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Jiménez C, Garrote-de-Barros A, López-Portugués C, Hernández-Sánchez M, Díez P. Characterization of Human B Cell Hematological Malignancies Using Protein-Based Approaches. Int J Mol Sci 2024; 25:4644. [PMID: 38731863 PMCID: PMC11083628 DOI: 10.3390/ijms25094644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The maturation of B cells is a complex, multi-step process. During B cell differentiation, errors can occur, leading to the emergence of aberrant versions of B cells that, finally, constitute a malignant tumor. These B cell malignancies are classified into three main groups: leukemias, myelomas, and lymphomas, the latter being the most heterogeneous type. Since their discovery, multiple biological studies have been performed to characterize these diseases, aiming to define their specific features and determine potential biomarkers for diagnosis, stratification, and prognosis. The rise of advanced -omics approaches has significantly contributed to this end. Notably, proteomics strategies appear as promising tools to comprehensively profile the final molecular effector of these cells. In this narrative review, we first introduce the main B cell malignancies together with the most relevant proteomics approaches. Then, we describe the core studies conducted in the field and their main findings and, finally, we evaluate the advantages and drawbacks of flow cytometry, mass cytometry, and mass spectrometry for the profiling of human B cell disorders.
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Affiliation(s)
- Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain;
| | - Alba Garrote-de-Barros
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.G.-d.-B.); (M.H.-S.)
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, 28029 Madrid, Spain
| | - Carlos López-Portugués
- Department of Physical and Analytical Chemistry Chemistry, Faculty of Chemistry, University of Oviedo, 33006 Oviedo, Spain;
- Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.G.-d.-B.); (M.H.-S.)
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, 28029 Madrid, Spain
| | - Paula Díez
- Department of Physical and Analytical Chemistry Chemistry, Faculty of Chemistry, University of Oviedo, 33006 Oviedo, Spain;
- Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
- Department of Functional Biology, Faculty of Medicine and Health Science, University of Oviedo, 33006 Oviedo, Spain
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2
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Janowski M, Łuczkowska K, Gniot M, Lewandowski K, Safranow K, Helbig G, Machaliński B, Paczkowska E. The Depth of the Molecular Response in Patients with Chronic Myeloid Leukemia Correlates with Changes in Humoral Immunity. J Clin Med 2024; 13:2353. [PMID: 38673624 PMCID: PMC11051126 DOI: 10.3390/jcm13082353] [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: 03/12/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Background and Objectives: The effective treatment of chronic myeloid leukemia leads to the restoration of proper immune system function. We aimed to investigate fluctuations in circulating cytokines, angiogenic factors and complement components in patients with CML during the first year of treatment with TKI and correlate them with the degree of achieved molecular response. Material and Methods: We recruited 31 patients with newly diagnosed CML. Peripheral blood and bone marrow samples were obtained, and concentrations of serum proteins were measured using an immunology multiplex assay. Results: The study cohort was divided into two groups of optimal or non-optimal in accordance with the European Leukemia Net (ELN) guidelines. We found significantly higher concentrations of C1q, C4 and C5a in serum after 3 months of TKI treatment in patients who achieved optimal responses in the 6 months after diagnosis. The most alterations were observed during 12 months of therapy. Patients in the optimal response group were characterized by higher serum concentrations of TGF-β, EGF, VEGF, Angiopoietin 1, IFN-γ and IL-8. Conclusions: The later plasma concentrations of complement components were significantly increased in patients with optimal responses. The changes after 12 months of treatment were particularly significant. Similar changes in bone marrow samples were observed.
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Affiliation(s)
- Michał Janowski
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (M.J.); (K.Ł.); (B.M.)
| | - Karolina Łuczkowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (M.J.); (K.Ł.); (B.M.)
| | - Michał Gniot
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznań, Poland; (M.G.); (K.L.)
| | - Krzysztof Lewandowski
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznań, Poland; (M.G.); (K.L.)
| | - Krzysztof Safranow
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Grzegorz Helbig
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 40-027 Katowice, Poland;
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (M.J.); (K.Ł.); (B.M.)
| | - Edyta Paczkowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (M.J.); (K.Ł.); (B.M.)
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Xiao Y, Yu X, Wang Y, Song G, Liu M, Wang D, Wang H. A novel immune-related gene signature for diagnosis and potential immunotherapy of microsatellite stable endometrial carcinoma. Sci Rep 2024; 14:3738. [PMID: 38355782 PMCID: PMC10867009 DOI: 10.1038/s41598-024-53338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
An immune-related gene signature (IRGS) was established to better understand the molecular and immunologic characteristics of microsatellite instable (MSI) and microsatellite stable (MSS) endometrial carcinoma (EC), and provide potential immunotherapy directions for MSS patients. Top 20 immune-related hub genes were screened by weight gene coexpression network analysis (WGCNA), and an IRGS was further established through Cox regression analysis. The molecular and immune characteristics were clarified in IRGS high and low risk groups. Expression and MS status validation of the IRGS were conducted through quantitative real-time Polymerase Chain Reaction (rt-qPCR) and immunohistochemistry (IHC) analysis. The IRGS includes 2 oncogenes (AGTR1 and HTR3C) and 2 tumor suppressor genes (CD3E and SERPIND1). Patients in IRGS high-risk group were more with MSS status, higher tumor grade, later FIGO stage, serous histology and elder ages compared with IRGS low-risk group (P < 0.05). Besides, patients in MSS group were more FIGO stages II-IV (42.7% vs. 26%), serous histology (35.7% vs. 5.3%) and with higher IRGS risk score (1.51 ± 3.11 vs. 1.02 ± 0.67) (P < 0.05) than patients in MSI group. Furthermore, patients in IRGS high-risk group had higher tumor purity, more Macrophages M1 and Macrophages M2 infiltrating, higher proportion of Macrophages M2 and Dendritic cells activated, lower proportion of T cells regulatory (Tregs), lower tumor mutation burden (TMB). Correspondingly, subjects in IRGS low-risk group had higher immunphenoscores than IRGS high-risk group. The relative mRNA level of AGTR1 and HTR3C were gradually increase, while CD3E and SERPIND1 were reversed in rt-qPCR. Through IHC experiments, AGTR1(69.2% vs 30%, P = 0.074) and HTR3C (76.9% vs 30%, P = 0.024) had higher positive staining rates in ECs than non-ECs. While SERPIND1 (84.6% vs 20%, P = 0.003) and CD3E (61.5% vs 40%, P = 0.000) had higher positive staining rates in non-ECs. IRGS is a potential diagnostic and prognostic biomarker for EC. IRGS low risk group might benefit from immune checkpoint inhibitors, while IRGS high risk group deserve other potential immunotherapy.
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Affiliation(s)
- Yunyun Xiao
- Department of Gynecology and Obstetrics, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China
| | - XiaoChuan Yu
- Department of Gynecology and Obstetrics, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China
| | - Yaping Wang
- Department of Pathology, Dalian Maternal and Children's Medical Group, Dalian, 116033, Liaoning, China
| | - Guangyao Song
- Department of Pathology, Dalian Maternal and Children's Medical Group, Dalian, 116033, Liaoning, China
| | - Ming Liu
- Department of Pathology, Dalian Maternal and Children's Medical Group, Dalian, 116033, Liaoning, China
| | - Daqing Wang
- Department of Oncology, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China.
| | - Huali Wang
- Department of Gynecology and Obstetrics, Dalian Maternal and Children's Medical Group, No. 1 Dunhuang Street, Shahekou District, Dalian, 116033, Liaoning, China.
