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Jajula S, Naik V, Kalita B, Yanamandra U, Sharma S, Chatterjee T, Bhanuse S, Bhavsar PP, Taunk K, Rapole S. Integrative proteome analysis of bone marrow interstitial fluid and serum reveals candidate signature for acute myeloid leukemia. J Proteomics 2024; 303:105224. [PMID: 38866132 DOI: 10.1016/j.jprot.2024.105224] [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: 04/11/2024] [Revised: 05/27/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Acute myeloid leukemia (AML) is an aggressive form of blood cancer and clinically highly heterogeneous characterized by the accumulation of clonally proliferative immature precursors of myeloid lineage leading to bone marrow failure. Although, the current diagnostic methods for AML consist of cytogenetic and molecular assessment, there is a need for new markers that can serve as useful candidates in diagnosis, prognosis and understanding the pathophysiology of the disease. This study involves the investigation of alterations in the bone marrow interstitial fluid and serum proteome of AML patients compared to controls using label-free quantitative proteomic approach. A total of 201 differentially abundant proteins were identified in AML BMIF, while in the case of serum 123 differentially abundant proteins were identified. The bioinformatics analysis performed using IPA revealed several altered pathways including FAK signalling, IL-12 signalling and production of macrophages etc. Verification experiments were performed in a fresh independent cohort of samples using MRM assays led to the identification of a panel of three proteins viz., PPBP, APOH, ENOA which were further validated in a new cohort of serum samples by ELISA. The three-protein panel could be helpful in the diagnosis, prognosis and understanding of the pathophysiology of AML in the future. BIOLOGICAL SIGNIFICANCE: Acute Myeloid Leukemia (AML) is a type haematological malignancy which constitute one third of total leukemias and it is the most common acute leukemia in adults. In the current clinical practice, the evaluation of diagnosis and progression of AML is largely based on morphologic, immunophenotypic, cytogenetic and molecular assessment. There is a need for new markers/signatures which can serve as useful candidates in diagnosis and prognosis. The present study aims to identify and validate candidate biosignature for AML which can be useful in diagnosis, prognosis and understand the pathophysiology of the disease. Here, we identified 201 altered proteins in AML BMIF and 123 in serum. Among these altered proteins, a set of three proteins viz., pro-platelet basic protein (CXCL7), enolase 1 (ENO1) and beta-2-glycoprotein 1 (APOH) were significantly increased in AML BMIF and serum suggest that this panel of proteins could help in future AML disease management and thereby improving the survival expectancy of AML patients.
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Affiliation(s)
- Saikiran Jajula
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Venkateshwarlu Naik
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India; Amrita Research Centre, Amrita Vishwa Vidyapeetham, Faridabad, Haryana, 121002, India
| | - Uday Yanamandra
- Armed Forces Medical College, Pune 411007, Maharashtra, India
| | | | | | - Sadananad Bhanuse
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Praneeta Pradip Bhavsar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India; Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia 741249, West Bengal, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India.
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Zhang Z, Huang J, Zhang Z, Shen H, Tang X, Wu D, Bao X, Xu G, Chen S. Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia. Biomark Res 2024; 12:60. [PMID: 38858750 PMCID: PMC11165883 DOI: 10.1186/s40364-024-00600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Acute myeloid leukemia (AML) is the most frequent leukemia in adults with a high mortality rate. Current diagnostic criteria and selections of therapeutic strategies are generally based on gene mutations and cytogenetic abnormalities. Chemotherapy, targeted therapies, and hematopoietic stem cell transplantation (HSCT) are the major therapeutic strategies for AML. Two dilemmas in the clinical management of AML are related to its poor prognosis. One is the inaccurate risk stratification at diagnosis, leading to incorrect treatment selections. The other is the frequent resistance to chemotherapy and/or targeted therapies. Genomic features have been the focus of AML studies. However, the DNA-level aberrations do not always predict the expression levels of genes and proteins and the latter is more closely linked to disease phenotypes. With the development of high-throughput sequencing and mass spectrometry technologies, studying downstream effectors including RNA, proteins, and metabolites becomes possible. Transcriptomics can reveal gene expression and regulatory networks, proteomics can discover protein expression and signaling pathways intimately associated with the disease, and metabolomics can reflect precise changes in metabolites during disease progression. Moreover, omics profiling at the single-cell level enables studying cellular components and hierarchies of the AML microenvironment. The abundance of data from different omics layers enables the better risk stratification of AML by identifying prognosis-related biomarkers, and has the prospective application in identifying drug targets, therefore potentially discovering solutions to the two dilemmas. In this review, we summarize the existing AML studies using omics methods, both separately and combined, covering research fields of disease diagnosis, risk stratification, prognosis prediction, chemotherapy, as well as targeted therapy. Finally, we discuss the directions and challenges in the application of multi-omics in precision medicine of AML. Our review may inspire both omics researchers and clinical physicians to study AML from a different angle.
