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Pham DT, Tran TD. Drivergene.net: A Cytoscape app for the identification of driver nodes of large-scale complex networks and case studies in discovery of drug target genes. Comput Biol Med 2024; 179:108888. [PMID: 39047507 DOI: 10.1016/j.compbiomed.2024.108888] [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: 02/23/2024] [Revised: 06/15/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]
Abstract
There are no tools to identify driver nodes of large-scale networks in approach of competition-based controllability. This study proposed a novel method for this computation of large-scale networks. It implemented the method in a new Cytoscape plug-in app called Drivergene.net. Experiments of the software on large-scale biomolecular networks have shown outstanding speed and computing power. Interestingly, 86.67% of the top 10 driver nodes found on these networks are anticancer drug target genes that reside mostly at the innermost K-cores of the networks. Finally, compared method with those of five other researchers and confirmed that the proposed method outperforms the other methods on identification of anticancer drug target genes. Taken together, Drivergene.net is a reliable tool that efficiently detects not only drug target genes from biomolecular networks but also driver nodes of large-scale complex networks. Drivergene.net with a user manual and example datasets are available https://github.com/tinhpd/Drivergene.git.
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Affiliation(s)
- Duc-Tinh Pham
- Complex Systems and Bioinformatics Lab, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam; Graduate University of Science and Technology, Academy of Science and Technology Viet Nam, 18 Hoang Quoc Viet Street, Cau Giay District, Hanoi, Viet Nam
| | - Tien-Dzung Tran
- Complex Systems and Bioinformatics Lab, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam; Faculty of Information and Communication Technology, Hanoi University of Industry, 298 Cau Dien Street, Bac Tu Liem District, Hanoi, Viet Nam.
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2
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Jin M, Shi R, Gao D, Wang B, Li N, Li X, Sik A, Liu K, Zhang X. ErbB2 pY -1248 as a predictive biomarker for Parkinson's disease based on research with RPPA technology and in vivo verification. CNS Neurosci Ther 2024; 30:e14407. [PMID: 37564024 PMCID: PMC10848095 DOI: 10.1111/cns.14407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023] Open
Abstract
AIMS This study aims to reveal a promising biomarker for Parkinson's disease (PD) based on research with reverse phase protein array (RPPA) technology for the first time and in vivo verification, which gains time for early intervention in PD, thus increasing the effectiveness of treatment and reducing disease morbidity. METHODS AND RESULTS We employed RPPA technology which can assess both total and post-translationally modified proteins to identify biomarker candidates of PD in a cellular PD model. As a result, the phosphorylation (pY-1248) of the epidermal growth factor receptor (EGFR) ErbB2 is a promising biomarker candidate for PD. In addition, lapatinib, an ErbB2 tyrosine kinase inhibitor, was used to verify this PD biomarker candidate in vivo. We found that lapatinib-attenuated dopaminergic neuron loss and PD-like behavior in the zebrafish PD model. Accordingly, the expression of ErbB2pY-1248 significantly increased in the MPTP-induced mouse PD model. Our results suggest that ErbB2pY-1248 is a predictive biomarker for PD. CONCLUSIONS In this study, we found that ErbB2pY-1248 is a predictive biomarker of PD by using RPPA technology and in vivo verification. It offers a new perspective on PD diagnosing and treatment, which will be essential in identifying individuals at risk of PD. In addition, this study provides new ideas for digging into biomarkers of other neurodegenerative diseases.
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Affiliation(s)
- Meng Jin
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Ruidie Shi
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
- School of PsychologyNorth China University of Science and TechnologyTang'shanChina
| | - Daili Gao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Baokun Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Ning Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Xia Li
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd.Ji'nanChina
| | - Attila Sik
- Institute of Transdisciplinary Discoveries, Medical SchoolUniversity of PecsPécsHungary
- Institute of Clinical Sciences, Medical SchoolUniversity of BirminghamBirminghamUK
- Institute of Physiology, Medical SchoolUniversity of PecsPécsHungary
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Xiujun Zhang
- School of PsychologyNorth China University of Science and TechnologyTang'shanChina
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3
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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4
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Gild ML, Clifton-Bligh RJ, Wirth LJ, Robinson BG. Medullary Thyroid Cancer: Updates and Challenges. Endocr Rev 2023; 44:934-946. [PMID: 37204852 PMCID: PMC10656709 DOI: 10.1210/endrev/bnad013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/19/2023] [Accepted: 05/18/2023] [Indexed: 05/20/2023]
Abstract
A personalized approach to the management of medullary thyroid cancer (MTC) presents several challenges; however, in the past decade significant progress has been made in both diagnostic and treatment modalities. Germline rearranged in transfection (RET) testing in multiple endocrine neoplasia 2 and 3, and somatic RET testing in sporadic MTC have revolutionized the treatment options available to patients. Positron emission tomography imaging with novel radioligands has improved characterization of disease and a new international grading system can predict prognosis. Systemic therapy for persistent and metastatic disease has evolved significantly with targeted kinase therapy especially for those harboring germline or somatic RET variants. Selpercatinib and pralsetinib are highly selective RET kinase inhibitors that have shown improved progression-free survival with better tolerability than outcomes seen in earlier multikinase inhibitor studies. Here we discuss changes in paradigms for MTC patients: from determining RET alteration status upfront to novel techniques for the evaluation of this heterogenous disease. Successes and challenges with kinase inhibitor use will illustrate how managing this rare malignancy continues to evolve.