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4
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Min Y, Wu J, Hou W, Li X, Zhao X, Guan X, Qian X, Hao C, Ying W. Differential analysis of core-fucosylated glycoproteomics enabled by single-step truncation of N-glycans. Glycoconj J 2023; 40:541-549. [PMID: 37542637 DOI: 10.1007/s10719-023-10130-x] [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: 04/07/2023] [Revised: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 08/07/2023]
Abstract
Alpha-1,6 fucosylation of N-glycans (core fucosylation, CF) represents a unique form of N-glycans and is widely involved in disease progression. In order to accurately identify CF glycoproteins, several approaches have been developed based on sequential cleavage with different glycosidases to truncate the N-glycans. Since multi-step sample treatments may introduce quantitation bias and affect the practicality of these approaches in large-scale applications. Here, we systematically evaluated the performance of the single-step treatment of intact glycopeptides by endoglycosidase F3 for CF glycoproteome. The single-step truncation (SST) strategy demonstrated higher quantitative stability and higher efficiency compared with previous approaches. The strategy was further practiced on both cell lines and serum samples. The dysregulation of CF glycopeptides between preoperative and postoperative serum from patients with pancreatic ductal adenocarcinoma was revealed, and the CF modifications of BCHE_N369, CDH5_N112 and SERPIND1_N49 were found to be potential prognostic markers. This study thus provides an efficient solution for large-scale quantitative analysis of the CF glycoproteome.
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Affiliation(s)
- Yao Min
- School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Jianhui Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China
| | - Wenhao Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Xiaoyu Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Xiaoya Guan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Chunyi Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, 102206, China.
| | - Wantao Ying
- School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China.
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China.
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Álvarez-Zúñiga CD, Garza-Veloz I, Martínez-Rendón J, Ureño-Segura M, Delgado-Enciso I, Martinez-Fierro ML. Circulating Biomarkers Associated with the Diagnosis and Prognosis of B-Cell Progenitor Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:4186. [PMID: 37627214 PMCID: PMC10453581 DOI: 10.3390/cancers15164186] [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: 07/20/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a hematological disease characterized by the dysfunction of the hematopoietic system that leads to arrest at a specific stage of stem cells development, suppressing the average production of cellular hematologic components. BCP-ALL is a neoplasm of the B-cell lineage progenitor. BCP-ALL is caused and perpetuated by several mechanisms that provide the disease with its tumor potential and genetic and cytological characteristics. These pathological features are used for diagnosis and the prognostication of BCP-ALL. However, most of these paraclinical tools can only be obtained by bone marrow aspiration, which, as it is an invasive study, can delay the diagnosis and follow-up of the disease, in addition to the anesthetic risk it entails for pediatric patients. For this reason, it is crucial to find noninvasive and accessible ways to supply information concerning diagnosis, prognosis, and the monitoring of the disease, such as circulating biomarkers. In oncology, a biomarker is any measurable indicator that demonstrates the presence of malignancy, tumoral behavior, prognosis, or responses to treatments. This review summarizes circulating molecules associated with BCP-ALL with potential diagnostic value, classificatory capacity during monitoring specific clinic features of the disease, and/or capacity to identify each BCP-ALL stage regarding its evolution and outcome of the patients with BCP-ALL. In the same way, we provide and classify biomarkers that may be used in further studies focused on clinical approaches or therapeutic target identification for BCP-ALL.
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Affiliation(s)
- Claudia Daniela Álvarez-Zúñiga
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (C.D.Á.-Z.); (I.G.-V.); (J.M.-R.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (C.D.Á.-Z.); (I.G.-V.); (J.M.-R.)
| | - Jacqueline Martínez-Rendón
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (C.D.Á.-Z.); (I.G.-V.); (J.M.-R.)
| | - Misael Ureño-Segura
- Hematology Service, Hospital General Zacatecas “Luz González Cosío”, Servicios de Salud de Zacatecas, Zacatecas 98160, Mexico;
| | - Iván Delgado-Enciso
- Cancerology State Institute, Colima State Health Services, Colima 28085, Mexico;
- School of Medicine, University of Colima, Colima 28040, Mexico
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y C.S, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (C.D.Á.-Z.); (I.G.-V.); (J.M.-R.)
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6
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Naryzhny S, Ronzhina N, Zorina E, Kabachenko F, Klopov N, Zgoda V. Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers. Int J Mol Sci 2022; 23:ijms231911113. [PMID: 36232415 PMCID: PMC9569744 DOI: 10.3390/ijms231911113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
The use of tumor markers aids in the early detection of cancer recurrence and prognosis. There is a hope that they might also be useful in screening tests for the early detection of cancer. Here, the question of finding ideal tumor markers, which should be sensitive, specific, and reliable, is an acute issue. Human plasma is one of the most popular samples as it is commonly collected in the clinic and provides noninvasive, rapid analysis for any type of disease including cancer. Many efforts have been applied in searching for “ideal” tumor markers, digging very deep into plasma proteomes. The situation in this area can be improved in two ways—by attempting to find an ideal single tumor marker or by generating panels of different markers. In both cases, proteomics certainly plays a major role. There is a line of evidence that the most abundant, so-called “classical plasma proteins”, may be used to generate a tumor biomarker profile. To be comprehensive these profiles should have information not only about protein levels but also proteoform distribution for each protein. Initially, the profile of these proteins in norm should be generated. In our work, we collected bibliographic information about the connection of cancers with levels of “classical plasma proteins”. Additionally, we presented the proteoform profiles (2DE patterns) of these proteins in norm generated by two-dimensional electrophoresis with mass spectrometry and immunodetection. As a next step, similar profiles representing protein perturbations in plasma produced in the case of different cancers will be generated. Additionally, based on this information, different test systems can be developed.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
- Correspondence: ; Tel.: +7-911-176-4453
| | - Natalia Ronzhina
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
| | - Elena Zorina
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
| | - Fedor Kabachenko
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Nikolay Klopov
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
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Michelis R, Milhem L, Galouk E, Stemer G, Aviv A, Tadmor T, Shehadeh M, Shvidel L, Barhoum M, Braester A. Increased serum level of alpha-2 macroglobulin and its production by B-lymphocytes in chronic lymphocytic leukemia. Front Immunol 2022; 13:953644. [PMID: 36119042 PMCID: PMC9478581 DOI: 10.3389/fimmu.2022.953644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL), the most common adult’s leukemia in the western world, is caused in 95% of the cases by uncontrolled proliferation of monoclonal B-lymphocytes. The complement system in CLL is chronically activated at a low level via the classical pathway (CP). This chronic activation is induced by IgG-hexamers, which are formed after binding to alpha-2-macroglobulin (A2M). The study investigated for the first time the serum levels of A2M in CLL patients, their association with the disease severity, and A2M production by the malignant B-lymphocytes. Blood samples were collected from 65 CLL patients and 30 normal controls (NC) subjects, and used for quantifications of the A2M levels, the complement activation marker (sC5b-9), the complement components C2, C3 and C4, and clinical biochemistry and hematology parameters. The production of A2M was studied in B-lymphocytes isolated from blood samples as well as in CLL and non-CLL cell lines.The serum A2M levels were significantly higher in CLL patients vs NCs, showing values of 3.62 ± 0.22 and 1.97 ± 0.10 mg/ml, respectively. Within the CLL group, A2M levels correlated significantly with the disease stage, with sC5b-9, and with clinical indicators of the disease severity. Increased A2M production was showed in three out of four CLL B-lymphocytic lines that were studied, as compared to non-CLL lines, to a non-lymphocytic line, and to blood-derived primary B-lymphocytes. A2M production was further increased both in primary cells and in the CLL cell-line after incubation with CLL sera, compared to NC sera. This study shows for the first time that serum A2M levels in CLL are significantly increased, likely due to A2M production by the malignant B-lymphocytes, and are correlated with the disease severity and with chronic complement activation. The moderate change in A2M production after incubation with NC sera in-vitro supports the hypothesis that inhibition of excess A2M production can be achieved, and that this may potentially down-regulate the IgG-hexamerization and the resulting chronic CP activation. This may also help restore complement system activity, and eventually improve complement activity and immunotherapy outcomes in CLL.