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Affiliation(s)
- Zhiyu Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jiayi Huang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhibo Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hongjie Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaowen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
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Guru Murthy GS, Zhang T, Bolon YT, Spellman S, Dong J, Auer P, Saber W. Proteomics to predict relapse in patients with myelodysplastic neoplasms undergoing allogeneic hematopoietic cell transplantation. Biomark Res 2024; 12:10. [PMID: 38273355 PMCID: PMC10809608 DOI: 10.1186/s40364-023-00550-0] [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: 10/09/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Disease relapse remains a major barrier to success after allogeneic hematopoietic cell transplantation (allo-HCT) in myelodysplastic neoplasms (MDS). While certain high risk genomic alterations are associated with increased risk of relapse, there is a lack of clinically applicable tools to analyze the downstream cellular events that are associated with relapse. We hypothesized that unique proteomic signatures in MDS patients undergoing allo-HCT could serve as a tool to understand this aspect and predict relapse. Using the Center for International Blood and Marrow Transplant Research (CIBMTR) database, we identified 52 MDS patients who underwent allo-HCT and analyzed their proteomic profile from pretransplant blood samples in a matched case-control design. Twenty-six patients without disease relapse after allo-HCT (controls) were matched with 26 patients who experienced relapse (cases). Proteomics assessment was conducted using the Slow Off-rate Modified Aptamers (SOMAmer) based assay. In gene set enrichment analysis, we noted that expression in the hallmark complement, and hallmark allograft rejection pathways were statistically enriched among patients who had disease relapse post-transplant. In addition, correlation analyses showed that methylation array probes in cis- and transcription regulatory elements of immune pathway genes were modulated and differentially sensitize the immune response. These findings suggest that proteomic analysis could serve as a novel tool for prediction of relapse after allo-HCT in MDS.
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Affiliation(s)
| | - Tao Zhang
- National Marrow Donor Program/Be the Match, Minneapolis, Minnesota, USA
| | - Yung-Tsi Bolon
- National Marrow Donor Program/Be the Match, Minneapolis, Minnesota, USA
| | - Stephen Spellman
- National Marrow Donor Program/Be the Match, Minneapolis, Minnesota, USA
| | - Jing Dong
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Paul Auer
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Wael Saber
- CIBMTR® (Center for International Blood and Marrow Transplant Research), Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Shama A, Soni T, Jawanda IK, Upadhyay G, Sharma A, Prabha V. The Latest Developments in Using Proteomic Biomarkers from Urine and Serum for Non-Invasive Disease Diagnosis and Prognosis. Biomark Insights 2023; 18:11772719231190218. [PMID: 37528936 PMCID: PMC10387783 DOI: 10.1177/11772719231190218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
Due to diagnostic improvements, medical diagnostics is demanding non-invasive or minimally invasive methods. Non-invasively obtained body fluids (eg., Urine, serum) can replace cerebral fluid, amniotic fluid, synovial fluid, bronchoalveolar lavage fluid, and others for diagnostic reasons. Many illnesses are induced by perturbations of cellular signaling pathways and associated pathway networks as a result of genetic abnormalities. These disturbances are represented by a shift in the protein composition of the fluids surrounding the tissues and organs that is, tissue interstitial fluid (TIF). These variant proteins may serve as diagnostic "signatures" for a variety of disorders. This review provides a concise summary of urine and serum biomarkers that may be used for the diagnosis and prognosis of a variety of disorders, including cancer, brain diseases, kidney diseases, and other system diseases. The studies reviewed in this article suggest that serum and urine biomarkers of various illnesses may be therapeutically useful for future diagnostics. Correct illness management is crucial for disease prognosis, hence non-invasive serum and urine biomarkers have been extensively studied for diagnosis, subclassification, monitoring disease activity, and predicting treatment results and consequences.
