- Correspondence:
| | - Giuseppe Stefano Netti
- Unit of Clinical Pathology, Center for Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Unit of Nephology, Dialysis and Transplantation, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Giovanni Stallone
- Unit of Nephology, Dialysis and Transplantation, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Elena Ranieri
- Unit of Clinical Pathology, Center for Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Unit of Nephology, Dialysis and Transplantation, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
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Host Cell Signatures of the Envelopment Site within Beta-Herpes Virions. Int J Mol Sci 2022; 23:ijms23179994. [PMID: 36077391 PMCID: PMC9456339 DOI: 10.3390/ijms23179994] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
Beta-herpesvirus infection completely reorganizes the membrane system of the cell. This system is maintained by the spatiotemporal arrangement of more than 3000 cellular proteins that continuously adapt the configuration of membrane organelles according to cellular needs. Beta-herpesvirus infection establishes a new configuration known as the assembly compartment (AC). The AC membranes are loaded with virus-encoded proteins during the long replication cycle and used for the final envelopment of the newly formed capsids to form infectious virions. The identity of the envelopment membranes is still largely unknown. Electron microscopy and immunofluorescence studies suggest that the envelopment occurs as a membrane wrapping around the capsids, similar to the growth of phagophores, in the area of the AC with the membrane identities of early/recycling endosomes and the trans-Golgi network. During wrapping, host cell proteins that define the identity and shape of these membranes are captured along with the capsids and incorporated into the virions as host cell signatures. In this report, we reviewed the existing information on host cell signatures in human cytomegalovirus (HCMV) virions. We analyzed the published proteomes of the HCMV virion preparations that identified a large number of host cell proteins. Virion purification methods are not yet advanced enough to separate all of the components of the rich extracellular material, including the large amounts of non-vesicular extracellular particles (NVEPs). Therefore, we used the proteomic data from large and small extracellular vesicles (lEVs and sEVs) and NVEPs to filter out the host cell proteins identified in the viral proteomes. Using these filters, we were able to narrow down the analysis of the host cell signatures within the virions and determine that envelopment likely occurs at the membranes derived from the tubular recycling endosomes. Many of these signatures were also found at the autophagosomes, suggesting that the CMV-infected cell forms membrane organelles with phagophore growth properties using early endosomal host cell machinery that coordinates endosomal recycling.
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Li Q, Gu Y, Gao X, Guo X, Huang C, Liu P, Hu G, Li G, Fang W, Mai W, Wu C, Xu Z, Huang F, Liu P. Preparation of polyclonal antibody against phosphatidylethanolamine binding protein 1 recombinant protein and its functional verification in pulmonary hypertension syndrome in broilers. Int J Biol Macromol 2022; 213:19-26. [DOI: 10.1016/j.ijbiomac.2022.05.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/04/2022] [Accepted: 05/22/2022] [Indexed: 11/26/2022]
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Genomic Survey of PEBP Gene Family in Rice: Identification, Phylogenetic Analysis, and Expression Profiles in Organs and under Abiotic Stresses. PLANTS 2022; 11:plants11121576. [PMID: 35736727 PMCID: PMC9228618 DOI: 10.3390/plants11121576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Phosphatidylethanolamine-binding-protein (PEBP) domain-containing proteins play important roles in multiple developmental processes of plants; however, functions of few members in the PEBP gene family have been elucidated in rice and other crops. In this study, we found that twenty OsPEBPs genes identified in rice are not evenly distributed on the chromosomes. Four colinear pairs are identified, suggesting the duplication of OsPEBPs during evolution. The OsPEBPs are classified into six subgroups by phylogenetic analysis. The structure of all the OsPEBP genes and encoded proteins are similar. The 262 PEBP domain-containing proteins from crops are divided into six groups. The number of colinear pairs varies between rice and other crops. More than thirty cis-acting elements in the promoter region of OsPEBPs are discovered. Expression profiles of OsPEBP genes are differential. Most of the OsPEBPs expression can be regulated by NaCl, ABA, JA, and light, indicating that OsPEBPs may be involved in the control of the response to the environmental signals. These results lay sound foundation to further explore their functions in development of rice and crops.