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Affiliation(s)
- Regina Michelis
- The Institute for Medical Research, Galilee Medical Center, Nahariya, Israel
- *Correspondence: Regina Michelis,
| | - Lama Milhem
- The Institute for Medical Research, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Evleen Galouk
- The Institute for Medical Research, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Galia Stemer
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- Institute of Hematology, Galilee Medical Center, Nahariya, Israel
| | - Ariel Aviv
- Department of Hematology, Emek Medical Center, Afula, Israel
| | - Tamar Tadmor
- Hematology Unit, Bnai Zion Medical Center, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Mona Shehadeh
- Biochemistry Laboratory, Galilee Medical Center, Nahariya, Israel
| | - Lev Shvidel
- Hematology Institute, Kaplan Medical Center, Rehovot, Israel
- Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Masad Barhoum
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Andrei Braester
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- Institute of Hematology, Galilee Medical Center, Nahariya, Israel
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8
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Prediction of Type 2 Diabetes at Pre-diabetes Stage by Mass Spectrometry: A Preliminary Study. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10419-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Yu R, Cheng L, Yang S, Liu Y, Zhu Z. iTRAQ-Based Proteomic Analysis Reveals Potential Serum Biomarkers for Pediatric Non-Hodgkin's Lymphoma. Front Oncol 2022; 12:848286. [PMID: 35371990 PMCID: PMC8970600 DOI: 10.3389/fonc.2022.848286] [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: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 11/20/2022] Open
Abstract
Non-Hodgkin’s lymphoma (NHL) is the third most common malignant tumor among children. However, at initial NHL diagnosis, most cases are at an advanced stage because of nonspecific clinical manifestations and currently limited diagnostic methods. This study aimed to screen and verify potential serum biomarkers of pediatric NHL using isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis. Serum protein expression profiles from children with B-NHL (n=20) and T-NHL (n=20) and healthy controls (n=20) were detected by utilizing iTRAQ in combination with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC–MS/MS) and analyzed by applying Ingenuity Pathway Analysis (IPA). The candidate biomarkers S100A8 and LRG1 were further validated by using enzyme-linked immunosorbent assays (ELISAs). Receiver operating characteristic (ROC) analysis based on ELISA data was used to evaluate diagnostic efficacy. In total, 534 proteins were identified twice using iTRAQ combined with 2D LC–MS/MS. Further analysis identified 79 and 73 differentially expressed proteins in B-NHL and T-NHL serum, respectively, compared with control serum according to our defined criteria; 34 proteins were overexpressed and 45 proteins underexpressed in B-NHL, whereas 45 proteins were overexpressed and 28 proteins underexpressed in T-NHL (p < 0.05). IPA demonstrated a variety of signaling pathways, including acute phase response signaling and liver X receptor/retinoid X receptor (LXR/RXR) activation, to be strongly associated with pediatric NHL. S100A8 and LRG1 were elevated in NHL patients compared to normal controls according to ELISA (p < 0.05), which was consistent with iTRAQ results. The areas under the ROC curves of S100A8, LRG1, and the combination of S100A8 and LRG1 were 0.873, 0.898 and 0.970, respectively. Our findings indicate that analysis of the serum proteome using iTRAQ combined with 2D LC–MS/MS is a feasible approach for biomarker discovery. Serum S100A8 and LRG1 are promising candidate biomarkers for pediatric NHL, and these differential proteins illustrate a novel pathogenesis and may be clinically helpful for NHL diagnosis in the future.
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Affiliation(s)
- Runhong Yu
- Henan Provincial People's Hospital, Institute of Hematology of Henan Provincial People's Hospital, Zhengzhou, China.,Henan Provincial People's Hospital, Henan Key laboratory of Stem Cell Differentiation and Modification, Zhengzhou, China
| | - Linna Cheng
- Henan Provincial People's Hospital, Institute of Hematology of Henan Provincial People's Hospital, Zhengzhou, China.,Henan Provincial People's Hospital, Henan Key laboratory of Stem Cell Differentiation and Modification, Zhengzhou, China
| | - Shiwei Yang
- Henan Provincial People's Hospital, Institute of Hematology of Henan Provincial People's Hospital, Zhengzhou, China.,Henan Provincial People's Hospital, Henan Key laboratory of Stem Cell Differentiation and Modification, Zhengzhou, China
| | - Yufeng Liu
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zunmin Zhu
- Henan Provincial People's Hospital, Institute of Hematology of Henan Provincial People's Hospital, Zhengzhou, China.,Henan Provincial People's Hospital, Henan Key laboratory of Stem Cell Differentiation and Modification, Zhengzhou, China.,Department of Hematology, People's Hospital of Zhengzhou University, Zhengzhou, China
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10
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Oncogenic Mutation BRAF V600E Changes Phenotypic Behavior of THLE-2 Liver Cells through Alteration of Gene Expression. Int J Mol Sci 2022; 23:ijms23031548. [PMID: 35163468 PMCID: PMC8836259 DOI: 10.3390/ijms23031548] [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: 11/22/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
The accumulation of mutations in cancer driver genes, such as tumor suppressors or proto-oncogenes, affects cellular homeostasis. Disturbances in the mechanism controlling proliferation cause significant augmentation of cell growth and division due to the loss of sensitivity to the regulatory signals. Nowadays, an increasing number of cases of liver cancer are observed worldwide. Data provided by the International Cancer Genome Consortium (ICGC) have indicated many alterations within gene sequences, whose roles in tumor development are not well understood. A comprehensive analysis of liver cancer (virus-associated hepatocellular carcinoma) samples has identified new and rare mutations in B-Raf proto-oncogene (BRAF) in Japanese HCC patients, as well as BRAF V600E mutations in French HCC patients. However, their function in liver cancer has never been investigated. Here, using functional analysis and next generation sequencing, we demonstrate the tumorigenic effect of BRAF V600E on hepatocytes (THLE-2 cell line). Moreover, we identified genes such as BMP6, CXCL11, IL1B, TBX21, RSAD2, MMP10, and SERPIND1, which are possibly regulated by the BRAF V600E-mediated, mitogen-activated protein kinases/extracellular signal-regulated kinases (MAPK/ERK) signaling pathway. Through several functional assays, we demonstrate that BRAF L537M, D594A, and E648G mutations alone are not pathogenic in liver cancer. The investigation of genome mutations and the determination of their impact on cellular processes and functions is crucial to unraveling the molecular mechanisms of liver cancer development.
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Camilli C, Hoeh AE, De Rossi G, Moss SE, Greenwood J. LRG1: an emerging player in disease pathogenesis. J Biomed Sci 2022; 29:6. [PMID: 35062948 PMCID: PMC8781713 DOI: 10.1186/s12929-022-00790-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
The secreted glycoprotein leucine-rich α-2 glycoprotein 1 (LRG1) was first described as a key player in pathogenic ocular neovascularization almost a decade ago. Since then, an increasing number of publications have reported the involvement of LRG1 in multiple human conditions including cancer, diabetes, cardiovascular disease, neurological disease, and inflammatory disorders. The purpose of this review is to provide, for the first time, a comprehensive overview of the LRG1 literature considering its role in health and disease. Although LRG1 is constitutively expressed by hepatocytes and neutrophils, Lrg1-/- mice show no overt phenotypic abnormality suggesting that LRG1 is essentially redundant in development and homeostasis. However, emerging data are challenging this view by suggesting a novel role for LRG1 in innate immunity and preservation of tissue integrity. While our understanding of beneficial LRG1 functions in physiology remains limited, a consistent body of evidence shows that, in response to various inflammatory stimuli, LRG1 expression is induced and directly contributes to disease pathogenesis. Its potential role as a biomarker for the diagnosis, prognosis and monitoring of multiple conditions is widely discussed while dissecting the mechanisms underlying LRG1 pathogenic functions. Emphasis is given to the role that LRG1 plays as a vasculopathic factor where it disrupts the cellular interactions normally required for the formation and maintenance of mature vessels, thereby indirectly contributing to the establishment of a highly hypoxic and immunosuppressive microenvironment. In addition, LRG1 has also been reported to affect other cell types (including epithelial, immune, mesenchymal and cancer cells) mostly by modulating the TGFβ signalling pathway in a context-dependent manner. Crucially, animal studies have shown that LRG1 inhibition, through gene deletion or a function-blocking antibody, is sufficient to attenuate disease progression. In view of this, and taking into consideration its role as an upstream modifier of TGFβ signalling, LRG1 is suggested as a potentially important therapeutic target. While further investigations are needed to fill gaps in our current understanding of LRG1 function, the studies reviewed here confirm LRG1 as a pleiotropic and pathogenic signalling molecule providing a strong rationale for its use in the clinic as a biomarker and therapeutic target.