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Affiliation(s)
- Matti L Gild
- Faculty of Health and Medicine, University of Sydney, Sydney 2006, Australia
- Department of Diabetes and Endocrinology, Royal North Shore Hospital, Sydney 2065, Australia
- Cancer Genetics, Kolling Institute of Medical Research, Sydney 2065, Australia
| | - Roderick J Clifton-Bligh
- Faculty of Health and Medicine, University of Sydney, Sydney 2006, Australia
- Department of Diabetes and Endocrinology, Royal North Shore Hospital, Sydney 2065, Australia
- Cancer Genetics, Kolling Institute of Medical Research, Sydney 2065, Australia
| | - Lori J Wirth
- Department of Medicine, Massachusetts General Hospital, & Harvard Medical School, Boston 02114, USA
| | - Bruce G Robinson
- Faculty of Health and Medicine, University of Sydney, Sydney 2006, Australia
- Department of Diabetes and Endocrinology, Royal North Shore Hospital, Sydney 2065, Australia
- Cancer Genetics, Kolling Institute of Medical Research, Sydney 2065, Australia
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5
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Ganesh BP, Peesh P, Blasco MP, Hamamy AE, Khan R, Guzman G, Honarpisheh P, Mohan EC, Goodman GW, Nguyen JN, Banerjee A, Ko KA, Korf J, Tan C, Fan H, Colpo G, Ahnstedt H, Couture L, Kofler J, Moruno-Manchon J, Maniskas M, Aronowski J, Lee J, Li J, Bryan RM, Chauhan A, Venna VR, McCullough L. Restoring a balanced pool of host-derived and microbiota-derived ligands of the aryl hydrocarbon receptor is beneficial after stroke. RESEARCH SQUARE 2023:rs.3.rs-3143015. [PMID: 37790313 PMCID: PMC10543021 DOI: 10.21203/rs.3.rs-3143015/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Stroke is a major cause of morbidity and mortality, and its incidence increases with age. While acute therapies for stroke are currently limited to intravenous thrombolytics and endovascular thrombectomy, recent studies have implicated an important role for the gut microbiome in post-stroke neuroinflammation. After stroke, several immuno-regulatory pathways, including the aryl hydrocarbon receptor (AHR) pathway, become activated. AHR is a master regulatory pathway that mediates neuroinflammation. Among various cell types, microglia (MG), as the resident immune cells of the brain, play a vital role in regulating post-stroke neuroinflammation and antigen presentation. Activation of AHR is dependent on a dynamic balance between host-derived and microbiota-derived ligands. While previous studies have shown that activation of MG AHR by host-derived ligands, such as kynurenine, is detrimental after stroke, the effects of post-stroke changes in microbiota-derived ligands of AHR, such as indoles, is unknown. Our study builds on the concept that differential activation of MG AHR by host-derived versus microbiome-derived metabolites affects outcomes after ischemic stroke. We examined the link between stroke-induced dysbiosis and loss of essential microbiota-derived AHR ligands. We hypothesize that restoring the balance between host-derived (kynurenine) and microbiota-derived (indoles) ligands of AHR is beneficial after stroke, offering a new potential avenue for therapeutic intervention in post-stroke neuroinflammation. Method We performed immunohistochemical analysis of brain samples from stroke patients to assess MG AHR expression after stroke. We used metabolomics analysis of plasma samples from stroke and non-stroke control patients with matched comorbidities to determine the levels of indole-based AHR ligands after stroke. We performed transient middle cerebral artery occlusion (MCAO) in aged (18 months) wild-type (WT) and germ-free (GF) mice to investigate the effects of post-stroke treatment with microbiota-derived indoles on outcome. To generate our results, we employed a range of methodologies, including flow cytometry, metabolomics, and 16S microbiome sequencing. Results We found that MG AHR expression is increased in human brain after stroke and after ex vivo oxygen-glucose deprivation and reperfusion (OGD/R). Microbiota-derived ligands of AHR are decreased in the human plasma at 24 hours after ischemic stroke. Kynurenine and indoles exhibited differential effects on aged WT MG survival after ex vivoOGD/R. We found that specific indole-based ligands of AHR (indole-3-propionic acid and indole-3-aldehyde) were absent in GF mice, thus their production depends on the presence of a functional gut microbiota. Additionally, a time-dependent decrease in the concentration of these indole-based AHR ligands occurred in the brain within the first 24 hours after stroke in aged WT mice. Post-stroke treatment of GF mice with a cocktail of microbiota-derived indole-based ligands of AHR regulated MG-mediated neuroinflammation and molecules involved in antigen presentation (increased CD80, MHC-II, and CD11b). Post-stroke treatment of aged WT mice with microbiota-derived indole-based ligands of AHR reduced both infarct volume and neurological deficits at 24 hours. Conclusion Our novel findings provide compelling evidence that the restoration of a well-balanced pool of host-derived kynurenine-based and microbiota-derived indole-based ligands of AHR holds considerable therapeutic potential for the treatment of ischemic stroke.