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Zemlianskaia N, Gauderman WJ, Lewinger JP. A scalable hierarchical lasso for gene-environment interactions. J Comput Graph Stat 2022; 31:1091-1103. [PMID: 36793591 PMCID: PMC9928188 DOI: 10.1080/10618600.2022.2039161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We describe a regularized regression model for the selection of gene-environment (G×E) interactions. The model focuses on a single environmental exposure and induces a main-effect-before-interaction hierarchical structure. We propose an efficient fitting algorithm and screening rules that can discard large numbers of irrelevant predictors with high accuracy. We present simulation results showing that the model outperforms existing joint selection methods for (G×E) interactions in terms of selection performance, scalability and speed, and provide a real data application. Our implementation is available in the gesso R package.
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Affiliation(s)
- Natalia Zemlianskaia
- Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - W. James Gauderman
- Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Juan Pablo Lewinger
- Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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Dihydroartemisinin Induces Ferroptosis in HCC by Promoting the Formation of PEBP1/15-LO. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:3456725. [PMID: 34925691 PMCID: PMC8683180 DOI: 10.1155/2021/3456725] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/26/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022]
Abstract
Relevant researches have recognized the vital role of inducing ferroptosis in the treatment of tumor. The latest findings indicate that PEBP1/15-LO can play an essential role in the process of cell death. However, its role in regulating ferroptosis in hepatocellular carcinoma (simplified by HCC) remains unclear. The previous research of our team has proved that DHA can induce ferroptosis of hepatic stellate cells. In this study, we found that DHA could also induce ferroptosis in HCC cells. Interestingly, DHA induced ferroptosis by promoting the formation of PEBP1/15-LO and promoting cell membrane lipid peroxidation. In addition, we also found that DHA had no obvious regulatory effect on 15-LO, but it could promote PEBP1 protein expression. Importantly, we discovered the upregulation of PEBP1 induced by DHA was related to the inhibition of its ubiquitination degradation. In vivo experiments have also obtained consistent results that DHA can inhibit tumor growth and affect the expression of ferroptosis markers in tumor tissues, which would be partially offset by interference with PEBP1.
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Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation. TOXICS 2021; 9:toxics9120338. [PMID: 34941772 PMCID: PMC8708250 DOI: 10.3390/toxics9120338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/19/2023]
Abstract
Exposure to ambient air pollution during pregnancy has been associated with an increased risk of preeclampsia (PE). Some suggested mechanisms behind this association are changes in placental DNA methylation and gene expression. The objective of this study was to identify how early pregnancy exposure to ambient nitrogen oxides (NOx) among PE cases and normotensive controls influence DNA methylation (EPIC array) and gene expression (RNA-seq). The study included placentas from 111 women (29 PE cases/82 controls) in Scania, Sweden. First-trimester NOx exposure was assessed at the participants’ residence using a dispersion model and categorized via median split into high or low NOx. Placental gestational epigenetic age was derived from the DNA methylation data. We identified six differentially methylated positions (DMPs, q < 0.05) comparing controls with low NOx vs. cases with high NOx and 14 DMPs comparing cases and controls with high NOx. Placentas with female fetuses showed more DMPs (N = 309) than male-derived placentas (N = 1). Placentas from PE cases with high NOx demonstrated gestational age deceleration compared to controls with low NOx (p = 0.034). No differentially expressed genes (DEGs, q < 0.05) were found. In conclusion, early pregnancy exposure to NOx affected placental DNA methylation in PE, resulting in placental immaturity and showing sexual dimorphism.
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Cho JH, Park S, Kim S, Kang SM, Woo TG, Yoon MH, Lee H, Jeong M, Park YH, Kim H, Han YT, Suh YG, Kim BH, Kwon Y, Yun H, Park BJ. RKIP Induction Promotes Tumor Differentiation via SOX2 Degradation in NF2-Deficient Conditions. Mol Cancer Res 2021; 20:412-424. [PMID: 34728553 DOI: 10.1158/1541-7786.mcr-21-0373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/16/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022]
Abstract
Loss of NF2 (merlin) has been suggested as a genetic cause of neurofibromatosis type 2 and malignant peripheral nerve sheath tumor (MPNST). Previously, we demonstrated that NF2 sustained TGFβ receptor 2 (TβR2) expression and reduction or loss of NF2 activated non-canonical TGFβ signaling, which reduced Raf kinase inhibitor protein (RKIP) expression via TβR1 kinase activity. Here, we show that a selective RKIP inducer (novel chemical, Nf18001) inhibits tumor growth and promotes schwannoma cell differentiation into mature Schwann cells under NF2-deficient conditions. In addition, Nf18001 is not cytotoxic to cells expressing NF2 and is not disturb canonical TGFβ signaling. Moreover, the novel chemical induces expression of SOX10, a marker of differentiated Schwann cells, and promotes nuclear export and degradation of SOX2, a stem cell factor. Treatment with Nf18001 inhibited tumor growth in an allograft model with mouse schwannoma cells. These results strongly suggest that selective RKIP inducers could be useful for the treatment of neurofibromatosis type 2 as well as NF2-deficient MPNST. IMPLICATIONS: This study identifies that a selective RKIP inducer inhibits tumor growth and promotes schwannoma cell differentiation under NF2-deficient conditions by reducing SOX2 and increasing SOX10 expression.