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Affiliation(s)
- Carlotta Camilli
- Institute of Ophthalmology, University College London, London, UK.
| | - Alexandra E Hoeh
- Institute of Ophthalmology, University College London, London, UK
| | - Giulia De Rossi
- Institute of Ophthalmology, University College London, London, UK
| | - Stephen E Moss
- Institute of Ophthalmology, University College London, London, UK
| | - John Greenwood
- Institute of Ophthalmology, University College London, London, UK
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12
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Vanner RJ, Dobson SM, Gan OI, McLeod J, Schoof EM, Grandal I, Wintersinger JA, Garcia-Prat L, Hosseini M, Xie SZ, Jin L, Mbong N, Voisin V, Chan-Seng-Yue M, Kennedy JA, Waanders E, Morris Q, Porse B, Chan SM, Guidos CJ, Danska JS, Minden MD, Mullighan CG, Dick JE. Multiomic Profiling of Central Nervous System Leukemia Identifies mRNA Translation as a Therapeutic Target. Blood Cancer Discov 2022; 3:16-31. [PMID: 35019858 PMCID: PMC9783958 DOI: 10.1158/2643-3230.bcd-20-0216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/29/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
Central nervous system (CNS) dissemination of B-precursor acute lymphoblastic leukemia (B-ALL) has poor prognosis and remains a therapeutic challenge. Here we performed targeted DNA sequencing as well as transcriptional and proteomic profiling of paired leukemia-infiltrating cells in the bone marrow (BM) and CNS of xenografts. Genes governing mRNA translation were upregulated in CNS leukemia, and subclonal genetic profiling confirmed this in both BM-concordant and BM-discordant CNS mutational populations. CNS leukemia cells were exquisitely sensitive to the translation inhibitor omacetaxine mepesuccinate, which reduced xenograft leptomeningeal disease burden. Proteomics demonstrated greater abundance of secreted proteins in CNS-infiltrating cells, including complement component 3 (C3), and drug targeting of C3 influenced CNS disease in xenografts. CNS-infiltrating cells also exhibited selection for stemness traits and metabolic reprogramming. Overall, our study identifies targeting of mRNA translation as a potential therapeutic approach for B-ALL leptomeningeal disease. SIGNIFICANCE: Cancer metastases are often driven by distinct subclones with unique biological properties. Here we show that in B-ALL CNS disease, the leptomeningeal environment selects for cells with unique functional dependencies. Pharmacologic inhibition of mRNA translation signaling treats CNS disease and offers a new therapeutic approach for this condition.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Robert J Vanner
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Ildiko Grandal
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jeff A Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mohsen Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Veronique Voisin
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Genetics, University Medical Center, Utrecht, the Netherlands
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Quaid Morris
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cynthia J Guidos
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jayne S Danska
- Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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de Klaver W, Wisse PHA, van Wifferen F, Bosch LJW, Jimenez CR, van der Hulst RWM, Fijneman RJA, Kuipers EJ, Greuter MJE, Carvalho B, Spaander MCW, Dekker E, Coupé VMH, de Wit M, Meijer GA. Clinical Validation of a Multitarget Fecal Immunochemical Test for Colorectal Cancer Screening : A Diagnostic Test Accuracy Study. Ann Intern Med 2021; 174:1224-1231. [PMID: 34280333 DOI: 10.7326/m20-8270] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND The fecal immunochemical test (FIT) is used in colorectal cancer (CRC) screening, yet it leaves room for improvement. OBJECTIVE To develop a multitarget FIT (mtFIT) with better diagnostic performance than FIT. DESIGN Diagnostic test accuracy study. SETTING Colonoscopy-controlled series. PARTICIPANTS Persons (n = 1284) from a screening (n = 1038) and referral (n = 246) population were classified by their most advanced lesion (CRC [n = 47], advanced adenoma [n = 135], advanced serrated polyp [n = 30], nonadvanced adenoma [n = 250], and nonadvanced serrated polyp [n = 53]), along with control participants (n = 769). MEASUREMENTS Antibody-based assays were developed and applied to leftover FIT material. Classification and regression tree (CART) analysis was applied to biomarker concentrations to identify the optimal combination for detecting advanced neoplasia. Performance of this combination, the mtFIT, was cross-validated using a leave-one-out approach and compared with FIT at equal specificity. RESULTS The CART analysis showed a combination of hemoglobin, calprotectin, and serpin family F member 2-the mtFIT-to have a cross-validated sensitivity for advanced neoplasia of 42.9% (95% CI, 36.2% to 49.9%) versus 37.3% (CI, 30.7% to 44.2%) for FIT (P = 0.025), with equal specificity of 96.6%. In particular, cross-validated sensitivity for advanced adenomas increased from 28.1% (CI, 20.8% to 36.5%) to 37.8% (CI, 29.6% to 46.5%) (P = 0.006). On the basis of these results, early health technology assessment indicated that mtFIT-based screening could be cost-effective compared with FIT. LIMITATION Study population is enriched with persons from a referral population. CONCLUSION Compared with FIT, the mtFIT showed better diagnostic accuracy in detecting advanced neoplasia because of an increased detection of advanced adenomas. Moreover, early health technology assessment indicated that these results provide a sound basis to pursue further development of mtFIT as a future test for population-based CRC screening. A prospective screening trial is in preparation. PRIMARY FUNDING SOURCE Stand Up to Cancer/Dutch Cancer Society, Dutch Digestive Foundation, and HealthHolland.
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Affiliation(s)
- Willemijn de Klaver
- Netherlands Cancer Institute and Amsterdam University Medical Centers, location Academic Medical Center, Amsterdam, the Netherlands (W.d.K.)
| | - Pieter H A Wisse
- Netherlands Cancer Institute, Amsterdam, and Erasmus MC University Medical Center, Rotterdam, the Netherlands (P.H.W.)
| | - Francine van Wifferen
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | - Linda J W Bosch
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Connie R Jimenez
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | | | - Remond J A Fijneman
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Ernst J Kuipers
- Erasmus MC University Medical Center, Rotterdam, the Netherlands (E.J.K., M.C.S.)
| | - Marjolein J E Greuter
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | - Beatriz Carvalho
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Manon C W Spaander
- Erasmus MC University Medical Center, Rotterdam, the Netherlands (E.J.K., M.C.S.)
| | - Evelien Dekker
- Amsterdam University Medical Centers, location Academic Medical Center, Amsterdam, the Netherlands (E.D.)
| | - Veerle M H Coupé
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | - Meike de Wit
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Gerrit A Meijer
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
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14
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Dunphy K, O’Mahoney K, Dowling P, O’Gorman P, Bazou D. Clinical Proteomics of Biofluids in Haematological Malignancies. Int J Mol Sci 2021; 22:ijms22158021. [PMID: 34360786 PMCID: PMC8348619 DOI: 10.3390/ijms22158021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/25/2022] Open
Abstract
Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Kelly O’Mahoney
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
- Correspondence:
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15
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Kumari M, Singh P, Singh N, Bal A, Srinivasan R, Ghosh S. Identification and characterization of non-small cell lung cancer associated sialoglycoproteins. J Proteomics 2021; 248:104336. [PMID: 34298184 DOI: 10.1016/j.jprot.2021.104336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/18/2022]
Abstract
Aberrantly sialylated cellular glycoconjugates were found to be involved in different processes during tumorigenesis. Such alteration was also noted in case of lung cancer, an important cause of cancer-related death throughout the world. Thus, study on lung cancer associated sialoglycoproteins is of paramount relevance to have a deeper insight into the mechanism of the disease pathogenesis. In the present study, sialic acid specific lectin (Maackia amurensis agglutinin and Sambcus nigra agglutinin)-based affinity chromatography followed by 2D-PAGE and MALDI-TOF/TOF mass spectrometric analysis were done to explore the disease-associated serum proteins of squamous cell carcinoma and adenocarcinoma [the major two subtypes of NSCLC (non-small cell lung carcinoma)] patients. Among seven identified proteins, α1-antitrypsin and haptoglobin-β were preferred for further studies. These two proteins were characterized as the disease associated serum-sialoglycoproteins of NSCLC-patients by western immunoblotting using each lectin specific inhibitor. The presence of these sialoglycoproteins was found on NSCLC cell lines (NCI-H520 & A549) by confocal microscopy. Both these proteins were also present in tissue samples of NSCLC origin and involved in proliferation, invasion and migration of NSCLC cells. Our findings suggest that α1-antitrypsin and haptoglobin-β may be the disease-associated sialoglycoproteins in NSCLC, which seem to be involved in disease progression. SIGNIFICANCE: Our contribution regarding the identification of the NSCLC associated sialoglycoproteins may provide a new vision towards the development of clinically useful newer strategies for the treatment of this disease.