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Affiliation(s)
- Bhanu Priya Ganesh
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Pedram Peesh
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Maria Pilar Blasco
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Ahmad El Hamamy
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Romeesa Khan
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Gary Guzman
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Parisa Honarpisheh
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Eric C Mohan
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Grant W Goodman
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Justin N Nguyen
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | | | - Kyung Ae Ko
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | - Janelle Korf
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | | | - Huihui Fan
- The University of Texas Health Science Center at Houston
| | - Gabriela Colpo
- The University of Texas McGovern Medical School at Houston, 77030, TX
| | - Hilda Ahnstedt
- The University of Texas Health Science Center at Houston
| | - Lucy Couture
- The University of Texas McGovern Medical School at Houston, 77030, TX
| | | | - Jose Moruno-Manchon
- Department of Neurobiology and Anatomy, the University of Texas McGovern Medical School at Houston, 77030, TX
| | - Michael Maniskas
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | | | - Juneyoung Lee
- The University of Texas Health Science Center at Houston
| | - Jun Li
- McGovern Medical School, The University of Texas Health Science Center at Houston
| | | | | | | | - Louise McCullough
- McGovern Medical School/University of Texas Health Science Center at Houston
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6
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Gupta P, Herring B, Kumar N, Telange R, Garcia-Buntley SS, Caceres TW, Colantonio S, Williams F, Kurup P, Carter AM, Lin D, Chen H, Rose B, Jaskula-Sztul R, Mukhtar S, Reddy S, Bibb JA. Faulty Metabolism: A Potential Instigator of an Aggressive Phenotype in Cdk5-dependent Medullary Thyroid Carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544755. [PMID: 37398342 PMCID: PMC10312670 DOI: 10.1101/2023.06.13.544755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mechanistic modeling of cancers such as Medullary Thyroid Carcinoma (MTC) to emulate patient-specific phenotypes is challenging. The discovery of potential diagnostic markers and druggable targets in MTC urgently requires clinically relevant animal models. Here we established orthotopic mouse models of MTC driven by aberrantly active Cdk5 using cell-specific promoters. Each of the two models elicits distinct growth differences that recapitulate the less or more aggressive forms of human tumors. The comparative mutational and transcriptomic landscape of tumors revealed significant alterations in mitotic cell cycle processes coupled with the slow-growing tumor phenotype. Conversely, perturbation in metabolic pathways emerged as critical for aggressive tumor growth. Moreover, an overlapping mutational profile was identified between mouse and human tumors. Gene prioritization revealed putative downstream effectors of Cdk5 which may contribute to the slow and aggressive growth in the mouse MTC models. In addition, Cdk5/p25 phosphorylation sites identified as biomarkers for Cdk5-driven neuroendocrine tumors (NETs) were detected in both slow and rapid onset models and were also histologically present in human MTC. Thus, this study directly relates mouse and human MTC models and uncovers vulnerable pathways potentially responsible for differential tumor growth rates. Functional validation of our findings may lead to better prediction of patient-specific personalized combinational therapies.
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Affiliation(s)
- Priyanka Gupta
- Department of Translational Neuroscience, University of Arizona School of Medicine in Phoenix, Phoenix, AZ 85004-2230, USA
| | - Brendon Herring
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rahul Telange
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ford Williams
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Pradeep Kurup
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Angela M. Carter
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Diana Lin
- Department of Pathology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Herbert Chen
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Bart Rose
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Renata Jaskula-Sztul
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sushanth Reddy
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - James A. Bibb
- Department of Translational Neuroscience, University of Arizona School of Medicine in Phoenix, Phoenix, AZ 85004-2230, USA
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7
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Umfress A, Chakraborti A, Priya Sudarsana Devi S, Adams R, Epstein D, Massicano A, Sorace A, Singh S, Iqbal Hossian M, Andrabi SA, Crossman DK, Kumar N, Shahid Mukhtar M, Luo H, Simpson C, Abell K, Stokes M, Wiederhold T, Rosen C, Lu H, Natarajan A, Bibb JA. Cdk5 mediates rotational force-induced brain injury. Sci Rep 2023; 13:3394. [PMID: 36854738 PMCID: PMC9974974 DOI: 10.1038/s41598-023-29322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/02/2023] [Indexed: 03/02/2023] Open
Abstract
Millions of traumatic brain injuries (TBIs) occur annually. TBIs commonly result from falls, traffic accidents, and sports-related injuries, all of which involve rotational acceleration/deceleration of the brain. During these injuries, the brain endures a multitude of primary insults including compression of brain tissue, damaged vasculature, and diffuse axonal injury. All of these deleterious effects can contribute to secondary brain ischemia, cellular death, and neuroinflammation that progress for weeks, months, and lifetime after injury. While the linear effects of head trauma have been extensively modeled, less is known about how rotational injuries mediate neuronal damage following injury. Here, we developed a new model of repetitive rotational head trauma in rodents and demonstrated acute and prolonged pathological, behavioral, and electrophysiological effects of rotational TBI (rTBI). We identify aberrant Cyclin-dependent kinase 5 (Cdk5) activity as a principal mediator of rTBI. We utilized Cdk5-enriched phosphoproteomics to uncover potential downstream mediators of rTBI and show pharmacological inhibition of Cdk5 reduces the cognitive and pathological consequences of injury. These studies contribute meaningfully to our understanding of the mechanisms of rTBI and how they may be effectively treated.
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Affiliation(s)
- Alan Umfress
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ayanabha Chakraborti
- Department of Translational Neuroscience, University of Arizona College of Medicine in Phoeni, Biomedical Sciences Partnership Bldg, Phoenix, AZ, 85004 , USA
| | | | - Raegan Adams
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel Epstein
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adriana Massicano
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases University of Nebraska Medical Center, Omaha, NE, USA
| | - M Iqbal Hossian
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shaida A Andrabi
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Shahid Mukhtar
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | | | - Charles Rosen
- OSF Healthcare Illinois Neurological Institute, Peoria, IL, USA
| | - Hongbing Lu
- Department of Mechanical Engineering, University of Texas at Dallas, Dallas, TX, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases University of Nebraska Medical Center, Omaha, NE, USA
| | - James A Bibb
- Department of Translational Neuroscience, University of Arizona College of Medicine in Phoeni, Biomedical Sciences Partnership Bldg, Phoenix, AZ, 85004 , USA.