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Affiliation(s)
- Anurag Shama
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Thomson Soni
- Department of Microbiology, Panjab University, Chandigarh, India
| | | | - Garima Upadhyay
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Anshika Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Vijay Prabha
- Department of Microbiology, Panjab University, Chandigarh, India
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Yin DM, Yuan D, Sun RJ, Xu HZ, Hun SY, Sui XH, Shan NN. Identification of ORM1, vWF, SPARC, and PPBP as immune-related proteins involved in immune thrombocytopenia by quantitative LC-MS/MS. Clin Proteomics 2023; 20:24. [PMID: 37355563 DOI: 10.1186/s12014-023-09413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/03/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Immune thrombocytopenia (ITP) is a common autoimmune disease characterized by loss of immune tolerance to platelet autoantigens leading to excessive destruction and insufficient production of platelets. METHOD Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) was performed to detect the differentially expressed proteins in bone marrow samples from active ITP patients and normal controls. RESULT Our bioinformatic analysis identified two upregulated proteins (ORM1 and vWF) and two downregulated proteins (PPBP and SPARC) related to immune function. The four proteins were all found to be related to the tumor necrosis factor (TNF) -α signalling pathway and involved in the pathogenesis of ITP in KEGG pathway analysis. CONCLUSION Bioinformatics analysis identified differentially expressed proteins in bone marrow that are involved in the TNF-α signalling pathway and are related to the activation of immune function in ITP patients. These findings could provide new ideas for research on the loss of immune tolerance in ITP patients.
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Affiliation(s)
- Dong-Mei Yin
- Department of Blood Transfusion, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Blood Transfusion, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Dai Yuan
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jing Wu Rd, Jinan, 250021, Shandong, China
| | - Rui-Jie Sun
- Department of Rheumatology, Clinical Immunology Center, Peking Union Medical College Hospital, Beijing, 100000, China
| | - Hong-Zhi Xu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jing Wu Rd, Jinan, 250021, Shandong, China
| | - Shou-Yong Hun
- Department of Blood Transfusion, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Blood Transfusion, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Xiao-Hui Sui
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jing Wu Rd, Jinan, 250021, Shandong, China
| | - Ning-Ning Shan
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jing Wu Rd, Jinan, 250021, Shandong, China.
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Wu Q, Tu H, Li J. Multifaceted Roles of Chemokine C-X-C Motif Ligand 7 in Inflammatory Diseases and Cancer. Front Pharmacol 2022; 13:914730. [PMID: 35837284 PMCID: PMC9273993 DOI: 10.3389/fphar.2022.914730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Over recent years, C-X-C motif ligand 7 (CXCL7) has received widespread attention as a chemokine involved in inflammatory responses. Abnormal production of the chemokine CXCL7 has been identified in different inflammatory diseases; nevertheless, the exact role of CXCL7 in the pathogenesis of inflammatory diseases is not fully understood. Persistent infection or chronic inflammation can induce tumorigenesis and progression. Previous studies have shown that the pro-inflammatory chemokine CXCL7 is also expressed by malignant tumor cells and that binding of CXCL7 to its cognate receptors C-X-C chemokine receptor 1 (CXCR1) and C-X-C chemokine receptor 2 (CXCR2) can influence tumor biological behavior (proliferation, invasion, metastasis, and tumor angiogenesis) in an autocrine and paracrine manner. CXCL7 and its receptor CXCR1/CXCR2, which are aberrantly expressed in tumors, may represent new targets for clinical tumor immunotherapy.