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Affiliation(s)
- Munmun Kumari
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Praveen Singh
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amanjit Bal
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Radhika Srinivasan
- Department of Cytology & Gynecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sujata Ghosh
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Broto GE, Corrêa S, Trigo FC, Dos Santos EC, Tomiotto-Pelissier F, Pavanelli WR, Silveira GF, Abdelhay E, Panis C. Comparative Analysis of Systemic and Tumor Microenvironment Proteomes From Children With B-Cell Acute Lymphocytic Leukemia at Diagnosis and After Induction Treatment. Front Oncol 2021; 10:550213. [PMID: 33381445 PMCID: PMC7769010 DOI: 10.3389/fonc.2020.550213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/06/2020] [Indexed: 12/03/2022] Open
Abstract
Among the childhood diseases, B-cell acute lymphocytic leukemia (B-ALL) is the most frequent type of cancer. Despite recent advances concerning disease treatment, cytotoxic chemotherapy remains the first line of treatment in several countries, and the modifications induced by such drugs in the organism are still poorly understood. In this context, the present study provided a comparative high-throughput proteomic analysis of the cumulative changes induced by chemotherapeutic drugs used in the induction phase of B-ALL treatment in both peripheral blood (PB) and bone marrow compartment (BM) samples. To reach this goal, PB and BM plasma samples were comparatively analyzed by using label-free proteomics at two endpoints: at diagnosis (D0) and the end of the cumulative induction phase treatment (D28). Proteomic data was available via ProteomeXchange with identifier PXD021584. The resulting differentially expressed proteins were explored by bioinformatics approaches aiming to identify the main gene ontology processes, pathways, and transcription factors altered by chemotherapy, as well as to understand B-ALL biology in each compartment at D0. At D0, PB was characterized as a pro-inflammatory environment, with the involvement of several downregulated coagulation proteins as KNG, plasmin, and plasminogen. D28 was characterized predominantly by immune response-related processes and the super expression of the transcription factor IRF3 and transthyretin. RUNX1 was pointed out as a common transcription factor found in both D0 and D28. We chose to validate the proteins transthyretin and interferon-gamma (IFN-γ) by commercial kits and expressed the results as PB/BM ratios. Transthyretin ratio was augmented after induction chemotherapy, while IFN-γ was reduced at the end of the treatment. Considering that most of these proteins were not yet described in B-ALL literature, these findings added to understanding disease biology at diagnosis and highlighted a possible role for transthyretin and IFN-γ as mechanisms related to disease resolution.
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Affiliation(s)
- Geise Ellen Broto
- Programa de Pós-graduação em Patologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná, UNIOESTE, Francisco Beltrão, Brazil
| | - Stephany Corrêa
- Laboratório de Células-Tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Everton Cruz Dos Santos
- Laboratório de Células-Tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Wander Rogério Pavanelli
- Programa de Pós-graduação em Patologia Experimental Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Eliana Abdelhay
- Laboratório de Células-Tronco, Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Carolina Panis
- Programa de Pós-graduação em Patologia Clínica e Laboratorial, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná, UNIOESTE, Francisco Beltrão, Brazil.,Programa de Pós-graduação em Patologia Experimental Universidade Estadual de Londrina, Londrina, Brazil.,Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Universidade Estadual do Oeste do Paraná, UNIOESTE, Francisco Beltrão, Brazil
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Dysregulation of Key Proteins Associated with Sperm Motility and Fertility Potential in Cancer Patients. Int J Mol Sci 2020; 21:ijms21186754. [PMID: 32942548 PMCID: PMC7554694 DOI: 10.3390/ijms21186754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/26/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cancer has adverse effects on male reproductive health. Conventional semen analysis does not explain the molecular changes in the spermatozoa of cancer patients. Currently, proteomics is being widely used to identify the fertility-associated molecular pathways affected in spermatozoa. The objective of this study was to evaluate the sperm proteome of patients with various types of cancer. Cryopreserved semen samples from patients (testicular cancer, n = 40; Hodgkin’s disease, n = 32; lymphoma, n = 20; leukemia, n = 17) before starting therapy were used for proteomic analysis, while samples from fertile donors (n = 19) were included as controls. The proteomic profiling of sperm was carried out by liquid chromatography-tandem mass spectrometry, and differentially expressed proteins involved in the reproductive processes were validated by Western blotting. Bioinformatic analysis revealed that proteins associated with mitochondrial dysfunction, oxidative phosphorylation, and Sirtuin signaling pathways were dysregulated in cancer patients, while oxidative phosphorylation and tricarboxylic acid cycle were predicted to be deactivated. Furthermore, the analysis revealed dysregulation of key proteins associated with sperm fertility potential and motility (NADH:Ubiquinone oxidoreductase core subunit S1, superoxide dismutase 1, SERPINA5, and cytochrome b-c1 complex subunit 2) in the cancer group, which were further validated by Western blot. Dysfunctional molecular mechanisms essential for fertility in cancer patients prior to therapy highlight the potential impact of cancer phenotype on male fertility.
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18
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Aberuyi N, Rahgozar S, Ghodousi ES, Ghaedi K. Drug Resistance Biomarkers and Their Clinical Applications in Childhood Acute Lymphoblastic Leukemia. Front Oncol 2020; 9:1496. [PMID: 32010613 PMCID: PMC6978753 DOI: 10.3389/fonc.2019.01496] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Biomarkers are biological molecules found in body fluids or tissues, which can be considered as indications of a normal or abnormal process, or of a condition or disease. There are various types of biomarkers based on their application and molecular alterations. Treatment-sensitivity or drug resistance biomarkers include prognostic and predictive molecules with utmost importance in selecting appropriate treatment protocols and improving survival rates. Acute lymphoblastic leukemia (ALL) is the most prevalent hematological malignancy diagnosed in children with nearly 80% cure rate. Despite the favorable survival rates of childhood ALL (chALL), resistance to chemotherapeutic agents and, as a consequence, a dismal prognosis develops in a significant number of patients. Therefore, there are urgent needs to have robust, sensitive, and disease-specific molecular prognostic and predictive biomarkers, which could allow better risk classification and then better clinical results. In this article, we review the currently known drug resistance biomarkers, including somatic or germ line nucleic acids, epigenetic alterations, protein expressions and metabolic variations. Moreover, biomarkers with potential clinical applications are discussed.
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Affiliation(s)
- Narges Aberuyi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Soheila Rahgozar
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Elaheh Sadat Ghodousi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technologies, University of Isfahan, Isfahan, Iran
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19
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Guo Q, Zhu L, Wang C, Wang S, Nie X, Liu J, Liu Q, Hao Y, Li X, Lin B. SERPIND1 Affects the Malignant Biological Behavior of Epithelial Ovarian Cancer via the PI3K/AKT Pathway: A Mechanistic Study. Front Oncol 2019; 9:954. [PMID: 31637210 PMCID: PMC6788328 DOI: 10.3389/fonc.2019.00954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/09/2019] [Indexed: 01/31/2023] Open
Abstract
Serpin family D member 1 (SERPIND1) belongs to the serine protease inhibitor family. Its role in cancers has gradually attracted interest from researchers in recent years. However, the role of SERPIND1 in the development of epithelial ovarian cancer remains poorly understood. This studied aimed to investigate the expression and clinical significance of SERPIND1 in epithelial ovarian cancer, as well as its effect on the malignant biological behavior of ovarian cancer cells and the related regulatory mechanisms. We found that SERPIND1 expression was significantly elevated in epithelial ovarian cancer. Patients with higher expression of SERPIND1 in ovarian cancer tissues had poor prognoses. SERPIND1 promoted the proliferation, migration, invasion, G1-to-S phase transition, and epithelial–mesenchymal transition of ovarian cancer cells and inhibited their apoptosis by promoting phosphorylation in the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) pathway. Meanwhile, the inhibition of SERPIND1 expression in ovarian cancer cells resulted in opposite effects. The addition of the PI3K/AKT pathway inhibitor LY294002 to SERPIND1-overexpressing cells could reverse the promoting effect of SERPIND1 on the malignant biological behavior of ovarian cancer cells. Further, nuclear factor kappa B subunit 1, a transcription factor could bind to the promoter region of SERPIND1 and regulate SERPIND1 expression. In conclusion, our results indicated that SERPIND1 could be an effective marker for assessing the prognosis of ovarian cancer. By elucidating its mechanism underlying the promotion of malignant biological behavior of ovarian cancer by SERPIND1, we demonstrated that SERPIND1 could potentially serve as a novel drug target.