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Emerging Role of Plant-Based Dietary Components in Post-Translational Modifications Associated with Colorectal Cancer. Life (Basel) 2023; 13:life13020264. [PMID: 36836621 PMCID: PMC9962725 DOI: 10.3390/life13020264] [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: 12/30/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. Its main modifiable risk factors are diet, alcohol consumption, and smoking. Thus, the right approach through lifestyle changes may lead to its prevention. In fact, some natural dietary components have exhibited chemopreventive activity through modulation of cellular processes involved in CRC development. Although cancer is a multi-factorial process, the study of post-translational modifications (PTMs) of proteins associated with CRC has recently gained interest, as inappropriate modification is closely related to the activation of cell signalling pathways involved in carcinogenesis. Therefore, this review aimed to collect the main PTMs associated with CRC, analyse the relationship between different proteins that are susceptible to inappropriate PTMs, and review the available scientific literature on the role of plant-based dietary compounds in modulating CRC-associated PTMs. In summary, this review suggested that some plant-based dietary components such as phenols, flavonoids, lignans, terpenoids, and alkaloids may be able to correct the inappropriate PTMs associated with CRC and promote apoptosis in tumour cells.
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9
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Fan L, Tang Y, Li J, Huang W. Increased expression of TBC1D10B as a potential prognostic and immunotherapy relevant biomarker in liver hepatocellular carcinoma. Sci Rep 2023; 13:335. [PMID: 36611046 PMCID: PMC9825366 DOI: 10.1038/s41598-022-20341-1] [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: 02/07/2022] [Accepted: 09/12/2022] [Indexed: 01/09/2023] Open
Abstract
The TBC1 domain family member 10B (EPI64B/TBC1D10B), a member of the RabGAP EPI64 subfamily, contains a TBC domain that confers GTPase-activating protein activity. Even though overexpression of TBC1D10B has been reported to promote tumor invasion and metastasis in gastric adenocarcinoma, the prognostic value of TBC1D10B and its correlation with DNA methylation and immune infiltration in hepatocellular carcinoma are still not known. Transcriptional expression profiles of TBC1D10B between hepatocellular carcinoma tissues and normal tissues were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus. The Clinical Proteomic Tumor Analysis Consortium and the Human Protein Atlas were used to assess the TBC1D10B protein expression. The biological functions of TBC1D10B were evaluated by the Metascape database and by Gene Set Enrichment Analysis (GSEA). Receiver operating characteristic (ROC) curve analysis was used to distinguish hepatocellular carcinoma from adjacent normal tissues. The effect of TBC1D10B on survival was estimated using the Kaplan-Meier method. DNA methylation in the TBC1D10B gene was assessed using the online MEXPRESS and MethSurv tools. The association between TBC1D10B mRNA expression and immune cell infiltration was investigated by the TIMER2 web server, tumor immune estimation resource and single-sample GSEA. This study found that TBC1D10B is highly expressed in hepatocellular carcinoma and that increased TBC1D10B mRNA expression is associated with female sex, lower Body Mass Index, high level of alpha fetal protein, and worse clinical stages. The mRNA and protein levels of TBC1D10B were verified in cells. Functional annotation indicated enrichment with negative regulation of the cell cycle, extracellular matrix, and corresponding pathways in the high-TBC1D10B phenotype. The ROC curve analysis showed that, with a cutoff level of 2.912, the accuracy, sensitive, and specificity in differentiate TBC1D10B hepatocellular carcinoma from adjacent controls were 0.931, 0.920, and 0.802, respectively. Kaplan-Meier survival analysis showed that hepatocellular carcinoma patients with high TBC1D10B had a worse prognosis than those with low TBC1D10B, especially in patients with a weight below 70 kg, height above 170 cm, and histological G2 and G3. We also found that the methylation of TBC1D10B was associated with the prognosis in patients with hepatocellular carcinoma. Moreover, correlation analysis indicated that TBC1D10B mRNA expression was positively correlated with infiltration levels of most immune cells, but negatively correlated with Th17 and cytotoxic cells infiltration. Our study indicates that increased TBC1D10B expression in hepatocellular carcinoma may play a role in tumorigenesis by regulating the cell cycle and extracellular matrix. TBC1D10B may be a novel prognostic and predictive marker and immune therapeutic target in hepatocellular carcinoma patients.
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Affiliation(s)
- Li Fan
- grid.477238.dDepartment of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001 Guangxi China
| | - Yongmei Tang
- grid.477238.dDepartment of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001 Guangxi China
| | - Jingjing Li
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China.
| | - Wenjie Huang
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China.