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Affiliation(s)
- Qianmiao Wu
- Department of Hematology, Second Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Medicine, Nanchang University, Nanchang, China
| | - Huaijun Tu
- Department of Neurology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Li
- Department of Hematology, Second Affiliated Hospital of Nanchang University, Nanchang, China
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Moura AA, Bezerra MJB, Martins AMA, Borges DP, Oliveira RTG, Oliveira RM, Farias KM, Viana AG, Carvalho GGC, Paier CRK, Sousa MV, Fontes W, Ricart CAO, Moraes MEA, Magalhães SMM, Furtado CLM, Moraes-Filho MO, Pessoa C, Pinheiro RF. Global Proteomics Analysis of Bone Marrow: Establishing Talin-1 and Centrosomal Protein of 55 kDa as Potential Molecular Signatures for Myelodysplastic Syndromes. Front Oncol 2022; 12:833068. [PMID: 35814389 PMCID: PMC9257025 DOI: 10.3389/fonc.2022.833068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a hematological disorder characterized by abnormal stem cell differentiation and a high risk of acute myeloid leukemia transformation. Treatment options for MDS are still limited, making the identification of molecular signatures for MDS progression a vital task. Thus, we evaluated the proteome of bone marrow plasma from patients (n = 28) diagnosed with MDS with ring sideroblasts (MDS-RS) and MDS with blasts in the bone marrow (MDS-EB) using label-free mass spectrometry. This strategy allowed the identification of 1,194 proteins in the bone marrow plasma samples. Polyubiquitin-C (UBC), moesin (MSN), and Talin-1 (TLN1) showed the highest abundances in MDS-EB, and centrosomal protein of 55 kDa (CEP55) showed the highest relative abundance in the bone marrow plasma of MDS-RS patients. In a follow-up, in the second phase of the study, expressions of UBC, MSN, TLN1, and CEP55 genes were evaluated in bone marrow mononuclear cells from 45 patients by using qPCR. This second cohort included only seven patients from the first study. CEP55, MSN, and UBC expressions were similar in mononuclear cells from MDS-RS and MDS-EB individuals. However, TLN1 gene expression was greater in mononuclear cells from MDS-RS (p = 0.049) as compared to MDS-EB patients. Irrespective of the MDS subtype, CEP55 expression was higher (p = 0.045) in MDS patients with abnormal karyotypes, while MSN, UBC, and TALIN1 transcripts were similar in MDS with normal vs. abnormal karyotypes. In conclusion, proteomic and gene expression approaches brought evidence of altered TLN1 and CEP55 expressions in cellular and non-cellular bone marrow compartments of patients with low-risk (MDS-RS) and high-risk (MDS-EB) MDSs and with normal vs. abnormal karyotypes. As MDS is characterized by disrupted apoptosis and chromosomal alterations, leading to mitotic slippage, TLN1 and CEP55 represent potential markers for MDS prognosis and/or targeted therapy.
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Affiliation(s)
- Arlindo A. Moura
- Graduate Program in Animal Science, Federal University of Ceará, Fortaleza, Brazil
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Biotechnology (Renorbio), Federal University of Ceará, Fortaleza, Brazil
- *Correspondence: Arlindo A. Moura, ; Claudia Pessoa, ; Ronald F. Pinheiro,
| | - Maria Julia B. Bezerra
- Graduate Program in Animal Science, Federal University of Ceará, Fortaleza, Brazil
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Aline M. A. Martins
- Laboratory of Protein Chemistry and Biochemistry, The University of Brasília, Brasília, Brazil
| | - Daniela P. Borges
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Medical Sciences, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Roberta T. G. Oliveira
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Medical Sciences, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Raphaela M. Oliveira
- Laboratory of Protein Chemistry and Biochemistry, The University of Brasília, Brasília, Brazil
| | - Kaio M. Farias
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Biotechnology (Renorbio), Federal University of Ceará, Fortaleza, Brazil
| | - Arabela G. Viana
- Graduate Program in Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Guilherme G. C. Carvalho
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Pharmacology, Federal University of Ceará, Fortaleza, Brazil
| | - Carlos R. K. Paier
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Translational Medicine, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Marcelo V. Sousa
- Laboratory of Protein Chemistry and Biochemistry, The University of Brasília, Brasília, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, The University of Brasília, Brasília, Brazil