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Affiliation(s)
- Qian Guo
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Benxi, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China
| | - Liancheng Zhu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Caixia Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xin Nie
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Juanjuan Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yingying Hao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bei Lin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Benxi, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Benxi, China
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20
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Citalan-Madrid AF, Cabral-Pacheco GA, Martinez-de-Villarreal LE, Villarreal-Martinez L, Ibarra-Ramirez M, Garza-Veloz I, Cardenas-Vargas E, Marino-Martinez I, Martinez-Fierro ML. Proteomic tools and new insights for the study of B-cell precursor acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2019; 24:637-650. [PMID: 31514680 DOI: 10.1080/16078454.2019.1664127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a hematological malignancy of immature B-cell precursors, affecting children more often than adults. The etiology of BCP-ALL is still unknown, but environmental factors, sex, race or ethnicity, and genomic alterations influence the development of the disease. Tools based on protein detection, such as flow cytometry, mass spectrometry, mass cytometry and reverse phase protein array, represent an opportunity to investigate BCP-ALL pathogenesis and to identify new biomarkers of disease. This review aims to document the recent advancements with respect to applications of proteomic technologies to study mechanisms of leukemogenesis, how this information could be used in the discovery of biological targets, and finally we describe the challenges of application of proteomic tools for the approach of BCP-ALL.
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Affiliation(s)
- Alí F Citalan-Madrid
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| | - Griselda A Cabral-Pacheco
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| | | | - Laura Villarreal-Martinez
- Hematology Service, Hospital Universitario 'Dr. José Eleuterio González', Universidad Autonoma de Nuevo Leon , Monterrey , Mexico
| | - Marisol Ibarra-Ramirez
- Departamento de Genetica, Facultad de Medicina, Universidad Autónoma de Nuevo Leon , Monterrey , Mexico
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
| | - Edith Cardenas-Vargas
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Hospital General Zacatecas 'Luz González Cosío' , Zacatecas , Mexico
| | - Ivan Marino-Martinez
- Departamento de Patologia, Facultad de Medicina, Universidad Autonoma de Nuevo Leon , Monterrey , Mexico
| | - Margarita L Martinez-Fierro
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico.,Program of Doctorate in Sciences with Orientation in Molecular Medicine, Academic Unit of Human Medicine and Health Sciences, Zacatecas Autonomous University , Zacatecas , Mexico
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21
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Kim SW, Choi JW, Yun JW, Chung IS, Cho HC, Song SE, Im SS, Song DK. Proteomics approach to identify serum biomarkers associated with the progression of diabetes in Korean patients with abdominal obesity. PLoS One 2019; 14:e0222032. [PMID: 31504048 PMCID: PMC6736247 DOI: 10.1371/journal.pone.0222032] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/20/2019] [Indexed: 12/25/2022] Open
Abstract
Type 2 diabetes is a metabolic disease with a group of metabolic derangements and inflammatory reactants in the serum. Despite the substantial public health implications, markers of diabetes progression with abdominal obesity are still needed to facilitate early detection and treatment. In this study, we performed a proteomic approach to identify differential target proteins underlying diabetes progression in patients with abdominal obesity. Proteomic differences were investigated in the serum of controls and patients with prediabetes or diabetes with or without abdominal obesity by 2-DE combined with MALDI-TOF-MS. Proteomics data were validated by western blot analyses and major protein-protein interactions were assessed using a network analysis with String database. Among 245 matched protein spots, 36 exhibited marked differences in normal patients with abdominal obesity, prediabetes, and diabetes compared to levels in normal patients without abdominal obesity. Seven (Alpha-1-antichymotrypsin, Alpha-1-antitrypsin, Apolipoprotein A-I, haptoglobin, retinol-binding protein 4, transthyretin, and zinc-alpha2-glycoprotein) of these spots exhibited significant differences between normal and prediabetes/diabetes patients. After a network analysis, functional annotation using Gene Ontology indicated that most of the identified proteins were involved in lipid transport, lipid localization, and the regulation of serum lipoprotein particle levels. Our results indicated that variation in the levels of these identified protein biomarkers has been reported in normal, prediabetes and diabetic Assessment of the levels of these biomarkers may contribute to the development of biomarkers for not only early diagnosis but also in prognosis of diabetes mellitus type 2.
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Affiliation(s)
- Sang Woo Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, South Korea
- Catholic Kwandong University, International St. Mary’s Hospital, Incheon Metropolitan City, South Korea
| | - Jung-Won Choi
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, South Korea
- Catholic Kwandong University, International St. Mary’s Hospital, Incheon Metropolitan City, South Korea
| | - Jong Won Yun
- Department of Biotechnology, Daegu University, Kyungsan, Kyungbuk, South Korea
| | - In-Sung Chung
- Division of Occupational and Environmental Medicine and Department of Preventive Medicine, Keimyung, University School of Medicine, Daegu, South Korea
| | - Ho Chan Cho
- Department of Internal Medicine, Keimyung, University School of Medicine, Daegu, South Korea
| | - Seung-Eun Song
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
| | - Seung-Soon Im
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
- * E-mail: (SSI); (DKS)
| | - Dae-Kyu Song
- Department of Physiology and Obesity-mediated Disease Research Center, Keimyung, University School of Medicine, Daegu, South Korea
- * E-mail: (SSI); (DKS)
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22
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A New Approach for the Diagnosis of Myelodysplastic Syndrome Subtypes Based on Protein Interaction Analysis. Sci Rep 2019; 9:12647. [PMID: 31477761 PMCID: PMC6718656 DOI: 10.1038/s41598-019-49084-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematological malignancies with a high risk of transformation to acute myeloid leukemia (AML). MDS are associated with posttranslational modifications of proteins and variations in the protein expression levels. In this work, we present a novel interactomic diagnostic method based on both protein array and surface plasmon resonance biosensor technology, which enables monitoring of protein-protein interactions in a label-free manner. In contrast to conventional methods based on the detection of individual biomarkers, our presented method relies on measuring interactions between arrays of selected proteins and patient plasma. We apply this method to plasma samples obtained from MDS and AML patients, as well as healthy donors, and demonstrate that even a small protein array comprising six selected proteins allows the method to discriminate among different MDS subtypes and healthy donors.
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23
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Yu R, Zhang J, Zang Y, Zeng L, Zuo W, Bai Y, Liu Y, Sun K, Liu Y. iTRAQ-based quantitative protein expression profiling of biomarkers in childhood B-cell and T-cell acute lymphoblastic leukemia. Cancer Manag Res 2019; 11:7047-7063. [PMID: 31440093 PMCID: PMC6664257 DOI: 10.2147/cmar.s210093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/18/2019] [Indexed: 01/01/2023] Open
Abstract
Purpose This study screened serum proteins to identify potential biomarkers for childhood B-cell and T-cell acute lymphoblastic leukemia (ALL). Patients and methods Serum collected from 20 newly diagnosed B-cell ALL, 20 T-cell ALL and 20 healthy children. The peptides from these samples were subjected to iTRAQ. Differentially expressed proteins (DEPs) were further validated by ELISA in 24 B-ALL, 24 T-ALL, and 24 healthy children. Results Bioinformatics analysis revealed several pathways, including atherosclerosis signaling, interleukin signaling and production in macrophages and clathrin-mediated endocytosis signaling, that were closely related to childhood T-cell ALL. Furthermore, four selected proteins, namely LRG1, S100A8, SPARC and sL-selectin, were verified by ELISA. These results were consistent with the results of the proteomics analysis. Conclusion Serum S100A8 may serve as new diagnostic biomarkers in childhood B-cell ALL and T-cell ALL.
