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Lim S, Ha Y, Lee B, Shin J, Rhim T. Calnexin as a dual-role biomarker: antibody-based diagnosis and therapeutic targeting in lung cancer. BMB Rep 2024; 57:155-160. [PMID: 38303563 PMCID: PMC10979343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Lung cancer carries one of the highest mortality rates among all cancers. It is often diagnosed at more advanced stages with limited treatment options compared to other malignancies. This study focuses on calnexin as a potential biomarker for diagnosis and treatment of lung cancer. Calnexin, a molecular chaperone integral to N-linked glycoprotein synthesis, has shown some associations with cancer. However, targeted therapeutic or diagnostic methods using calnexin have been proposed. Through 1D-LCMSMS, we identified calnexin as a biomarker for lung cancer and substantiated its expression in human lung cancer cell membranes using Western blotting, flow cytometry, and immunocytochemistry. Anti-calnexin antibodies exhibited complement-dependent cytotoxicity to lung cancer cell lines, resulting in a notable reduction in tumor growth in a subcutaneous xenograft model. Additionally, we verified the feasibility of labeling tumors through in vivo imaging using antibodies against calnexin. Furthermore, exosomal detection of calnexin suggested the potential utility of liquid biopsy for diagnostic purposes. In conclusion, this study establishes calnexin as a promising target for antibody-based lung cancer diagnosis and therapy, unlocking novel avenues for early detection and treatment. [BMB Reports 2024; 57(3): 155-160].
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Affiliation(s)
- Soyeon Lim
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Korea
| | - Youngeun Ha
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Korea
| | - Boram Lee
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Korea
| | - Junho Shin
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Korea
| | - Taiyoun Rhim
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Korea
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2
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Azzawri AA, Yildirim IH, Yegin Z, Dusak A. Expression of GRP78 and its copartners in HEK293 and pancreatic cancer cell lines (BxPC-3/PANC-1) exposed to MRI and CT contrast agents. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:391-416. [PMID: 37787049 DOI: 10.1080/15257770.2023.2263496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Endoplasmic reticulum (ER) stress-associated chaperones trigger a defense mechanism called as unfolded protein response (UPR) which can manage apoptosis and be determinative in cell fate. Both anticancer drug effects and potential toxicity effects of magnetic resonance imaging (MRI) and computed tomography (CT) contrast agents were aimed to be evaluated. For this purpose, we investigated expression profiles of endoplasmic reticulum stress-associated chaperone molecules in human pancreatic tumor lines BxPC-3 and PANC-1 and control human embryonic kidney cells 293 (HEK293) induced with a variety of gadolinium and iohexol contrast agents. Protein expression levels of ER stress-associated chaperones (master regulator: GRP78/Bip and its copartners: Calnexin, Ero1, PDI, CHOP, IRE1α and PERK) were evaluated with Western blotting. Expression levels at mRNA level were also assessed for GRP78/Bip and CHOP with real-time PCR. Induction of cells was carried out with four different Gd-based contrast agents (GBCAs): (Dotarem, Optimark, Primovist and Gadovist) and two different iohexol agents (Omnipol, Omnipaque). CT contrast agents tested in the study did not result in significant ER stress in HEK293 cells. However, they do not seem to have theranostic potential in pancreas cancer through ER pathway. The potential efficiency of macrocyclic MRI contrast agents to provoke apoptosis via ER stress-associated chaperones in BxPC-3 cells lends credibility for their future theranostic use in pancreas cancer as long as undesired toxicity effects were carefully considered. ER stress markers and/or contrast agents seem to have promising potential to be translated into the clinical practice to manage pancreas cancer progression.
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Affiliation(s)
| | | | - Zeynep Yegin
- Medical Laboratory Techniques Program, Vocational School of Health Services, Sinop University, Sinop, Turkey
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3
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Bujang MA. An Elaboration on Sample Size Planning for Performing a One-Sample Sensitivity and Specificity Analysis by Basing on Calculations on a Specified 95% Confidence Interval Width. Diagnostics (Basel) 2023; 13:diagnostics13081390. [PMID: 37189491 DOI: 10.3390/diagnostics13081390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 05/17/2023] Open
Abstract
Sample size calculation based on a specified width of 95% confidence interval will offer researchers the freedom to set the level of accuracy of the statistics that they aim to achieve for a particular study. This paper provides a description of the general conceptual context for performing sensitivity and specificity analysis. Subsequently, sample size tables for sensitivity and specificity analysis based on a specified 95% confidence interval width is then provided. Such recommendations for sample size planning are provided based on two different scenarios: one for a diagnostic purpose and another for a screening purpose. Further discussion on all the other relevant considerations for the determination of a minimum sample size requirement and on how to draft the sample size statement for performing sensitivity and specificity analysis are also provided.
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Affiliation(s)
- Mohamad Adam Bujang
- Clinical Research Centre, Sarawak General Hospital, Ministry of Health Malaysia, Kuching 93586, Malaysia
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4
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Alteration in Levels of Specific miRNAs and Their Potential Protein Targets between Human Pancreatic Cancer Samples, Adjacent Normal Tissue, and Xenografts Derived from These Tumors. Life (Basel) 2023; 13:life13030608. [PMID: 36983764 PMCID: PMC10057657 DOI: 10.3390/life13030608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Herein, we describe the global comparison of miRNAs in human pancreatic cancer tumors, adjacent normal tissue, and matched patient-derived xenograft models using microarray screening. RNA was extracted from seven tumor, five adjacent normal, and eight FI PDX tumor samples and analyzed by Affymetrix GeneChip miRNA 4.0 array. A transcriptome analysis console (TAC) was used to generate comparative lists of up- and downregulated miRNAs for the comparisons, tumor vs. normal and F1 PDX vs. tumor. Particular attention was paid to miRNAs that were changed in the same direction in both comparisons. We identified the involvement in pancreatic tumor tissue of several miRNAs, including miR4534, miR3154, and miR4742, not previously highlighted as being involved in this type of cancer. Investigation in the parallel mRNA and protein lists from the same samples allowed the elimination of proteins where altered expression correlated with corresponding mRNA levels and was thus less likely to be miRNA regulated. Using the remaining differential expression protein lists for proteins predicted to be targeted for differentially expressed miRNA on our list, we were able to tentatively ascribe specific protein changes to individual miRNA. Particularly interesting target proteins for miRs 615-3p, 2467-3p, 4742-5p, 509-5p, and 605-3p were identified. Prominent among the protein targets are enzymes involved in aldehyde metabolism and membrane transport and trafficking. These results may help to uncover vulnerabilities that could enable novel approaches to treating pancreatic cancer.