| | - Carlos A. O. Ricart
- Laboratory of Protein Chemistry and Biochemistry, The University of Brasília, Brasília, Brazil
| | - Maria Elisabete A. Moraes
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Translational Medicine, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Silvia M. M. Magalhães
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Medical Sciences, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Cristiana L. M. Furtado
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Translational Medicine, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Experimental Biology Center, NUBEX, The University of Fortaleza (Unifor), Fortaleza, Brazil
| | - Manoel O. Moraes-Filho
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Translational Medicine, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Claudia Pessoa
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Biotechnology (Renorbio), Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Pharmacology, Federal University of Ceará, Fortaleza, Brazil
- *Correspondence: Arlindo A. Moura, ; Claudia Pessoa, ; Ronald F. Pinheiro,
| | - Ronald F. Pinheiro
- Drug Research and Development Center (NPDM), The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- Graduate Program in Medical Sciences, The School of Medicine, Federal University of Ceará, Fortaleza, Brazil
- *Correspondence: Arlindo A. Moura, ; Claudia Pessoa, ; Ronald F. Pinheiro,
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Assessing the Prognosis of Patients with Myelodysplastic Syndromes (MDS). Cancers (Basel) 2022; 14:cancers14081941. [PMID: 35454847 PMCID: PMC9032854 DOI: 10.3390/cancers14081941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 01/27/2023] Open
Abstract
Prognostic stratification in patients with myelodysplastic syndrome (MDS) relies on a number of key factors. Combining such patient-related and disease-related prognostic parameters into useful assessment tools remains a challenge. The most widely used scoring systems include the international prognostic scoring system (IPSS), the revised IPSS (IPSS-R), the World Health Organization (WHO) Prognostic Scoring System (WPSS), and the new molecular IPSS (IPSS-M). Similar to the IPSS-R and the IPSS-M, the chronic myelomonocytic leukemia (CMML) prognostic scoring system (CPSS) and the CPSS molecular (CPSS-mol) are powerful and reliable prognostic tools that help to assess the individual prognosis of patients with CMML. The well-established prognostic assessment of MDS and CMML may be further augmented by additional disease-related parameters, such as somatic mutations, or patient-related factors, such as comorbidities. In this article, we briefly describe useful prognostic scoring systems for myelodysplastic syndromes and identify some open questions that require further investigation.
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10
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Szóstek-Mioduchowska A, Kordowitzki P. Shedding Light on the Possible Link between ADAMTS13 and Vaccine-Induced Thrombotic Thrombocytopenia. Cells 2021; 10:cells10102785. [PMID: 34685765 PMCID: PMC8535032 DOI: 10.3390/cells10102785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
Several recent reports have highlighted the onset of vaccine-induced thrombotic thrombocytopaenia (VITT) in some recipients (approximately 1 case out of 100k exposures) of the ChAdOx1 nCoV-19 vaccine (AstraZeneca). Although the underlying events leading to this blood-clotting phenomenon has yet to be elucidated, several critical observations present a compelling potential mechanism. Thrombus formation requires the von Willebrand (VWF) protein to be in ultra-large multimeric state. The conservation of this state is controlled by the ADAMTS13 enzyme, whose proteolytic activity reduces the size of VWF multimers, keeping blood clotting at bay. However, ADAMTS13 cannot act on VWF that is bound to platelet factor 4 (PF4). As such, it is of particular interest to note that a common feature between subjects presenting with VITT is high titres of antibodies against PF4. This raises the possibility that these antibodies preserve the stability of ultra-large VWF complexes, leading to the formation of endothelium-anchored VWF strings, which are capable of recruiting circulating platelets and causing uncontrolled thrombosis in terminal capillaries. Here, we share our viewpoint about the current understanding of the VITT pathogenesis involving the prevention of ADAMTS13's activity on VWF by PF4 antibody-mediated stabilisation/ protection of the PF4-VWF complex.