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Affiliation(s)
- Jung-Hyun Cho
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, Republic of Korea
| | - Soyoung Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, Republic of Korea
| | - Soyeong Kim
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, Republic of Korea
| | - Tae-Gyun Woo
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, Republic of Korea
| | - Min-Ho Yoon
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, Republic of Korea
| | - Hyunkee Lee
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Myeonggyo Jeong
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Yeong Hye Park
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Heegyu Kim
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Young Taek Han
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy, CHA University, Pocheon, Gyeonggi-do, Republic of Korea
| | - Bae-Hoon Kim
- Rare Disease R&D Center, PRG S&T Co., Ltd. Busan, Republic of Korea
| | - Yonghoon Kwon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, Republic of Korea.
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, Republic of Korea.
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Zhu J, Kong W, Xie Z. Expression and Prognostic Characteristics of Ferroptosis-Related Genes in Colon Cancer. Int J Mol Sci 2021; 22:ijms22115652. [PMID: 34073365 PMCID: PMC8199073 DOI: 10.3390/ijms22115652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Ferroptosis is a new type of programmed cell death, which occurs with iron dependence. Previous studies have showed that ferroptosis plays an important regulatory role in the occurrence and development of tumors. Colon cancer is one of the major morbidities and causes of mortality in the world. This study used RNA-seq and colon cancer clinical data to explore the relationship between ferroptosis-related genes and colon cancer. Based on the fifteen prognostic ferroptosis-related genes, two molecular subgroups of colon cancer were identified. Surprisingly, we also found cluster2 was characterized by lower mutation burden and expression of checkpoint genes, better survival, and higher expression of NOX1. Moreover, cluster2 has fewer BRAF mutations. We also found the expression of NOX1 is related to the status of BRAF. Finally, using 15 ferroptosis-related genes from The Cancer Genome Atlas cohort, we constructed a prognosis model, and this model may be used to predict the prognosis of patients in clinics.
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Affiliation(s)
- Jie Zhu
- Department of Pharmacology and International Cancer Institute, School of Basic Medical Sciences, Peking University, Beijing 100191, China;
| | - Weikaixin Kong
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing 100191, China;
| | - Zhengwei Xie
- Department of Pharmacology and International Cancer Institute, School of Basic Medical Sciences, Peking University, Beijing 100191, China;
- Correspondence:
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Nilsson J, Gobom J, Sjödin S, Brinkmalm G, Ashton NJ, Svensson J, Johansson P, Portelius E, Zetterberg H, Blennow K, Brinkmalm A. Cerebrospinal fluid biomarker panel for synaptic dysfunction in Alzheimer's disease. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12179. [PMID: 33969172 PMCID: PMC8087978 DOI: 10.1002/dad2.12179] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Synaptic dysfunction and degeneration is one of the earliest events in Alzheimer's disease (AD) and the best correlate of cognitive decline. Thus, identification and validation of biomarkers reflecting synaptic degeneration to be used as prognostic biomarkers are greatly needed. METHOD Solid-phase extraction and parallel reaction monitoring mass spectrometry were used to quantify 17 synaptic proteins in CSF, in two cross-sectional studies including AD (n = 52) and controls (n = 37). RESULTS Increased concentrations of beta-synuclein, gamma-synuclein, neurogranin, phosphatidylethanolamine-binding protein 1, and 14-3-3 proteins were observed in AD patients compared to controls, while neuronal pentraxin-2 and neuronal pentraxin receptor were decreased. DISCUSSION We have established a method with a novel panel of synaptic proteins as biomarkers of synaptic dysfunction. The results indicate that several of the proteins included in the panel may serve as synaptic biomarkers for AD.