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5
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Calnexin, More Than Just a Molecular Chaperone. Cells 2023; 12:cells12030403. [PMID: 36766745 PMCID: PMC9913998 DOI: 10.3390/cells12030403] [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: 01/04/2023] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Calnexin is a type I integral endoplasmic reticulum (ER) membrane protein with an N-terminal domain that resides in the lumen of the ER and a C-terminal domain that extends into the cytosol. Calnexin is commonly referred to as a molecular chaperone involved in the folding and quality control of membrane-associated and secreted proteins, a function that is attributed to its ER- localized domain with a structure that bears a strong resemblance to another luminal ER chaperone and Ca2+-binding protein known as calreticulin. Studies have discovered that the cytosolic C-terminal domain of calnexin undergoes distinct post-translational modifications and interacts with a variety of proteins. Here, we discuss recent findings and hypothesize that the post-translational modifications of the calnexin C-terminal domain and its interaction with specific cytosolic proteins play a role in coordinating ER functions with events taking place in the cytosol and other cellular compartments.
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6
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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7
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Huang H, Yang Y, Zhu Y, Chen H, Yang Y, Zhang L, Li W. Blood protein biomarkers in lung cancer. Cancer Lett 2022; 551:215886. [PMID: 35995139 DOI: 10.1016/j.canlet.2022.215886] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Lung cancer has consistently ranked first as the cause of cancer-associated mortality. The 5-year survival rate has risen slowly, and the main obstacle to improving the prognosis of patients has been that lung cancer is usually diagnosed at an advanced or incurable stage. Thus, early detection and timely intervention are the most effective ways to reduce lung cancer mortality. Tumor-specific molecules and cellular elements are abundant in circulation, providing real-time information in a noninvasive and cost-effective manner during lung cancer development. These circulating biomarkers are emerging as promising tools for early detection of lung cancer and can be used to supplement computed tomography screening, as well as for prognosis prediction and treatment response monitoring. Serum and plasma are the main sources of circulating biomarkers, and protein biomarkers have been most extensively studied. In this review, we summarize the research progress on three most common types of blood protein biomarkers (tumor-associated antigens, autoantibodies, and exosomal proteins) in lung cancer. This review will potentially guide researchers toward a more comprehensive understanding of candidate lung cancer protein biomarkers in the blood to facilitate their translation to the clinic.
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Affiliation(s)
- Hong Huang
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yongfeng Yang
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yihan Zhu
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Hongyu Chen
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Ying Yang
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Li Zhang
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, 610041, China.
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8
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Hirano S, Matsumoto K, Tanaka K, Amano N, Koguchi D, Ikeda M, Shimizu Y, Tsuchiya B, Nagashio R, Sato Y, Iwamura M. DJ-1 Expression Might Serve as a Biologic Marker in Patients with Bladder Cancer. Cancers (Basel) 2022; 14:2535. [PMID: 35626138 PMCID: PMC9139869 DOI: 10.3390/cancers14102535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/03/2023] Open
Abstract
The overexpression of DJ-1 protein and its secretion into the bloodstream has been reported in various neoplasms. However, serum levels and the subcellular localization of DJ-1 have not been analyzed in detail in bladder cancer (BC). Our comprehensive analysis of these variables started with the measurement of DJ-1 in serum from 172 patients with BC, 20 patients with urolithiasis and 100 healthy participants. Next, an immunohistochemical study of DJ-1 expression and localization was conducted in 92 patients with BC, and associations with clinicopathologic factors and patient outcomes were evaluated. Serum DJ-1 was significantly higher in patients with BC than in those with urolithiasis or in healthy participants. Immunohistochemically, a cytoplasm-positive (Cy+) and nucleus-negative (N-) DJ-1 pattern was associated with age and pathologic stage. Log-rank tests indicated that the Cy+, N- pattern was significantly associated with overall survival (OS), recurrence-free survival (RFS), and cancer specific survival (CSS). In addition, the Cy+, N- pattern was an independent prognostic factor in the multivariate analysis adjusted for the effects of the clinicopathologic outcomes. The investigation of DJ-1 expression might help physicians to make decisions regarding further follow-up and additional treatments.
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Affiliation(s)
- Shuhei Hirano
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Kazumasa Matsumoto
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Kei Tanaka
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Noriyuki Amano
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Dai Koguchi
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Masaomi Ikeda
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Yuriko Shimizu
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Benio Tsuchiya
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
| | - Ryo Nagashio
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
| | - Yuichi Sato
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
| | - Masatsugu Iwamura
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
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9
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Mercier R, LaPointe P. The role of cellular proteostasis in anti-tumor immunity. J Biol Chem 2022; 298:101930. [PMID: 35421375 PMCID: PMC9108985 DOI: 10.1016/j.jbc.2022.101930] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/25/2022] Open
Abstract
Immune checkpoint blockade therapy is perhaps the most important development in cancer treatment in recent memory. It is based on decades of investigation into the biology of immune cells and the role of the immune system in controlling cancer growth. While the molecular circuitry that governs the immune system in general - and anti-tumor immunity in particular - is intensely studied, far less attention has been paid to the role of cellular stress in this process. Proteostasis, intimately linked to cell stress responses, refers to the dynamic regulation of the cellular proteome and is maintained through a complex network of systems that govern the synthesis, folding, and degradation of proteins in the cell. Disruption of these systems can result in the loss of protein function, altered protein function, the formation of toxic aggregates, or pathologies associated with cell stress. However, the importance of proteostasis extends beyond its role in maintaining proper protein function; proteostasis governs how tolerant cells may be to mutations in protein coding genes and the overall half-life of proteins. Such gene expression changes may be associated with human diseases including neurodegenerative diseases, metabolic disease, and cancer and manifest at the protein level against the backdrop of the proteostasis network in any given cellular environment. In this review, we focus on the role of proteostasis in regulating immune responses against cancer as well the role of proteostasis in determining immunogenicity of cancer cells.
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Affiliation(s)
- Rebecca Mercier
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada.