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10
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Phosphorylated Proteins from Serum: A Promising Potential Diagnostic Biomarker of Cancer. Int J Mol Sci 2022; 23:ijms232012359. [PMID: 36293212 PMCID: PMC9604268 DOI: 10.3390/ijms232012359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is a fatal disease worldwide. Each year ten million people are diagnosed around the world, and more than half of patients eventually die from it in many countries. A majority of cancer remains asymptomatic in the earlier stages, with specific symptoms appearing in the advanced stages when the chances of adequate treatment are low. Cancer screening is generally executed by different imaging techniques like ultrasonography (USG), mammography, CT-scan, and magnetic resonance imaging (MRI). Imaging techniques, however, fail to distinguish between cancerous and non-cancerous cells for early diagnosis. To confirm the imaging result, solid and liquid biopsies are done which have certain limitations such as invasive (in case of solid biopsy) or missed early diagnosis due to extremely low concentrations of circulating tumor DNA (in case of liquid biopsy). Therefore, it is essential to detect certain biomarkers by a noninvasive approach. One approach is a proteomic or glycoproteomic study which mostly identifies proteins and glycoproteins present in tissues and serum. Some of these studies are approved by the Food and Drug Administration (FDA). Another non-expensive and comparatively easier method to detect glycoprotein biomarkers is by ELISA, which uses lectins of diverse specificities. Several of the FDA approved proteins used as cancer biomarkers do not show optimal sensitivities for precise diagnosis of the diseases. In this regard, expression of phosphoproteins is associated with a more specific stage of a particular disease with high sensitivity and specificity. In this review, we discuss the expression of different serum phosphoproteins in various cancers. These phosphoproteins are detected either by phosphoprotein enrichment by immunoprecipitation using phosphospecific antibody and metal oxide affinity chromatography followed by LC-MS/MS or by 2D gel electrophoresis followed by MALDI-ToF/MS analysis. The updated knowledge on phosphorylated proteins in clinical samples from various cancer patients would help to develop these serum phophoproteins as potential diagnostic/prognostic biomarkers of cancer.
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Wang X, Shi X, Lu H, Zhang C, Li X, Zhang T, Shen J, Wen J. Succinylation Inhibits the Enzymatic Hydrolysis of the Extracellular Matrix Protein Fibrillin 1 and Promotes Gastric Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200546. [PMID: 35901491 PMCID: PMC9507347 DOI: 10.1002/advs.202200546] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/03/2022] [Indexed: 06/15/2023]
Abstract
Extracellular matrix (ECM) remodeling is crucial in the regulation of gastric cancer (GC) progression. This work aims to reveal novel posttranslational modifications and their relevant mechanisms in GC. In 3D matrix culture and animal models, it is found that fibrillin 1 (FBN1) expression is increased in advanced GC and has succinylation modification. The succinylation modification of FBN1 blocks its degradation by matrix metalloproteinases (MMPs). The long-term accumulation and deposition of FBN1 enhance tumor progression by activating TGF-β1 and intracellular PI3K/Akt pathway. The FBN1 succinylation site monoclonal antibody can effectively intervene the effect of succinylation modification and inhibit GC progression. FBN1 is specifically upregulated in the progression of GC compared with other tumors. In conclusion, FBN1 is widely present in the form of K672-succinylated modifications in GC. Besides, the succinyl group of FBN1 blocks its binding to MMP2, inhibits its degradation by MMP2, and leads to the accumulation of FBN1, which poses a long-term risk to the poor prognosis of GC.
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Affiliation(s)
- Xingyun Wang
- Department of General SurgeryFirst Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
- Hongqiao International Institute of MedicineTongren HospitalShanghai Jiao Tong University School of MedicineNo. 1111, XianXia RoadShanghai200336China
| | - Xiao Shi
- Department of GastroenterologyZhongda HospitalSchool of MedicineSoutheast UniversityNanjing210009China
| | - Hongcheng Lu
- Department of UrologyZhongda Hospital Affiliated to Southeastern China UniversityNanjing210029China
| | - Chen Zhang
- Department of BiotherapyMedical Center for Digestive DiseasesSecond Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Xiang Li
- Department of Surgical OncologyJiangsu Province Hospital of Chinese MedicineAffiliated Hospital of Nanjing University of Chinese MedicineNanjing210029China
| | - Tiancheng Zhang
- Department of Surgical OncologyJiangsu Province Hospital of Chinese MedicineAffiliated Hospital of Nanjing University of Chinese MedicineNanjing210029China
| | - Jiajia Shen
- Department of General SurgeryFirst Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
| | - Jianfei Wen
- Department of General SurgeryFirst Affiliated Hospital of Nanjing Medical UniversityNanjing210029China
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12
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Gupta P, Strange K, Telange R, Guo A, Hatch H, Sobh A, Elie J, Carter AM, Totenhagen J, Tan C, Sonawane YA, Neuzil J, Natarajan A, Ovens AJ, Oakhill JS, Wiederhold T, Pacak K, Ghayee HK, Meijer L, Reddy S, Bibb JA. Genetic impairment of succinate metabolism disrupts bioenergetic sensing in adrenal neuroendocrine cancer. Cell Rep 2022; 40:111218. [PMID: 35977518 DOI: 10.1016/j.celrep.2022.111218] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 01/11/2023] Open
Abstract
Metabolic dysfunction mutations can impair energy sensing and cause cancer. Loss of function of the mitochondrial tricarboxylic acid (TCA) cycle enzyme subunit succinate dehydrogenase B (SDHB) results in various forms of cancer typified by pheochromocytoma (PC). Here we delineate a signaling cascade where the loss of SDHB induces the Warburg effect, triggers dysregulation of [Ca2+]i, and aberrantly activates calpain and protein kinase Cdk5, through conversion of its cofactor from p35 to p25. Consequently, aberrant Cdk5 initiates a phospho-signaling cascade where GSK3 inhibition inactivates energy sensing by AMP kinase through dephosphorylation of the AMP kinase γ subunit, PRKAG2. Overexpression of p25-GFP in mouse adrenal chromaffin cells also elicits this phosphorylation signaling and causes PC. A potent Cdk5 inhibitor, MRT3-007, reverses this phospho-cascade, invoking a senescence-like phenotype. This therapeutic approach halted tumor progression in vivo. Thus, we reveal an important mechanistic feature of metabolic sensing and demonstrate that its dysregulation underlies tumor progression in PC and likely other cancers.