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Affiliation(s)
- Anna Szóstek-Mioduchowska
- Department for Immunology and Pathology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima Street 10, 10-243 Olsztyn, Poland;
| | - Paweł Kordowitzki
- Department for Immunology and Pathology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima Street 10, 10-243 Olsztyn, Poland;
- Faculty of Biology and Veterinary Medicine, Nicolaus Copernicus University, Gagarina Street 1, 87-100 Torun, Poland
- Correspondence: ; Tel.: +48-89-539-31-28
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11
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Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN. Blood 2021; 136:2051-2064. [PMID: 32726410 DOI: 10.1182/blood.2019004095] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/26/2020] [Indexed: 12/22/2022] Open
Abstract
Primary myelofibrosis (PMF) is a myeloproliferative neoplasm (MPN) that leads to progressive bone marrow (BM) fibrosis. Although the cellular mutations involved in the pathogenesis of PMF have been extensively investigated, the sequential events that drive stromal activation and fibrosis by hematopoietic-stromal cross-talk remain elusive. Using an unbiased approach and validation in patients with MPN, we determined that the differential spatial expression of the chemokine CXCL4/platelet factor-4 marks the progression of fibrosis. We show that the absence of hematopoietic CXCL4 ameliorates the MPN phenotype, reduces stromal cell activation and BM fibrosis, and decreases the activation of profibrotic pathways in megakaryocytes, inflammation in fibrosis-driving cells, and JAK/STAT activation in both megakaryocytes and stromal cells in 3 murine PMF models. Our data indicate that higher CXCL4 expression in MPN has profibrotic effects and is a mediator of the characteristic inflammation. Therefore, targeting CXCL4 might be a promising strategy to reduce inflammation in PMF.
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12
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Zhou Y, Tan Z, Xue P, Wang Y, Li X, Guan F. High-throughput, in-depth and estimated absolute quantification of plasma proteome using data-independent acquisition/mass spectrometry ("HIAP-DIA"). Proteomics 2021; 21:e2000264. [PMID: 33460299 DOI: 10.1002/pmic.202000264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Mass spectrometry-based plasma proteomics has been demonstrated to be a useful tool capable of quantifying hundreds of proteins in a single LC-MS/MS experiment, for biomarker discovery or elucidation of disease mechanisms. We developed a novel data-independent acquisition (DIA)/MS-based workflow for high-throughput, in-depth and estimated absolute quantification of plasma proteins (termed HIAP-DIA), without depleting high-abundant proteins, in a single-shot experiment. In HIAP-DIA workflow, we generated an ultra-deep cumulative undepleted and depleted spectral library which contained 55,157 peptides and 5,328 proteins, optimized column length (50 cm) and gradient (90 min) of liquid chromatography instrumentation, optimized 50 DIA segments with average isolation window 17 Th, and selected reference proteins for estimated absolute quantification of all plasma proteins. A total of 606 proteins were quantified in triplicate, and 427 proteins were quantified with CV <20% in plasma proteome. R-squared value of overlapped 208 endogenous PQ500 estimated protein amounts from HIAP-DIA and absolute quantification with internal standards was 0.82, indicating high quantification accuracy of HIAP-DIA. As a pilot study, the HIAP-DIA approach described here was applied to a myelodysplastic syndromes (MDS) disease cohort. We achieved absolute quantification of 789 plasma proteins in 22 clinical plasma samples, spanning less than six orders of magnitude with quantification limit 10-20 ng/mL, and discovered 95 differentially expressed proteins providing insights into MDS pathophysiology.