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10
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Taylor BC, Balko JM. Mechanisms of MHC-I Downregulation and Role in Immunotherapy Response. Front Immunol 2022; 13:844866. [PMID: 35296095 PMCID: PMC8920040 DOI: 10.3389/fimmu.2022.844866] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
Immunotherapy has become a key therapeutic strategy in the treatment of many cancers. As a result, research efforts have been aimed at understanding mechanisms of resistance to immunotherapy and how anti-tumor immune response can be therapeutically enhanced. It has been shown that tumor cell recognition by the immune system plays a key role in effective response to T cell targeting therapies in patients. One mechanism by which tumor cells can avoid immunosurveillance is through the downregulation of Major Histocompatibility Complex I (MHC-I). Downregulation of MHC-I has been described as a mechanism of intrinsic and acquired resistance to immunotherapy in patients with cancer. Depending on the mechanism, the downregulation of MHC-I can sometimes be therapeutically restored to aid in anti-tumor immunity. In this article, we will review current research in MHC-I downregulation and its impact on immunotherapy response in patients, as well as possible strategies for therapeutic upregulation of MHC-I.
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Affiliation(s)
- Brandie C. Taylor
- Department of Medicine, Cancer Biology, Vanderbilt University, Nashville, TN, United States
| | - Justin M. Balko
- Department of Medicine, Cancer Biology, Vanderbilt University, Nashville, TN, United States
- Department of Medicine, Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, United States
- *Correspondence: Justin M. Balko,
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11
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Abstract
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
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12
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Zhang G, Zhang L, Sun S, Chen M. Identification of a Novel Defined Immune-Autophagy-Related Gene Signature Associated With Clinical and Prognostic Features of Kidney Renal Clear Cell Carcinoma. Front Mol Biosci 2022; 8:790804. [PMID: 34988121 PMCID: PMC8721006 DOI: 10.3389/fmolb.2021.790804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/22/2021] [Indexed: 12/23/2022] Open
Abstract
Background: As a common cancer of the urinary system in adults, renal clear cell carcinoma is metastatic in 30% of patients, and 1-2 years after diagnosis, 60% of patients die. At present, the rapid development of tumor immunology and autophagy had brought new directions to the treatment of renal cancer. Therefore, it was extremely urgent to find potential targets and prognostic biomarkers for immunotherapy combined with autophagy. Methods: Through GSE168845, immune-related genes, autophagy-related genes, and immune-autophagy-related differentially expressed genes (IAR-DEGs) were identified. Independent prognostic value of IAR-DEGs was determined by differential expression analysis, prognostic analysis, and univariate and multivariate Cox regression analyses. Then, the lasso Cox regression model was established to evaluate the correlation of IAR-DEGs with the immune score, immune checkpoint, iron death, methylation, and one-class logistic regression (OCLR) score. Results: In this study, it was found that CANX, BID, NAMPT, and BIRC5 were immune-autophagy-related genes with independent prognostic value, and the risk prognostic model based on them was well constructed. Further analysis showed that CANX, BID, NAMPT, and BIRC5 were significantly correlated with the immune score, immune checkpoint, iron death, methylation, and OCLR score. Further experimental results were consistent with the bioinformatics analysis. Conclusion: CANX, BID, NAMPT, and BIRC5 were potential targets and effective prognostic biomarkers for immunotherapy combined with autophagy in kidney renal clear cell carcinoma.
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Affiliation(s)
- Guangyuan Zhang
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Lei Zhang
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Si Sun
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China.,Department of Urology, Nanjing Lishui District People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
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13
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Cordeiro YG, Mulder LM, van Zeijl RJM, Paskoski LB, van Veelen P, de Ru A, Strefezzi RF, Heijs B, Fukumasu H. Proteomic Analysis Identifies FNDC1, A1BG, and Antigen Processing Proteins Associated with Tumor Heterogeneity and Malignancy in a Canine Model of Breast Cancer. Cancers (Basel) 2021; 13:cancers13235901. [PMID: 34885011 PMCID: PMC8657005 DOI: 10.3390/cancers13235901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/13/2021] [Accepted: 11/19/2021] [Indexed: 12/24/2022] Open
Abstract
New insights into the underlying biological processes of breast cancer are needed for the development of improved markers and treatments. The complex nature of mammary cancer in dogs makes it a great model to study cancer biology since they present a high degree of tumor heterogeneity. In search of disease-state biomarkers candidates, we applied proteomic mass spectrometry imaging in order to simultaneously detect histopathological and molecular alterations whilst preserving morphological integrity, comparing peptide expression between intratumor populations in distinct levels of differentiation. Peptides assigned to FNDC1, A1BG, and double-matching keratins 18 and 19 presented a higher intensity in poorly differentiated regions. In contrast, we observed a lower intensity of peptides matching calnexin, PDIA3, and HSPA5 in poorly differentiated cells, which enriched for protein folding in the endoplasmic reticulum and antigen processing, assembly, and loading of class I MHC. Over-representation of collagen metabolism, coagulation cascade, extracellular matrix components, cadherin-binding and cell adhesion pathways also distinguished cell populations. Finally, an independent validation showed FNDC1, A1BG, PDIA3, HSPA5, and calnexin as significant prognostic markers for human breast cancer patients. Thus, through a spatially correlated characterization of spontaneous carcinomas, we described key proteins which can be further validated as potential prognostic biomarkers.
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Affiliation(s)
- Yonara G. Cordeiro
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, Brazil; (Y.G.C.); (L.B.P.); (R.F.S.)
| | - Leandra M. Mulder
- Center of Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.M.); (R.J.M.v.Z.); (P.v.V.); (A.d.R.); (B.H.)
| | - René J. M. van Zeijl
- Center of Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.M.); (R.J.M.v.Z.); (P.v.V.); (A.d.R.); (B.H.)
| | - Lindsay B. Paskoski
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, Brazil; (Y.G.C.); (L.B.P.); (R.F.S.)
| | - Peter van Veelen
- Center of Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.M.); (R.J.M.v.Z.); (P.v.V.); (A.d.R.); (B.H.)
| | - Arnoud de Ru
- Center of Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.M.); (R.J.M.v.Z.); (P.v.V.); (A.d.R.); (B.H.)
| | - Ricardo F. Strefezzi
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, Brazil; (Y.G.C.); (L.B.P.); (R.F.S.)
| | - Bram Heijs
- Center of Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.M.); (R.J.M.v.Z.); (P.v.V.); (A.d.R.); (B.H.)
| | - Heidge Fukumasu
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, Brazil; (Y.G.C.); (L.B.P.); (R.F.S.)