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Affiliation(s)
- Priyanka Gupta
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Keehn Strange
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Rahul Telange
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ailan Guo
- Cell Signaling Technology, Danvers, MA 01923, USA
| | - Heather Hatch
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Amin Sobh
- Department of Medicine, Division of Hematology and Oncology, University of Florida, Gainesville, FL 32608, USA
| | - Jonathan Elie
- Perha Pharmaceuticals, Hôtel de Recherche, Perharidy Peninsula, 29680 Roscoff, France
| | - Angela M Carter
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - John Totenhagen
- Department of Radiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - Chunfeng Tan
- UT Health Science Center at Houston, Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Yogesh A Sonawane
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jiri Neuzil
- Institute of Biotechnology, Czech Academy of Sciences, Prague-West 252 50, Czech Republic; School of Pharmacy Medical Science, Griffith University, Southport, QLD 4222, Australia
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ashley J Ovens
- Metabolic Signalling Laboratory, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Jonathan S Oakhill
- Metabolic Signalling Laboratory, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | | | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hans K Ghayee
- Department of Internal Medicine, Division of Endocrinology, University of Florida College of Medicine and Malcom Randall VA Medical Center, Gainesville, FL 32608, USA
| | - Laurent Meijer
- Perha Pharmaceuticals, Hôtel de Recherche, Perharidy Peninsula, 29680 Roscoff, France
| | - Sushanth Reddy
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - James A Bibb
- Department of Surgery, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center and the Department of Neurobiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA.
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Hermann J, Schurgers L, Jankowski V. Identification and characterization of post-translational modifications: Clinical implications. Mol Aspects Med 2022; 86:101066. [PMID: 35033366 DOI: 10.1016/j.mam.2022.101066] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Post-translational modifications (PTMs) generate marginally modified isoforms of native peptides, proteins and lipoproteins thereby regulating protein functions, molecular interactions, and localization. With a key role in functional proteomics, post-translational modifications are recently also associated with the onsets and progressions of various diseases, such as cancer, cardiovascular, renal, and metabolic diseases. With the impact of post-translational modifications becoming increasingly clear, its reliable detection and quantification remain a major obstacle in the translation of these novel pathological markers into clinical diagnosis. While current antibody-based clinical diagnostics struggle to detect and quantify these marginal protein and lipoprotein alterations, state-of-the-art mass spectrometric, proteomic approaches provide the mass accuracy and resolving power necessary to isolate, identify and quantify novel and pathological post-translational modifications; however clinical translation of mass spectrometric applications are still facing major challenges. Here we review the status quo of the clinical translation of mass-spectrometric applications as novel diagnostic tools for the identification and quantification of post-translational modifications and focus on the emerging role of mass spectrometric methods in the clinical assessment of PTMs in disease states.
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Affiliation(s)
- Juliane Hermann
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Leon Schurgers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200, MD, Maastricht, the Netherlands
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.
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Cdk5 drives formation of heterogeneous pancreatic neuroendocrine tumors. Oncogenesis 2021; 10:83. [PMID: 34862365 PMCID: PMC8642406 DOI: 10.1038/s41389-021-00372-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 01/07/2023] Open
Abstract
Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous population of neoplasms that arise from hormone-secreting islet cells of the pancreas and have increased markedly in incidence over the past four decades. Non-functional PanNETs, which occur more frequently than hormone-secreting tumors, are often not diagnosed until later stages of tumor development and have poorer prognoses. Development of successful therapeutics for PanNETs has been slow, partially due to a lack of diverse animal models for pre-clinical testing. Here, we report development of an inducible, conditional mouse model of PanNETs by using a bi-transgenic system for regulated expression of the aberrant activator of Cdk5, p25, specifically in β-islet cells. This model produces a heterogeneous population of PanNETs that includes a subgroup of well-differentiated, non-functional tumors. Production of these tumors demonstrates the causative potential of aberrantly active Cdk5 for generation of PanNETs. Further, we show that human PanNETs express Cdk5 pathway components, are dependent on Cdk5 for growth, and share genetic and transcriptional overlap with the INS-p25OE model. The utility of this model is enhanced by the ability to form tumor-derived allografts. This new model of PanNETs will facilitate molecular delineation of Cdk5-dependent PanNETs and the development of new targeted therapeutics.
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15
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Smith BJ, Silva-Costa LC, Martins-de-Souza D. Human disease biomarker panels through systems biology. Biophys Rev 2021; 13:1179-1190. [PMID: 35059036 PMCID: PMC8724340 DOI: 10.1007/s12551-021-00849-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/01/2021] [Indexed: 12/23/2022] Open
Abstract
As more uses for biomarkers are sought after for an increasing number of disease targets, single-target biomarkers are slowly giving way for biomarker panels. These panels incorporate various sources of biomolecular and clinical data to guarantee a higher robustness and power of separation for a clinical test. Multifactorial diseases such as psychiatric disorders show great potential for clinical use, assisting medical professionals during the analysis of risk and predisposition, disease diagnosis and prognosis, and treatment applicability and efficacy. More specific tests are also being developed to assist in ruling out, distinguishing between, and confirming suspicions of multifactorial diseases, as well as to predict which therapy option may be the best option for a given patient's biochemical profile. As more complex datasets are entering the field, involving multi-omic approaches, systems biology has stepped in to facilitate the discovery and validation steps during biomarker panel generation. Filtering biomolecules and clinical data, pre-validating and cross-validating potential biomarkers, generating final biomarker panels, and testing the robustness and applicability of those panels are all beginning to rely on machine learning and systems biology and research in this area will only benefit from advances in these approaches.