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Affiliation(s)
- Runhong Yu
- Department of Hematology, People's Hospital of Zhengzhou University/Henan Provincial People's Hospital, Zhengzhou 450003, Henan, People's Republic of China
| | - Jingyu Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
| | - Yuzhu Zang
- Department of Hematology, People's Hospital of Zhengzhou University/Henan Provincial People's Hospital, Zhengzhou 450003, Henan, People's Republic of China
| | - Li Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
| | - Wenli Zuo
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University/Henan Cancer Hospital, Zhengzhou 450008, Henan, People's Republic of China
| | - Yanliang Bai
- Department of Hematology, People's Hospital of Zhengzhou University/Henan Provincial People's Hospital, Zhengzhou 450003, Henan, People's Republic of China
| | - Yanhui Liu
- Department of Hematology, People's Hospital of Zhengzhou University/Henan Provincial People's Hospital, Zhengzhou 450003, Henan, People's Republic of China
| | - Kai Sun
- Department of Hematology, People's Hospital of Zhengzhou University/Henan Provincial People's Hospital, Zhengzhou 450003, Henan, People's Republic of China
| | - Yufeng Liu
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, People's Republic of China
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24
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Guo L, Ren H, Zeng H, Gong Y, Ma X. Proteomic analysis of cerebrospinal fluid in pediatric acute lymphoblastic leukemia patients: a pilot study. Onco Targets Ther 2019; 12:3859-3868. [PMID: 31190885 PMCID: PMC6527054 DOI: 10.2147/ott.s193616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Purpose Involvement of central nervous system in acute lymphoblastic leukemia (CNSL) remains one of the major causes of pediatric acute lymphoblastic leukemia (ALL) treatment failure. However, the current understanding of the pathological process of CNSL is still limited. This study aimed to better understand the protein expression in cerebrospinal fluid (CSF) of ALL and discover valuable prognostic biomarkers. Materials and methods CSF samples were obtained from ALL patients and healthy controls. Comparative proteomic profiling using label-free liquid chromatography-tandem mass spectrometry was performed to detect differentially expressed proteins. Results In the present study, 51 differentially expressed proteins were found. Among them, two core clusters including ten proteins (TIMP1, LGALS3BP, A2M, FN1, AHSG, HRG, ITIH4, CF I, C2, and C4a) might be crucial for tumorigenesis and progression of ALL and can be potentially valuable indicators of CNSL. Conclusion These differentially expressed proteins of ALL children with central nervous system involvement and normal children may work as diagnostic and prognostic factors of ALL patients.
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Affiliation(s)
- Linghong Guo
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, People's Republic of China, .,West China School of Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Honghong Ren
- West China School of Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Hao Zeng
- West China School of Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Yanqiu Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Xuelei Ma
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, People's Republic of China,
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25
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Serum proteomics identify potential biomarkers for nasopharyngeal carcinoma sensitivity to radiotherapy. Biosci Rep 2019; 39:BSR20190027. [PMID: 31040200 PMCID: PMC6522734 DOI: 10.1042/bsr20190027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 02/06/2023] Open
Abstract
Radiotherapy is the primary treatment option for nasopharyngeal carcinoma (NPC). Local recurrence and metastasis caused by radioresistance become a bottleneck of curative effect for patients with NPC. Currently, serum predictive biomarkers of radioresistance are scare. We enrolled NPC patients, who underwent radiotherapy in the Department of Oncology, Xiangya Hospital, Central Southern University, and analyzed the serum proteins profiles in NPC patients using with quantitative label-free proteomics using ultra-definition MS. Patients were divided into those who were radioresistant and radiosensitive by the overall reduction (≤50% or >50%, respectively) in tumor extent. The MS/MS spectrum database search identified 911 proteins and 809 proteins are quantitatable. Eight proteins significantly up-regulated and 12 serum proteins were significantly down-regulated in the radioresistance group compared with radiosensitivity group (P<0.05). Finally, five proteins entered the optimal models, including secreted protein acidic and cysteine rich (SPARC) (P =0.032), serpin family D member 1S (ERPIND1) (P =0.040), complement C4B (C4B) (P =0.017), peptidylprolyl Isomerase B (PPIB) (P =0.042), and family with sequence similarity 173 member A (FAM173A) (P =0.017). In all patient, the area under the curves (AUC) for SPARC, SERPIND, C4B, PPIB, and FAM173A were 0.716 (95% CI: 0.574-0.881), 0.697 (95% CI: 0.837-0.858), 0.686 (95% CI: 0.522-0.850), 0.668 (95% CI: 0.502-0.834) and 0.657 (95% CI: 0.512-0.825), respectively. The AUC of five selected proteins was 0.968 (95% CI: 0.918-1.000) with the sensitivity of 0.941 and the specificity of 0.926. Our result indicated that a panel including five serum protein (SPARC SERPIND1 C4B PPIB FAM173A) based on serum proteomics provided a high discrimination ability for radiotherapy effects in NPC patients. Studies with larger sample size and longer follow-up outcome are required.
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26
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Protein expression in the liver and blood serum in chickens in response to Salmonella Enteritidis infection. Vet Immunol Immunopathol 2018; 205:10-16. [PMID: 30458997 DOI: 10.1016/j.vetimm.2018.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/03/2018] [Accepted: 10/17/2018] [Indexed: 01/20/2023]
Abstract
Events occurring in the chicken caecum following Salmonella Enteritidis infection are relatively well-described. However, mechanisms of the immune response and defence beyond the intestinal tract are less well-described. In this study, we therefore determined changes in protein abundance in the liver and blood serum in response to S. Enteritidis infection using the unbiased approach of shotgun proteomics. Complement and coagulation cascades, TNF signalling, antigen processing and presentation was activated in the liver following infection with S. Enteritidis. Chicken proteins that decreased in the liver were involved in glycolysis, the citrate cycle, oxidative phosphorylation and fatty acid metabolism. No functional category was significantly activated or suppressed in the serum. Concerning individual proteins, VNN1, SAA, AVD, SERPINA3, SERPINB10, AGT, MRP126 or CP increased in abundance both in the liver and serum. MT4, MT3, PTGDS, GLRX and TGM4, though highly inducible in the liver, did not increase in the serum. PIGR, SERPINF2 and IGJ increased in the serum but not in the liver. SERPINA4, apoAIV, CLEC3B, SERPINF1, HRG, AHSG and ALB decreased both in the liver and serum. Avidin-like LOC431660, THRSP, GATM, GGACT, ACOX1, ALDOB or FABP7 decreased in the liver but not in the serum. Finally, CKM, CKB, PLTP, COMP, IGFALS, AMY1A or SERPIND1 decreased in the serum after S. Enteritidis infection but not in the liver. Differently abundant proteins characterise the chicken's response to infection and can be also used as markers of chicken health status.
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27
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Coudray A, Battenhouse AM, Bucher P, Iyer VR. Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data. PeerJ 2018; 6:e5362. [PMID: 30083469 PMCID: PMC6074801 DOI: 10.7717/peerj.5362] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023] Open
Abstract
To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of somatic mutations. However there has been little systematic evaluation of the utility of RNA-seq for identifying somatic mutations. Here, we develop and evaluate a pipeline for processing RNA-seq data from glioblastoma multiforme (GBM) tumors in order to identify somatic mutations. The pipeline entails the use of the STAR aligner 2-pass procedure jointly with MuTect2 from genome analysis toolkit (GATK) to detect somatic variants. Variants identified from RNA-seq data were evaluated by comparison against the COSMIC and dbSNP databases, and also compared to somatic variants identified by exome sequencing. We also estimated the putative functional impact of coding variants in the most frequently mutated genes in GBM. Interestingly, variants identified by RNA-seq alone showed better representation of GBM-related mutations cataloged by COSMIC. RNA-seq-only data substantially outperformed the ability of WES to reveal potentially new somatic mutations in known GBM-related pathways, and allowed us to build a high-quality set of somatic mutations common to exome and RNA-seq calls. Using RNA-seq data in parallel with WES data to detect somatic mutations in cancer genomes can thus broaden the scope of discoveries and lend additional support to somatic variants identified by exome sequencing alone.