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Affiliation(s)
- Yue Zhou
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zengqi Tan
- College of Life Science, Northwest University, Xi'an, China
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, Zürich, Switzerland
| | - Yi Wang
- Department of Hematology, Provincial People's Hospital, Xi'an, China
| | - Xiang Li
- College of Life Science, Northwest University, Xi'an, China
| | - Feng Guan
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,College of Life Science, Northwest University, Xi'an, China
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13
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Silva-Cardoso SC, Tao W, Angiolilli C, Lopes AP, Bekker CPJ, Devaprasad A, Giovannone B, van Laar J, Cossu M, Marut W, Hack E, de Boer RJ, Boes M, Radstake TRDJ, Pandit A. CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro. Front Immunol 2020; 11:2149. [PMID: 33042127 PMCID: PMC7527415 DOI: 10.3389/fimmu.2020.02149] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/07/2020] [Indexed: 12/25/2022] Open
Abstract
Fibrosis is a condition shared by numerous inflammatory diseases. Our incomplete understanding of the molecular mechanisms underlying fibrosis has severely hampered effective drug development. CXCL4 is associated with the onset and extent of fibrosis development in multiple inflammatory and fibrotic diseases. Here, we used monocyte-derived cells as a model system to study the effects of CXCL4 exposure on dendritic cell development by integrating 65 longitudinal and paired whole genome transcriptional and methylation profiles. Using data-driven gene regulatory network analyses, we demonstrate that CXCL4 dramatically alters the trajectory of monocyte differentiation, inducing a novel pro-inflammatory and pro-fibrotic phenotype mediated via key transcriptional regulators including CIITA. Importantly, these pro-inflammatory cells directly trigger a fibrotic cascade by producing extracellular matrix molecules and inducing myofibroblast differentiation. Inhibition of CIITA mimicked CXCL4 in inducing a pro-inflammatory and pro-fibrotic phenotype, validating the relevance of the gene regulatory network. Our study unveils that CXCL4 acts as a key secreted factor driving innate immune training and forming the long-sought link between inflammation and fibrosis.
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Affiliation(s)
- Sandra C Silva-Cardoso
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Weiyang Tao
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Chiara Angiolilli
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ana P Lopes
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Cornelis P J Bekker
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abhinandan Devaprasad
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Barbara Giovannone
- Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jaap van Laar
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Marta Cossu
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Wioleta Marut
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Erik Hack
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Marianne Boes
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Pediatrics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Timothy R D J Radstake
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Aridaman Pandit
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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14
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Dhakal B, Wang T, Kuxhausen M, Zhu F, Taylor C, Spellman SR, Verneris MR, Hsu K, Fleischhauer K, Lee SJ, Bolon YT, Carlson KS, Nazha A, Saber W. Prognostic impact of serum CXC chemokine ligands 4 and 7 on myelodysplastic syndromes post allogeneic hematopoietic cell transplant. Leuk Lymphoma 2020; 62:229-233. [PMID: 32924688 DOI: 10.1080/10428194.2020.1817446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Binod Dhakal
- Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tao Wang
- CIBMTR (Center for International Blood and Marrow Transplant Research), Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Biostatistics, Institute for Health and Society, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michelle Kuxhausen
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Fenlu Zhu
- Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Carolyn Taylor
- Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Michael R Verneris
- Children's Hospital Colorado, Division of Pediatric Hematology/Oncology/Bone Marrow Transplant, Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katharine Hsu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Yung-Tsi Bolon
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Karen-Sue Carlson
- Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aziz Nazha
- The Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Wael Saber
- CIBMTR (Center for International Blood and Marrow Transplant Research), Medical College of Wisconsin, Milwaukee, WI, USA
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15
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van Dijk AD, de Bont ESJM, Kornblau SM. Targeted therapy in acute myeloid leukemia: current status and new insights from a proteomic perspective. Expert Rev Proteomics 2020; 17:1-10. [PMID: 31945303 DOI: 10.1080/14789450.2020.1717951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: The biological heterogeneity of acute myeloid leukemia (AML) complicates personalized medicine. Individual prognosis is typically based on the presence of chromosomal and genetic lesions. Nevertheless, these classifications often lack a priori information about response to therapy. Since the protein expression landscape reflects the functional activity state of cells, we hypothesize that analyzing this can be used for the identification of protein activity markers to provide better risk stratification as well as may provide targeted therapeutic guidance in AML.Areas covered: Herein, we review recently new adopted drugs in the treatment for AML and discuss how quantitative proteomic techniques may contribute to better therapeutic selection in AML.Expert commentary: The net functional state of the cell is defined by the activity of protein within all the pathways that are active in the cell. Recognition of the proteomic profile of the leukemic blast could, therefore, complement current classification systems by providing a better a priori description of what pathways are important within a cell as a guide to the selection of therapy for the patient.