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Affiliation(s)
- Bradley J. Smith
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Licia C. Silva-Costa
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico E Tecnológico, Sao Paulo, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
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16
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Maharjan CK, Ear PH, Tran CG, Howe JR, Chandrasekharan C, Quelle DE. Pancreatic Neuroendocrine Tumors: Molecular Mechanisms and Therapeutic Targets. Cancers (Basel) 2021; 13:5117. [PMID: 34680266 PMCID: PMC8533967 DOI: 10.3390/cancers13205117] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/16/2022] Open
Abstract
Pancreatic neuroendocrine tumors (pNETs) are unique, slow-growing malignancies whose molecular pathogenesis is incompletely understood. With rising incidence of pNETs over the last four decades, larger and more comprehensive 'omic' analyses of patient tumors have led to a clearer picture of the pNET genomic landscape and transcriptional profiles for both primary and metastatic lesions. In pNET patients with advanced disease, those insights have guided the use of targeted therapies that inhibit activated mTOR and receptor tyrosine kinase (RTK) pathways or stimulate somatostatin receptor signaling. Such treatments have significantly benefited patients, but intrinsic or acquired drug resistance in the tumors remains a major problem that leaves few to no effective treatment options for advanced cases. This demands a better understanding of essential molecular and biological events underlying pNET growth, metastasis, and drug resistance. This review examines the known molecular alterations associated with pNET pathogenesis, identifying which changes may be drivers of the disease and, as such, relevant therapeutic targets. We also highlight areas that warrant further investigation at the biological level and discuss available model systems for pNET research. The paucity of pNET models has hampered research efforts over the years, although recently developed cell line, animal, patient-derived xenograft, and patient-derived organoid models have significantly expanded the available platforms for pNET investigations. Advancements in pNET research and understanding are expected to guide improved patient treatments.
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Affiliation(s)
- Chandra K. Maharjan
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Po Hien Ear
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (P.H.E.); (C.G.T.); (J.R.H.)
| | - Catherine G. Tran
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (P.H.E.); (C.G.T.); (J.R.H.)
| | - James R. Howe
- Department of Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (P.H.E.); (C.G.T.); (J.R.H.)
| | - Chandrikha Chandrasekharan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
| | - Dawn E. Quelle
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
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17
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Tabang DN, Cui Y, Tremmel DM, Ford M, Li Z, Sackett SD, Odorico JS, Li L. Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry. Mol Omics 2021; 17:652-664. [PMID: 34318855 PMCID: PMC8511275 DOI: 10.1039/d1mo00104c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The pancreas is a vital organ with digestive and endocrine roles, and diseases of the pancreas affect millions of people yearly. A better understanding of the pancreas proteome and its dynamic post-translational modifications (PTMs) is necessary to engineer higher fidelity tissue analogues for use in transplantation. The extracellular matrix (ECM) has major roles in binding and signaling essential to the viability of insulin-producing islets of Langerhans. To characterize PTMs in the pancreas, native and decellularized tissues from four donors were analyzed. N-Glycosylated and phosphorylated peptides were simultaneously enriched via electrostatic repulsion-hydrophilic interaction chromatography and analyzed with mass spectrometry, maximizing PTM information from one workflow. A modified surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion was used to maximize solubility of the ECM. The analysis resulted in the confident identification of 3650 proteins, including 517 N-glycoproteins and 148 phosphoproteins. We identified 214 ECM proteins, of which 99 were N-glycosylated, 18 were phosphorylated, and 9 were found to have both modifications. Collagens, a major component of the ECM, were the most highly glycosylated of the ECM proteins and several were also heavily phosphorylated, raising the possibility of structural and thus functional changes resulting from these modifications. To our knowledge, this work represents the first characterization of PTMs in pancreatic ECM proteins. This work provides a basal profile of PTMs in the healthy human pancreatic ECM, laying the foundation for future investigations to determine disease-specific changes such as in diabetes and pancreatic cancer, and potentially helping to guide the development of tissue replacement constructs. Data are available via ProteomeXchange with identifier PXD025048.
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Affiliation(s)
- Dylan Nicholas Tabang
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Daniel M Tremmel
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan Ford
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Sara Dutton Sackett
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jon S Odorico
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
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Gerritsen JS, White FM. Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Expert Rev Proteomics 2021; 18:661-674. [PMID: 34468274 PMCID: PMC8628306 DOI: 10.1080/14789450.2021.1976152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Many pathologies, including cancer, have been associated with aberrant phosphorylation-mediated signaling networks that drive altered cell proliferation, migration, metabolic regulation, and can lead to systemic inflammation. Phosphoproteomics, the large-scale analysis of protein phosphorylation sites, has emerged as a powerful tool to define signaling network regulation and dysregulation in normal and pathological conditions. AREAS COVERED We provide an overview of methodology for global phosphoproteomics as well as enrichment of specific subsets of the phosphoproteome, including phosphotyrosine and phospho-motif enrichment of kinase substrates. We review quantitative methods, advantages and limitations of different mass spectrometry acquisition formats, and computational approaches to extract biological insight from phosphoproteomics data. Throughout, we discuss various applications and their challenges in implementation. EXPERT OPINION Over the past 20 years the field of phosphoproteomics has advanced to enable deep biological and clinical insight through the quantitative analysis of signaling networks. Future areas of development include Clinical Laboratory Improvement Amendments (CLIA)-approved methods for analysis of clinical samples, continued improvements in sensitivity to enable analysis of small numbers of rare cells and tissue microarrays, and computational methods to integrate data resulting from multiple systems-level quantitative analytical methods.