- Correspondence: ; Tel.: +55-19-3565-6864
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Serum Epiplakin Might Be a Potential Serodiagnostic Biomarker for Bladder Cancer. Cancers (Basel) 2021; 13:cancers13205150. [PMID: 34680299 PMCID: PMC8534213 DOI: 10.3390/cancers13205150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 11/16/2022] Open
Abstract
Tumor markers that can be detected at an early stage are needed. Here, we evaluated the epiplakin expression levels in sera from patients with bladder cancer (BC). Using a micro-dot blot array, we evaluated epiplakin expression levels in 60 patients with BC, 20 patients with stone disease, and 28 healthy volunteers. The area under the curve (AUC) and best cut-off point were calculated using receiver-operating characteristic (ROC) analysis. Serum epiplakin levels were significantly higher in patients with BC than in those with stone disease (p = 0.0013) and in healthy volunteers (p < 0.0001). The AUC-ROC level for BC was 0.78 (95% confidence interval (CI) = 0.69-0.87). Using a cut-off point of 873, epiplakin expression levels exhibited 68.3% sensitivity and 79.2% specificity for BC. However, the serum epiplakin levels did not significantly differ by sex, age, pathological stage and grade, or urine cytology. We performed immunohistochemical staining using the same antibody on another cohort of 127 patients who underwent radical cystectomy. Univariate and multivariate analysis results showed no significant differences between epiplakin expression, clinicopathological findings, and patient prognoses. Our results showed that serum epiplakin might be a potential serodiagnostic biomarker in patients with BC.
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15
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Wu P, Xiang T, Wang J, Lv R, Ma S, Yuan L, Wu G, Che X. Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis. BMC Med Genomics 2021; 14:241. [PMID: 34620162 PMCID: PMC8499437 DOI: 10.1186/s12920-021-01092-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack of a clear understanding of the molecular mechanism. Hence, exploring the underlying mechanisms and seeking novel biomarkers for pursuing a precise prognostic biomarker and appropriate therapies are critical. Material and methods In our research, the differentially expressed genes (DEGs) were screened from the TCGA and GEO databases, and a total of 149 upregulated and 285 downregulated genes were sorted. This was followed by construction of functional enrichment and protein–protein interaction (PPI) network, and then the top 15 DEGs were selected for further analysis. The P4HB gene was chosen as our target gene by repetitively validating multiple datasets, and higher levels of P4HB expression predicted lower overall survival (OS) in patients with pRCC. Results We found that P4HB not only connects with immune cell infiltration and co-expression with PD-1, PD-L2, and CTLA-4, but also has a strong connection with the newly discovered hot gene, TOX. Conclusion We speculate that P4HB is a novel gene involved in the progression of pRCC through immunomodulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01092-w.
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Affiliation(s)
- Ping Wu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China
| | - Tingting Xiang
- Department of Rehabilitation, Liguang Rehabilitation Hospital of Dalian Development Zone, Dalian, 116600, China
| | - Jing Wang
- Department of Neurobiology, Harbin Medical University, Harbin, 150086, China
| | - Run Lv
- Department of Anesthesiology, Dalian Medical University, Dalian, 116044, China
| | - Shaoxin Ma
- Department of Anesthesiology, Dalian Medical University, Dalian, 116044, China
| | - Limei Yuan
- Department of Anesthesiology, Dalian Medical University, Dalian, 116044, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China.
| | - Xiangyu Che
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China.
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16
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Sun Z, Lu Z, Li R, Shao W, Zheng Y, Shi X, Li Y, Song J. Construction of a Prognostic Model for Hepatocellular Carcinoma Based on Immunoautophagy-Related Genes and Tumor Microenvironment. Int J Gen Med 2021; 14:5461-5473. [PMID: 34526813 PMCID: PMC8436260 DOI: 10.2147/ijgm.s325884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Background The aim of this study was to screen and identify immunoautophagy-related genes (IARGs) in HCC patients and clarify their potential prognostic value in HCC patients. Methods Immune-related genes and autophagy-related gene were downloaded from public databases. Cox regression analysis was used to selected several immunoautophagy-related genes to establish a prognostic model, and patients were divided into high- and low-risk groups based on median risk score. We analyzed the overall survival and clinicopathological characteristics between two groups. Meanwhile, internal validation dataset and external ICGC dataset were used to verify robustness of the model. Associations between six immune cells infiltrates and risk score were analyzed. Results A prognostic model was established based on CANX and HDAC1. The prognoses of the high-risk group were worse than low-risk group in both TCGA and ICGC datasets. Multivariate Cox regression analysis showed that risk score was an independent prognostic factor for HCC patients. Results showed that the risk score in young group was higher than elderly group. Patients with poorly differentiated tumor may have high risk score and poor survival. The score was positively correlated with immune cells. Conclusion Our study shows that immunoautophagy-related genes have potential prognostic value for patients with HCC and may provide new information and direction for targeted therapy.
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Affiliation(s)
- Zhen Sun
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Zhenhua Lu
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Rui Li
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Weiwei Shao
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Yangyang Zheng
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Xiaolei Shi
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Yao Li
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - Jinghai Song
- Department of General Surgery, Department of Hepato-Bilio-Pancreatic Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.,Graduate School of Peking Union Medical College, Beijing, 100730, People's Republic of China
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Preliminary Results of Robotic Lobectomy in Stage IIIA-N2 NSCLC after Induction Treatment: A Case Control Study. J Clin Med 2021; 10:jcm10163465. [PMID: 34441761 PMCID: PMC8396941 DOI: 10.3390/jcm10163465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 11/16/2022] Open
Abstract
Despite there already being many studies on robotic surgery as a minimally invasive approach for non-small-cell lung cancer (NSCLC) patients, the use of this technique for stage III disease is still poorly described. These are the preliminary results of our prospective study on the safety and effectiveness of robotic approaches in patients with locally advanced NSCLC in terms of postoperative complications and oncological outcomes. Since 2016, we prospectively investigated 19 consecutive patients with NSCLC stage IIIA-pN2 (diagnosed by EBUS-TBNA) who underwent lobectomy and radical lymph node dissection with robotic approaches after induction treatment. Furthermore, we matched a case-control study with 46 patients treated with open surgery during the same period of time, with similar age, comorbidities, clinical stage and tumor size. The individual matched population was composed of 16 robot-assisted thoracic surgeries and 16 patients who underwent open surgery. The median time range of resection was inferior in the open group compared to robotic lobectomy (243 vs. 161 min; p < 0.001). Lymph node resection and positivity were not significantly different (p = 0.96 and p = 0.57, respectively). Moreover, no difference was observed for PFS (p = 0.16) or OS (p = 0.41). In conclusion, we demonstrated that the early outcomes and oncological results of N2-patients after robotic lobectomy were similar to those who had open surgery. Considering the advantages of minimally invasive surgery, robot-assisted lobectomy appears to be a safe approach to patients with locally advanced diseases.