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Affiliation(s)
- Johanna Nilsson
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
| | - Johan Gobom
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
| | - Simon Sjödin
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
| | - Gunnar Brinkmalm
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
| | - Nicholas J. Ashton
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburgSweden
- Department of Old Age Psychiatry, Maurice Wohl Clinical Neuroscience InstituteKing's College LondonLondonUK
- NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia at South London and Maudsley NHS FoundationLondonUK
| | - Johan Svensson
- Department of Internal Medicine and Clinical Nutrition, Institute of MedicineThe Sahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Per Johansson
- Department of Internal Medicine and Clinical Nutrition, Institute of MedicineThe Sahlgrenska Academy at the University of GothenburgGothenburgSweden
- Department of Clinical SciencesLund UniversityLundSweden
| | - Erik Portelius
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
| | - Henrik Zetterberg
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
- UK Dementia Research Institute at UCLLondonUK
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - Kaj Blennow
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
| | - Ann Brinkmalm
- Institute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
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Penas C, Apraiz A, Muñoa I, Arroyo-Berdugo Y, Rasero J, Ezkurra PA, Velasco V, Subiran N, Bosserhoff AK, Alonso S, Asumendi A, Boyano MD. RKIP Regulates Differentiation-Related Features in Melanocytic Cells. Cancers (Basel) 2020; 12:cancers12061451. [PMID: 32503139 PMCID: PMC7352799 DOI: 10.3390/cancers12061451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 12/26/2022] Open
Abstract
Raf Kinase Inhibitor Protein (RKIP) has been extensively reported as an inhibitor of key signaling pathways involved in the aggressive tumor phenotype and shows decreased expression in several types of cancers. However, little is known about RKIP in melanoma or regarding its function in normal cells. We examined the role of RKIP in both primary melanocytes and malignant melanoma cells and evaluated its diagnostic and prognostic value. IHC analysis revealed a significantly higher expression of RKIP in nevi compared with early-stage (stage I–II, AJCC 8th) melanoma biopsies. Proliferation, wound healing, and collagen-coated transwell assays uncovered the implication of RKIP on the motility but not on the proliferative capacity of melanoma cells as RKIP protein levels were inversely correlated with the migration capacity of both primary and metastatic melanoma cells but did not alter other parameters. As shown by RNA sequencing, endogenous RKIP knockdown in primary melanocytes triggered the deregulation of cellular differentiation-related processes, including genes (i.e., ZEB1, THY-1) closely related to the EMT. Interestingly, NANOG was identified as a putative transcriptional regulator of many of the deregulated genes, and RKIP was able to decrease the activation of the NANOG promoter. As a whole, our data support the utility of RKIP as a diagnostic marker for early-stage melanomas. In addition, these findings indicate its participation in the maintenance of a differentiated state of melanocytic cells by modulating genes intimately linked to the cellular motility and explain the progressive decrease of RKIP often described in tumors.
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Affiliation(s)
- Cristina Penas
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain; (C.P.); (A.A.); (Y.A.-B.); (P.A.E.); (A.A.)
| | - Aintzane Apraiz
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain; (C.P.); (A.A.); (Y.A.-B.); (P.A.E.); (A.A.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
| | - Iraia Muñoa
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
- Department of Physiology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain
| | - Yoana Arroyo-Berdugo
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain; (C.P.); (A.A.); (Y.A.-B.); (P.A.E.); (A.A.)
| | - Javier Rasero
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
- Department of Psychology, Carnegie Mellon University, Pittsburg, PA 15213, USA
| | - Pilar A. Ezkurra
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain; (C.P.); (A.A.); (Y.A.-B.); (P.A.E.); (A.A.)
| | - Veronica Velasco
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
| | - Nerea Subiran
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
- Department of Physiology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain
| | - Anja K. Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany;
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054 Erlangen, Germany
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain;
| | - Aintzane Asumendi
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain; (C.P.); (A.A.); (Y.A.-B.); (P.A.E.); (A.A.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
| | - Maria D. Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940 Leioa, Spain; (C.P.); (A.A.); (Y.A.-B.); (P.A.E.); (A.A.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.M.); (J.R.); (V.V.); (N.S.)
- Correspondence: ; Tel.: +34-946015689
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