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Affiliation(s)
- Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
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Lee J, Chen R, Mohanakumar T, Bremner R, Mittal S, Fleming TP. Identification of Phospho-Tyrosine Targets as a Strategy for the Treatment of Esophageal Adenocarcinoma Cells. Onco Targets Ther 2021; 14:3813-3820. [PMID: 34188489 PMCID: PMC8232872 DOI: 10.2147/ott.s309388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/25/2021] [Indexed: 11/27/2022] Open
Abstract
Introduction Esophageal cancer (EC) is an aggressive cancer type that is increasing at a high rate in the US and worldwide. Extensive sequencing of EC specimens has shown that there are no consistent driver mutations that can impact treatment strategies. The goal of this study was to identify activated tyrosine kinase receptors (TKRs) in EC samples as potential targets in the treatment of EC. Methods Activated tyrosine kinase receptors were detected using a dot-blot array for human TK receptors. Human esophageal cancer cell lines were transplanted into immunocompromised mice, and tumor xenografts were subjected to tyrosine kinase inhibitors based on the dot-blot array data. Results Using the OE33 esophageal cancer cell line, we identified activated EGF receptor (EGFR), as well as ErbB2 and ErbB3. Treatment of this cell line with erlotinib, a specific inhibitor of EGFR, did not impact the growth of this tumor cell line. Treating the OE33 cell line with afatinib, a pan-EGFR family inhibitor resulted in the growth inhibition of OE33, indicating that the ErbB2 and ErbB3 receptors were contributing to tumor cell proliferation. Afatinib treatment of mice growing OE33 tumors inhibited growth of the OE33 tumor cells. Discussion Activated tyrosine kinase receptors were readily detected in both cancer cell lines and human esophageal cancer samples. By identifying the activated receptors and then using the appropriate tyrosine kinase inhibitors, we can block tumor growth in vitro and in animal xenografts. We propose that identifying and targeting activated TKRs can be used as a personalized EC tumor treatment strategy.
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Affiliation(s)
- John Lee
- Norton Thoracic Institute, St. Joseph Hospital, Phoenix, AZ, USA
| | - Rongbing Chen
- Norton Thoracic Institute, St. Joseph Hospital, Phoenix, AZ, USA
| | - T Mohanakumar
- Norton Thoracic Institute, St. Joseph Hospital, Phoenix, AZ, USA
| | - Ross Bremner
- Norton Thoracic Institute, St. Joseph Hospital, Phoenix, AZ, USA
| | - Sumeet Mittal
- Norton Thoracic Institute, St. Joseph Hospital, Phoenix, AZ, USA
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Zhu C, Wu J, Jin X, Yan Y, Ding CF, Tang K, Zhang D. Post-synthesis of biomimetic chitosan with honeycomb-like structure for sensitive recognition of phosphorylated peptides. J Chromatogr A 2021; 1643:462072. [PMID: 33789194 DOI: 10.1016/j.chroma.2021.462072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Chemical modification of biological materials is indispensable for enrichment of phosphorylated peptides. In this work, we synthesized a biomimetic honeycombed affinity chromatography (IMAC) adsorbent by preparing Crosslinked Chitosan, chelating aminomethyl phosphate decorated with Ti (IV) cation. The as-prepared CTSM@AMPA-Ti4+ composites with stable structure, low steric hindrance, and high Ti4+ loading amount were used as a promising adsorbent for enrichment of phosphopeptides. CTSM@AMPA-Ti4+ showed extremely high sensitivity (0.4 fmol) and selectivity at a low composition molar ratio of β-casein/BSA (1:1000). What's more, it can keep its performance in the case that used to capture phosphorylated peptides from standard protein ten times or soaking in the acid/base solution for a long time. In addition, CTSM@AMPA-Ti4+ successfully captured 35 phosphorylated peptides from human saliva. This study offers a way about diversiform functionalization of CTSM in phosphoproteome analysis and disease research.
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Affiliation(s)
- Canhong Zhu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Jiani Wu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Xueting Jin
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Di Zhang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
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Prunus spinosa Extract Loaded in Biomimetic Nanoparticles Evokes In Vitro Anti-Inflammatory and Wound Healing Activities. NANOMATERIALS 2020; 11:nano11010036. [PMID: 33375632 PMCID: PMC7824340 DOI: 10.3390/nano11010036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022]
Abstract
Prunus spinosa fruits (PSF) contain different phenolic compounds showing antioxidant and anti-inflammatory activities. Innovative drug delivery systems such as biomimetic nanoparticles could improve the activity of PSF extract by promoting (i) the protection of payload into the lipidic bilayer, (ii) increased accumulation to the diseased tissue due to specific targeting properties, (iii) improved biocompatibility, (iv) low toxicity and increased bioavailability. Using membrane proteins extracted from human monocyte cell line THP-1 cells and a mixture of phospholipids, we formulated two types of PSF-extract-loaded biomimetic vesicles differing from each other for the presence of either 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DOPG). The biological activity of free extract (PSF), compared to both types of extract-loaded vesicles (PSF-DOPCs and PSF-DOPGs) and empty vesicles (DOPCs and DOPGs), was evaluated in vitro on HUVEC cells. PSF-DOPCs showed preferential incorporation of the extract. When enriched into the nanovesicles, the extract showed a significantly increased anti-inflammatory activity, and a pronounced wound-healing effect (with PSF-DOPCs more efficient than PSF-DOPG) compared to free PSF. This innovative drug delivery system, combining nutraceutical active ingredients into a biomimetic formulation, represents a possible adjuvant therapy for the treatment of wound healing. This nanoplatform could be useful for the encapsulation/enrichment of other nutraceutical products with short stability and low bioavailability.
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