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18
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Moradpoor R, Gharebaghian A, Shahi F, Mousavi A, Salari S, Akbari ME, Ajdari S, Salimi M. Identification and Validation of Stage-Associated PBMC Biomarkers in Breast Cancer Using MS-Based Proteomics. Front Oncol 2020; 10:1101. [PMID: 32793473 PMCID: PMC7393188 DOI: 10.3389/fonc.2020.01101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
Background: It is well-described that the transcriptome of peripheral blood mononuclear cells (PBMCs) can be altered in the context of many malignancies to allow them avoid the effective immune response, which leads to cancer invasiveness. Here, we used an MS-based strategy to discover biomarkers in the PBMCs of breast cancer (BC) patients and validated them at different stages of BC. Methods: PBMCs were isolated from the breast cancer patients and were cultured alone or co-cultured with breast cancer cell lines. The role of PBMC in the invasion property of breast cancer cells was explored. NF-kB activity was also measured in the co-cultured breast cancer cells. Identification of protein profiles in the secretome and proteome of the co-cultured PBMCs was performed using SWATH mass spectrometry. Pathway enrichment and gene ontology analyses were carried out to look for the molecular pathways correlated with the protein expression profile of PBMCs in the breast cancer patients. Quantitative real-time polymerase chain reaction (qPCR) was performed to validate the candidate genes in the PBMC fraction of the breast cancer patients at the primary and metastatic stages. In silico survival analysis was performed to assess the potential clinical biomarkers in these PBMC subtypes. Results: PBMCs could significantly increase the invasion property of the BC cells concomitant with a decrease in E-cadherin and an increase in both Vimentin and N-cadherin expression. The NF-kB activity in the BC cells significantly increased following co-culturing implying the role of PBMCs in EMT induction. Enrichment analysis showed that the differentially expressed proteins in PBMCs are mainly associated with IL-17, PI3K-Akt, and HIF-1 signaling pathway, in which a set of seven proteins including TMSB4X, HSPA4, S100A9, SRSF6, THBS1, CUL4A, and CANX were frequently expressed. Finally, in silico analysis confirmed that a gene set consisting of S100A9, SRSF6, THBS1, CUL4A, and CANX were found to provide an insight for the identification of metastasis in breast cancer patients. Conclusion: In conclusion, our study revealed that the protein expression profile in PBMCs is a reflection of the proteins expressed in the BC tissue itself; however, the abundance level is different due to the stage of cancer.
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Affiliation(s)
- Raheleh Moradpoor
- Department of Basic Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Gharebaghian
- Laboratory Hematology and Blood Bank Department, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farhad Shahi
- Breast Disease Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Asadollah Mousavi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sina Salari
- Medical Oncology, Hematology and Bone Marrow Transplantation, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Soheila Ajdari
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Salimi
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
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19
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Soghli N, Qujeq D, Yousefi T, Soghli N. The regulatory functions of circular RNAs in osteosarcoma. Genomics 2020; 112:2845-2856. [DOI: 10.1016/j.ygeno.2020.03.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
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20
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Gutiérrez T, Qi H, Yap MC, Tahbaz N, Milburn LA, Lucchinetti E, Lou PH, Zaugg M, LaPointe PG, Mercier P, Overduin M, Bischof H, Burgstaller S, Malli R, Ballanyi K, Shuai J, Simmen T. The ER chaperone calnexin controls mitochondrial positioning and respiration. Sci Signal 2020; 13:13/638/eaax6660. [DOI: 10.1126/scisignal.aax6660] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chaperones in the endoplasmic reticulum (ER) control the flux of Ca2+ ions into mitochondria, thereby increasing or decreasing the energetic output of the oxidative phosphorylation pathway. An example is the abundant ER lectin calnexin, which interacts with sarco/endoplasmic reticulum Ca2+ ATPase (SERCA). We found that calnexin stimulated the ATPase activity of SERCA by maintaining its redox state. This function enabled calnexin to control how much ER Ca2+ was available for mitochondria, a key determinant for mitochondrial bioenergetics. Calnexin-deficient cells compensated for the loss of this function by partially shifting energy generation to the glycolytic pathway. These cells also showed closer apposition between the ER and mitochondria. Calnexin therefore controls the cellular energy balance between oxidative phosphorylation and glycolysis.
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Affiliation(s)
- Tomás Gutiérrez
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
| | - Megan C. Yap
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nasser Tahbaz
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leanne A. Milburn
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Eliana Lucchinetti
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Phing-How Lou
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael Zaugg
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Paul G. LaPointe
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Pascal Mercier
- Department of Biochemistry and National Field Nuclear Magnetic Resonance Centre (Nanuc), University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael Overduin
- Department of Biochemistry and National Field Nuclear Magnetic Resonance Centre (Nanuc), University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Helmut Bischof
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Sandra Burgstaller
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Roland Malli
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jianwei Shuai
- Department of Physics, and State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361005, China
| | - Thomas Simmen
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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21
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Regulation of Oncogenic Targets by miR-99a-3p (Passenger Strand of miR-99a-Duplex) in Head and Neck Squamous Cell Carcinoma. Cells 2019; 8:cells8121535. [PMID: 31795200 PMCID: PMC6953126 DOI: 10.3390/cells8121535] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022] Open
Abstract
To identify novel oncogenic targets in head and neck squamous cell carcinoma (HNSCC), we have analyzed antitumor microRNAs (miRNAs) and their controlled molecular networks in HNSCC cells. Based on our miRNA signature in HNSCC, both strands of the miR-99a-duplex (miR-99a-5p: the guide strand, and miR-99a-3p: the passenger strand) are downregulated in cancer tissues. Moreover, low expression of miR-99a-5p and miR-99a-3p significantly predicts poor prognosis in HNSCC, and these miRNAs regulate cancer cell migration and invasion. We previously showed that passenger strands of miRNAs have antitumor functions. Here, we screened miR-99a-3p-controlled oncogenes involved in HNSCC pathogenesis. Thirty-two genes were identified as miR-99a-3p-regulated genes, and 10 genes (STAMBP, TIMP4, TMEM14C, CANX, SUV420H1, HSP90B1, PDIA3, MTHFD2, BCAT1, and SLC22A15) significantly predicted 5-year overall survival. Notably, among these genes, STAMBP, TIMP4, TMEM14C, CANX, and SUV420H1 were independent prognostic markers of HNSCC by multivariate analyses. We further investigated the oncogenic function of STAMBP in HNSCC cells using knockdown assays. Our data demonstrated that the aggressiveness of phenotypes in HNSCC cells was attenuated by siSTAMBP transfection. Moreover, aberrant STAMBP expression was detected in HNSCC clinical specimens by immunohistochemistry. This strategy may contribute to the clarification of the molecular pathogenesis of this disease.