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Affiliation(s)
- Alexandre Coudray
- School of Life Sciences, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Anna M Battenhouse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Philipp Bucher
- School of Life Sciences, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Vishwanath R Iyer
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, TX, USA
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28
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Zorin NA, Zorina VN. Evolution of the macroglobulin protein family: from bacteria to primates. J EVOL BIOCHEM PHYS+ 2018. [DOI: 10.1134/s0022093017060011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome. Proteomes 2017; 5:proteomes5020013. [PMID: 28587287 PMCID: PMC5489773 DOI: 10.3390/proteomes5020013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3–10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7–20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.
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Quezada H, Guzmán-Ortiz AL, Díaz-Sánchez H, Valle-Rios R, Aguirre-Hernández J. Omics-based biomarkers: current status and potential use in the clinic. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.bmhime.2017.11.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Omics-based biomarkers: current status and potential use in the clinic. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2017; 74:219-226. [DOI: 10.1016/j.bmhimx.2017.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/17/2017] [Indexed: 12/20/2022] Open
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32
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Freitas CDT, Viana CA, Vasconcelos IM, Moreno FBB, Lima-Filho JV, Oliveira HD, Moreira RA, Monteiro-Moreira ACO, Ramos MV. First insights into the diversity and functional properties of chitinases of the latex of Calotropis procera. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:361-371. [PMID: 27521700 DOI: 10.1016/j.plaphy.2016.07.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/31/2016] [Indexed: 05/07/2023]
Abstract
Chitinases (EC 3.2.1.14) found in the latex of Calotropis procera (Ait) R. Br. were studied. The proteins were homogeneously obtained after two ion exchange chromatography steps. Most proteins were identified individually in 15 spots on 2-D gel electrophoresis with isoelectric points ranging from 4.6 to 6.0 and molecular masses extending from 27 to 30 kDa. Additionally, 66 kDa proteins were identified as chitinases in SDS-PAGE. Their identities were further confirmed by mass spectrometry (MS) analysis of the tryptic digests of each spot and MS analysis of the non-digested proteins. Positive reaction for Schiff's reagent suggested the proteins are glycosylated. The chitinases exhibited high catalytic activity toward to colloidal chitin at pH 5.0, and this activity underwent decay in the presence of increasing amounts of reducing agent dithiothreitol. Spore germination and hyphae growth of two phytopathogenic fungi were inhibited only marginally by the chitinases but were affected differently. This suggested a complex relationship might exist between the specificity of the proteins toward the fungal species. The chitinases showed potent insecticidal activity against the Bruchidae Callosobruchus maculatus, drastically reducing survival, larval weight and adult emergence. It is concluded that closely related chitinases are present in the latex of C. procera, and the first experimental evidence suggests these proteins are involved more efficiently in defence strategies against insects rather than fungi.
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Affiliation(s)
- Cleverson D T Freitas
- Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, Campus do Pici, Cx. Postal 6033, Fortaleza, CE CEP 60451-970, Brazil.
| | - Carolina A Viana
- Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, Campus do Pici, Cx. Postal 6033, Fortaleza, CE CEP 60451-970, Brazil
| | - Ilka M Vasconcelos
- Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, Campus do Pici, Cx. Postal 6033, Fortaleza, CE CEP 60451-970, Brazil
| | - Frederico B B Moreno
- Centro de Ciências da Saúde, Universidade de Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | - José V Lima-Filho
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Recife, PE, Brazil
| | - Hermogenes D Oliveira
- Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, Campus do Pici, Cx. Postal 6033, Fortaleza, CE CEP 60451-970, Brazil
| | - Renato A Moreira
- Centro de Ciências da Saúde, Universidade de Fortaleza (UNIFOR), Fortaleza, CE, Brazil
| | | | - Márcio V Ramos
- Departamento de Bioquímica e Biologia Molecular da Universidade Federal do Ceará, Campus do Pici, Cx. Postal 6033, Fortaleza, CE CEP 60451-970, Brazil.
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Zhu L, Guo Q, Jin S, Feng H, Zhuang H, Liu C, Tan M, Liu J, Li X, Lin B. Analysis of the gene expression profile in response to human epididymis protein 4 in epithelial ovarian cancer cells. Oncol Rep 2016; 36:1592-604. [PMID: 27430660 DOI: 10.3892/or.2016.4926] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 03/30/2016] [Indexed: 11/05/2022] Open
Abstract
Currently, there are emerging multiple studies on human epididymis protein 4 (HE4) in ovarian cancer. HE4 possesses higher sensitivity and specificity than CA125 in the confirmative early diagnosis for ovarian cancer. Although much attention has been given to explore its clinical application, research of the basic mechanisms of HE4 in ovarian cancer are still unclear. In the present study, we provide fundamental data to identify full-scale differentially expressed genes (DEGs) in response to HE4 by use of human whole-genome microarrays in human epithelial ovarian cancer cell line ES-2 following overexpression and silencing of HE4. We found that a total of 717 genes were upregulated and 898 genes were downregulated in the HE4-overexpressing cells vs. the HE4-Mock cells, and 166 genes were upregulated and 285 were downregulated in the HE4-silenced cells vs. the HE4-Mock cells. An overlap of 16 genes consistently upregulated and 8 genes downregulated in response to HE4 were noted. These DEGs were involved in MAPK, steroid biosynthesis, cell cycle, the p53 hypoxia pathway, and focal adhesion pathways. Interaction network analysis predicted that the genes participated in the regulatory connection. Highly differential expression of the FOXA2, SERPIND1, BDKRD1 and IL1A genes was verified by quantitative real-time PCR in 4 cell line samples. Finally, SERPIND1 (HCII) was validated at the protein level by immunohistochemistry in 107 paraffin-embedded ovarian tissues. We found that SERPIND1 may act as a potential oncogene in the development of ovarian cancer. The present study displayed the most fundamental and full-scale data to show DEGs in response to HE4. These identified genes may provide a theoretical basis for investigations of the underlying molecular mechanism of HE4 in ovarian cancer.
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Affiliation(s)
- Liancheng Zhu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Qian Guo
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Shan Jin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Huilin Feng
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Huiyu Zhuang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Cong Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Mingzi Tan
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Juanjuan Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xiao Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bei Lin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Inflammatory glycoproteins in cardiometabolic disorders, autoimmune diseases and cancer. Clin Chim Acta 2016; 459:177-186. [PMID: 27312321 DOI: 10.1016/j.cca.2016.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/08/2016] [Accepted: 06/11/2016] [Indexed: 12/25/2022]
Abstract
The physiological function initially attributed to the oligosaccharide moieties or glycans on inflammatory glycoproteins was to improve protein stability. However, it is now clear that glycans play a prominent role in glycoprotein structure and function and in some cases contribute to disease states. In fact, glycan processing contributes to pathogenicity not only in autoimmune disorders but also in atherosclerotic cardiovascular disease, diabetes and malignancy. While most clinical laboratory tests measure circulating levels of inflammatory proteins, newly developed diagnostic and prognostic tests are harvesting the information that can be gleaned by measuring the amount or structure of the attached glycans, which may be unique to individuals as well as various diseases. As such, these newer glycan-based tests may provide future means for more personalized approaches to patient stratification and improved patient care. Here we will discuss recent progress in high-throughput laboratory methods for glycomics (i.e. the study of glycan structures) and glycoprotein quantification by methods such as mass spectrometry and nuclear magnetic resonance spectroscopy. We will also review the clinical utility of glycoprotein and glycan measurements in the prediction of common low-grade inflammatory disorders including cardiovascular disease, diabetes and cancer, as well as for monitoring autoimmune disease activity.
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