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22
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Alam A, Taye N, Patel S, Thube M, Mullick J, Shah VK, Pant R, Roychowdhury T, Banerjee N, Chatterjee S, Bhattacharya R, Roy R, Mukhopadhyay A, Mogare D, Chattopadhyay S. SMAR1 favors immunosurveillance of cancer cells by modulating calnexin and MHC I expression. Neoplasia 2019; 21:945-962. [PMID: 31422285 PMCID: PMC6706529 DOI: 10.1016/j.neo.2019.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/17/2019] [Indexed: 01/17/2023] Open
Abstract
Down-regulation or loss of MHC class I expression is a major mechanism used by cancer cells to evade immunosurveillance and increase their oncogenic potential. MHC I mediated antigen presentation is a complex regulatory process, controlled by antigen processing machinery (APM) dictating immune response. Transcriptional regulation of the APM that can modulate gene expression profile and their correlation to MHC I mediated antigen presentation in cancer cells remain enigmatic. Here, we reveal that Scaffold/Matrix-Associated Region 1- binding protein (SMAR1), positively regulates MHC I surface expression by down-regulating calnexin, an important component of antigen processing machinery (APM) in cancer cells. SMAR1, a bonafide MAR binding protein acts as a transcriptional repressor of several oncogenes. It is down-regulated in higher grades of cancers either through proteasomal degradation or through loss of heterozygosity (LOH) at the Chr.16q24.3 locus where the human homolog of SMAR1 (BANP) has been mapped. It binds to a short MAR region of the calnexin promoter forming a repressor complex in association with GATA2 and HDAC1. A reverse correlation between SMAR1 and calnexin was thus observed in SMAR1-LOH cells and also in tissues from breast cancer patients. To further extrapolate our findings, influenza A (H1N1) virus infection assay was performed. Upon viral infection, the levels of SMAR1 significantly increased resulting in reduced calnexin expression and increased MHC I presentation. Taken together, our observations establish that increased expression of SMAR1 in cancers can positively regulate MHC I surface expression thereby leading to higher chances of tumor regression and elimination of cancer cells.
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Affiliation(s)
- Aftab Alam
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Nandaraj Taye
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Sonal Patel
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Milind Thube
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Jayati Mullick
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Richa Pant
- National Centre for Cell Science, Pune, Maharashtra, India
| | | | | | | | | | - Rini Roy
- Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | | | - Devraj Mogare
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Samit Chattopadhyay
- National Centre for Cell Science, Pune, Maharashtra, India; Indian Institute of Chemical Biology, Kolkata, India.
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23
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Chen Y, Ma D, Wang X, Fang J, Liu X, Song J, Li X, Ren X, Li Q, Li Q, Wen S, Luo L, Xia J, Cui J, Zeng G, Chen L, Cheng B, Wang Z. Calnexin Impairs the Antitumor Immunity of CD4 + and CD8 + T Cells. Cancer Immunol Res 2018; 7:123-135. [PMID: 30401678 DOI: 10.1158/2326-6066.cir-18-0124] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/06/2018] [Accepted: 11/02/2018] [Indexed: 11/16/2022]
Abstract
Elucidation of the mechanisms of T-cell-mediated antitumor responses will provide information for the rational design and development of cancer immunotherapies. Here, we found that calnexin, an endoplasmic reticulum (ER) chaperone protein, is significantly upregulated in oral squamous cell carcinoma (OSCC). Upregulation of its membranous expression on OSCC cells is associated with inhibited T-cell infiltration in tumor tissues and correlates with poor survival of patients with OSCC. We found that calnexin inhibits the proliferation of CD4+ and CD8+ T cells isolated from the whole blood of healthy donors and patients with OSCC and inhibits the secretion of IFNγ, TNFα, and IL2 from these cells. Furthermore, in a melanoma model, knockdown of calnexin enhanced the infiltration and effector functions of T cells in the tumor microenvironment and conferred better control of tumor growth, whereas treatment with a recombinant calnexin protein impaired the infiltration and effector functions of T cells and promoted tumor growth. We also found that calnexin enhanced the expression of PD-1 on CD4+ and CD8+ T cells by restraining the DNA methylation status of a CpG island in the PD-1 promoter. Thus, this work uncovers a mechanism by which T-cell antitumor responses are regulated by calnexin in tumor cells and suggests that calnexin might serve as a potential target for the improvement of antitumor immunotherapy.
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Affiliation(s)
- Yichen Chen
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Da Ma
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Xi Wang
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Juan Fang
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Xiangqi Liu
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Jingjing Song
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Xinye Li
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Xianyue Ren
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Qiusheng Li
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Qunxing Li
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Shuqiong Wen
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Liqun Luo
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Juan Xia
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, P.R. China
| | - Gucheng Zeng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Lieping Chen
- Department of Immunobiology and Yale Comprehensive Cancer Center, Yale University, New Haven, Connecticut
| | - Bin Cheng
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China.
| | - Zhi Wang
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Stomatological Hospital, Sun Yat-Sen University, Guangzhou, P.R. China.
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24
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Daskalaki I, Gkikas I, Tavernarakis N. Hypoxia and Selective Autophagy in Cancer Development and Therapy. Front Cell Dev Biol 2018; 6:104. [PMID: 30250843 PMCID: PMC6139351 DOI: 10.3389/fcell.2018.00104] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/13/2018] [Indexed: 01/07/2023] Open
Abstract
Low oxygen availability, a condition known as hypoxia, is a common feature of various pathologies including stroke, ischemic heart disease, and cancer. Hypoxia adaptation requires coordination of intricate pathways and mechanisms such as hypoxia-inducible factors (HIFs), the unfolded protein response (UPR), mTOR, and autophagy. Recently, great effort has been invested toward elucidating the interplay between hypoxia-induced autophagy and cancer cell metabolism. Although novel types of selective autophagy have been identified, including mitophagy, pexophagy, lipophagy, ERphagy and nucleophagy among others, their potential interface with hypoxia response mechanisms remains poorly understood. Autophagy activation facilitates the removal of damaged cellular compartments and recycles components, thus promoting cell survival. Importantly, tumor cells rely on autophagy to support self-proliferation and metastasis; characteristics related to poor disease prognosis. Therefore, a deeper understanding of the molecular crosstalk between hypoxia response mechanisms and autophagy could provide important insights with relevance to cancer and hypoxia-related pathologies. Here, we survey recent findings implicating selective autophagy in hypoxic responses, and discuss emerging links between these pathways and cancer pathophysiology.
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Affiliation(s)
- Ioanna Daskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Ilias Gkikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Basic Sciences, Medical School, University of Crete, Heraklion, Greece
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25
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Cytoskeleton-Associated Protein 4 Is a Novel Serodiagnostic Marker for Lung Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1328-1333. [PMID: 29751934 DOI: 10.1016/j.ajpath.2018.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/09/2018] [Accepted: 03/13/2018] [Indexed: 11/21/2022]
Abstract
Our aim was to develop a serodiagnostic marker for lung cancer. Monoclonal antibodies were generated, and one antibody designated as KU-Lu-1, recognizing cytoskeleton-associated protein 4 (CKAP4), was studied further. To evaluate the utility of KU-Lu-1 antibody as a serodiagnostic marker for lung cancer, reverse-phase protein array analysis was performed with sera of 271 lung cancer patients and 100 healthy controls. CKAP4 was detected in lung cancer cells and tissues, and its secretion into the culture supernatant was also confirmed. The serum CKAP4 levels of lung cancer patients were significantly higher than those of healthy controls (P < 0.0001), and the area under the curve of receiver-operating characteristic curve analysis was 0.890, with 81.1% sensitivity and 86.0% specificity. Furthermore, the serum CKAP4 levels were also higher in patients with stage I adenocarcinoma or squamous cell carcinoma than in healthy controls (P < 0.0001). Serum CKAP4 levels may differentiate lung cancer patients from healthy controls, and they may be detected early even in stage I non-small cell lung cancer. Serum CKAP4 levels were also significantly higher in lung cancer patients than in healthy controls in the validation set (P < 0.0001). The present results provide evidence that CKAP4 may be a novel early serodiagnostic marker for lung cancer.
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26
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Advani J, Subbannayya Y, Patel K, Khan AA, Patil AH, Jain AP, Solanki HS, Radhakrishnan A, Pinto SM, Sahasrabuddhe NA, Thomas JK, Mathur PP, Nair BG, Chang X, Prasad TSK, Sidransky D, Gowda H, Chatterjee A. Long-Term Cigarette Smoke Exposure and Changes in MiRNA Expression and Proteome in Non-Small-Cell Lung Cancer. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:390-403. [PMID: 28692419 DOI: 10.1089/omi.2017.0045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis. We identified 112 upregulated and 147 downregulated miRNAs (by twofold) in cigarette smoke-treated H292 cells. The liquid chromatography-tandem mass spectrometry analysis identified 3,959 proteins, of which, 303 proteins were overexpressed and 112 proteins downregulated (by twofold). We observed 39 miRNA target pairs (proven targets) that were differentially expressed in response to chronic cigarette smoke exposure. Gene ontology analysis of the target proteins revealed enrichment of proteins in biological processes driving metabolism, cell communication, and nucleic acid metabolism. Pathway analysis revealed the enrichment of phagosome maturation, antigen presentation pathway, nuclear factor erythroid 2-related factor 2-mediated oxidative stress response, and cholesterol biosynthesis pathways in cigarette smoke-exposed cells. In conclusion, this report makes an important contribution to knowledge on molecular changes in a lung cell line in response to long term cigarette smoke exposure. The findings might inform future strategies for drug target, biomarker and diagnostics innovation in lung cancer, and clinical oncology. These observations also call for further research on the extent to which continuing or stopping cigarette smoking in patients diagnosed with lung cancer translates into molecular and clinical outcomes.
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Affiliation(s)
- Jayshree Advani
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | - Yashwanth Subbannayya
- 2 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
| | - Krishna Patel
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,3 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Aafaque Ahmad Khan
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Arun H Patil
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,2 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .,4 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Ankit P Jain
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Hitendra S Solanki
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 School of Biotechnology, KIIT University , Bhubaneswar, India
| | | | - Sneha M Pinto
- 2 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
| | | | - Joji K Thomas
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | | | - Bipin G Nair
- 3 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Xiaofei Chang
- 5 Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - T S Keshava Prasad
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,2 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
| | - David Sidransky
- 5 Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Harsha Gowda
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,2 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
| | - Aditi Chatterjee
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,2 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
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27
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Novikova SE, Kurbatov LK, Zavialova MG, Zgoda VG, Archakov AI. [Omics technologies in diagnostics of lung adenocarcinoma]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:181-210. [PMID: 28781253 DOI: 10.18097/pbmc20176303181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To date lung adenocarcinoma (LAC) is the most common type of lung cancer. Numerous studies on LAC biology resulted in identification of crucial mutations in protooncogenes and activating neoplastic transformation pathways. Therapeutic approaches that significantly increase the survival rate of patients with LAC of different etiology have been developed and introduced into clinical practice. However, the main problem in the treatment of LAC is early diagnosis, taking into account both factors and mechanisms responsible in tumor initiation and progression. Identification of a wide biomarker repertoire with high specificity and reliability of detection appears to be a solution to this problem. In this context, proteins with differential expression in normal and pathological condition, suitable for detection in biological fluids are the most promising biomarkers. In this review we have analyzed literature data on studies aimed at search of LAC biomarkers. The major attention has been paid to protein biomarkers as the most promising and convenient subject of clinical diagnosis. The review also summarizes existing knowledge on posttranslational modifications, splice variants, isoforms, as well as model systems and transcriptome changes in LAC.
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Affiliation(s)
- S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - L K Kurbatov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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28
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Shin J, Song SY, Ahn HS, An BC, Choi YD, Yang EG, Na KJ, Lee ST, Park JI, Kim SY, Lee C, Lee SW. Integrative analysis for the discovery of lung cancer serological markers and validation by MRM-MS. PLoS One 2017; 12:e0183896. [PMID: 28837649 PMCID: PMC5570484 DOI: 10.1371/journal.pone.0183896] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/14/2017] [Indexed: 12/18/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) constitutes approximately 80% of all diagnosed lung cancers, and diagnostic markers detectable in the plasma/serum of NSCLC patients are greatly needed. In this study, we established a pipeline for the discovery of markers using 9 transcriptome datasets from publicly available databases and profiling of six lung cancer cell secretomes. Thirty-one out of 312 proteins that overlapped between two-fold differentially expressed genes and identified cell secretome proteins were detected in the pooled plasma of lung cancer patients. To quantify the candidates in the serum of NSCLC patients, multiple-reaction-monitoring mass spectrometry (MRM-MS) was performed for five candidate biomarkers. Finally, two potential biomarkers (BCHE and GPx3; AUC = 0.713 and 0.673, respectively) and one two-marker panel generated by logistic regression (BCHE/GPx3; AUC = 0.773) were identified. A validation test was performed by ELISA to evaluate the reproducibility of GPx3 and BCHE expression in an independent set of samples (BCHE and GPx3; AUC = 0.630 and 0.759, respectively, BCHE/GPx3 panel; AUC = 0.788). Collectively, these results demonstrate the feasibility of using our pipeline for marker discovery and our MRM-MS platform for verifying potential biomarkers of human diseases.
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Affiliation(s)
- Jihye Shin
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea
| | - Sang-Yun Song
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Hwasun Hospital, Hwasun-gun, Jeollanam-do, Korea
| | - Hee-Sung Ahn
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- KIST School, Korea University of Science and Technology, Daejeon, Korea
| | - Byung Chull An
- Department of Anatomy, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, Korea
| | - Yoo-Duk Choi
- Department of Pathology, Chonnam National University Hospital, Dong-gu, Gwangju, Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
| | - Kook-Joo Na
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Hwasun Hospital, Hwasun-gun, Jeollanam-do, Korea
| | - Seung-Taek Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea
| | - Jae-Il Park
- Animal Facility of Aging Science, Korea Basic Science Institute, Buk-gu, Gwangju, Korea
| | - Seon-Young Kim
- Personalized Genomic Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Korea
- KIST School, Korea University of Science and Technology, Daejeon, Korea
- * E-mail: (SL); (CL)
| | - Seung-won Lee
- Department of Anatomy, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, Korea
- * E-mail: (SL); (CL)
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29
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Hellström C, Dodig-Crnković T, Hong MG, Schwenk JM, Nilsson P, Sjöberg R. High-Density Serum/Plasma Reverse Phase Protein Arrays. Methods Mol Biol 2017; 1619:229-238. [PMID: 28674890 DOI: 10.1007/978-1-4939-7057-5_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.
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Affiliation(s)
- Cecilia Hellström
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden.
| | - Ronald Sjöberg
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
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30
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Tang ZM, Ling ZG, Wang CM, Wu YB, Kong JL. Serum tumor-associated autoantibodies as diagnostic biomarkers for lung cancer: A systematic review and meta-analysis. PLoS One 2017; 12:e0182117. [PMID: 28750095 PMCID: PMC5547718 DOI: 10.1371/journal.pone.0182117] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE We performed a comprehensive review and meta-analysis to evaluate the diagnostic values of serum single and multiplex tumor-associated autoantibodies (TAAbs) in patients with lung cancer (LC). METHODS We searched the MEDLINE and EMBASE databases for relevant studies investigating serum TAAbs for the diagnosis of LC. The primary outcomes included sensitivity, specificity and accuracy of the test. RESULTS The systematic review and meta-analysis included 31 articles with single autoantibody and 39 with multiplex autoantibodies. Enzyme-linked immunosorbent assay (ELISA) was the most common detection method. For the diagnosis of patients with all stages and early-stage LC, different single or combinations of TAAbs demonstrated different diagnostic values. Although individual TAAbs showed low diagnostic sensitivity, the combination of multiplex autoantibodies offered relatively high sensitivity. For the meta-analysis of a same panel of autoantibodies in patients at all stages of LC, the pooled results of the panel of 6 TAAbs (p53, NY-ESO-1, CAGE, GBU4-5, Annexin 1 and SOX2) were: sensitivity 38% (95% CI 0.35-0.40), specificity 89% (95% CI 0.86-0.91), diagnostic accuracy 65.9% (range 62.5-81.8%), AUC 0.52 (0.48-0.57), while the summary estimates of 7 TAAbs (p53, CAGE, NY-ESO-1, GBU4-5, SOX2, MAGE A4 and Hu-D) were: sensitivity 47% (95% CI 0.34-0.60), specificity 90% (95% CI 0.89-0.92), diagnostic accuracy 78.4% (range 67.5-88.8%), AUC 0.90 (0.87-0.93). For the meta-analysis of the same panel of autoantibodies in patients at early-stage of LC, the sensitivities of both panels of 7 TAAbs and 6 TAAbs were 40% and 29.7%, while their specificities were 91% and 87%, respectively. CONCLUSIONS Serum single or combinations of multiplex autoantibodies can be used as a tool for the diagnosis of LC patients at all stages or early-stage, but the combination of multiplex autoantibodies shows a higher detection capacity; the diagnostic value of the panel of 7 TAAbs is higher than the panel of 6 TAAbs, which may be used as potential biomarkers for the early detection of LC.
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Affiliation(s)
- Zhen-Ming Tang
- Department of Respiratory Medicine, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Zhou-Gui Ling
- Department of Respiratory Medicine, the Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
- * E-mail: (ZGL); (JLK)
| | - Chun-Mei Wang
- Department of Respiratory Medicine, the People's Hospital of Shenzhen Guangming New District, Shenzhen, China
| | - Yan-Bin Wu
- Institute of Respiratory Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jin-Liang Kong
- Institute of Respiratory Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
- * E-mail: (ZGL); (JLK)
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31
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Reeves E, James E. Antigen processing and immune regulation in the response to tumours. Immunology 2016; 150:16-24. [PMID: 27658710 DOI: 10.1111/imm.12675] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/18/2016] [Accepted: 09/19/2016] [Indexed: 12/12/2022] Open
Abstract
The MHC class I and II antigen processing and presentation pathways display peptides to circulating CD8+ cytotoxic and CD4+ helper T cells respectively to enable pathogens and transformed cells to be identified. Once detected, T cells become activated and either directly kill the infected / transformed cells (CD8+ cytotoxic T lymphocytes) or orchestrate the activation of the adaptive immune response (CD4+ T cells). The immune surveillance of transformed/tumour cells drives alteration of the antigen processing and presentation pathways to evade detection and hence the immune response. Evasion of the immune response is a significant event tumour development and considered one of the hallmarks of cancer. To avoid immune recognition, tumours employ a multitude of strategies with most resulting in a down-regulation of the MHC class I expression at the cell surface, significantly impairing the ability of CD8+ cytotoxic T lymphocytes to recognize the tumour. Alteration of the expression of key players in antigen processing not only affects MHC class I expression but also significantly alters the repertoire of peptides being presented. These modified peptide repertoires may serve to further reduce the presentation of tumour-specific/associated antigenic epitopes to aid immune evasion and tumour progression. Here we review the modifications to the antigen processing and presentation pathway in tumours and how it affects the anti-tumour immune response, considering the role of tumour-infiltrating cell populations and highlighting possible future therapeutic targets.
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Affiliation(s)
- Emma Reeves
- Cancer Sciences Unit, Southampton General Hospital, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Edward James
- Cancer Sciences Unit, Southampton General Hospital, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
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