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Affiliation(s)
- Anneke D van Dijk
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Eveline S J M de Bont
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Steven M Kornblau
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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16
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CXCL4 is a driver of cytokine mRNA stability in monocyte-derived dendritic cells. Mol Immunol 2019; 114:524-534. [DOI: 10.1016/j.molimm.2019.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/16/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022]
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17
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Bewersdorf JP, Ardasheva A, Podoltsev NA, Singh A, Biancon G, Halene S, Zeidan AM. From clonal hematopoiesis to myeloid leukemia and what happens in between: Will improved understanding lead to new therapeutic and preventive opportunities? Blood Rev 2019; 37:100587. [DOI: 10.1016/j.blre.2019.100587] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/22/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023]
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18
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Artuz CM, Knights AJ, Funnell APW, Gonda TJ, Ravid K, Pearson RCM, Quinlan KGR, Crossley M. Partial reprogramming of heterologous cells by defined factors to generate megakaryocyte lineage-restricted biomolecules. ACTA ACUST UNITED AC 2018; 20:e00285. [PMID: 30364711 PMCID: PMC6197760 DOI: 10.1016/j.btre.2018.e00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/30/2018] [Accepted: 09/29/2018] [Indexed: 11/17/2022]
Abstract
The ability of transcriptional regulators to drive lineage conversion of somatic cells offers great potential for the treatment of human disease. To explore the concept of switching on specific target genes in heterologous cells, we developed a model system to screen candidate factors for their ability to activate the archetypal megakaryocyte-specific chemokine platelet factor 4 (PF4) in fibroblasts. We found that co-expression of the transcriptional regulators GATA1 and FLI1 resulted in a significant increase in levels of PF4, which became magnified over time. This finding demonstrates that such combinations can be used to produce potentially beneficial chemokines in readily available heterologous cell types.
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Affiliation(s)
- Crisbel M Artuz
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales, 2052, Australia
| | - Alexander J Knights
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales, 2052, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales, 2052, Australia
| | - Thomas J Gonda
- School of Pharmacy, The University of Queensland, Queensland, 4102, Australia
| | - Katya Ravid
- Department of Medicine, Boston University School of Medicine, Massachusetts, 02118, United States
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales, 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales, 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, New South Wales, 2052, Australia
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19
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Lee NH, Nikfarjam M, He H. Functions of the CXC ligand family in the pancreatic tumor microenvironment. Pancreatology 2018; 18:705-716. [PMID: 30078614 DOI: 10.1016/j.pan.2018.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/06/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023]
Abstract
Therapeutic resistance is the major contributor to the poor prognosis of and low survival from pancreatic cancer (PC). Cancer progression is a complex process reliant on interactions between the tumor and the tumor microenvironment (TME). Members of the CXCL family of chemokines are present in the pancreatic TME and seem to play a vital role in regulating PC progression. As pancreatic tumors interact with the TME and with PC stem cells (CSCs), determining the roles of specific members of the CXCL family is vital to the development of improved therapies. This review highlights the roles of selected CXCLs in the interactions between pancreatic tumor and its stroma, and in CSC phenotypes, which can be used to identify potential treatment targets.
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Affiliation(s)
- Nien-Hung Lee
- Department of Surgery, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Mehrdad Nikfarjam
- Department of Surgery, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Hong He
- Department of Surgery, University of Melbourne, Austin Health, Melbourne, Victoria, Australia.
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20
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Ruytinx P, Proost P, Struyf S. CXCL4 and CXCL4L1 in cancer. Cytokine 2018; 109:65-71. [DOI: 10.1016/j.cyto.2018.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 02/07/2023]
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21
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Karshovska E, Weber C, Hundelshausen PV. Platelet chemokines in health and disease. Thromb Haemost 2017; 110:894-902. [DOI: 10.1160/th13-04-0341] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/17/2013] [Indexed: 12/12/2022]
Abstract
SummaryIn recent years, it has become clear that platelets and platelet-derived chemokines, beyond their role in thrombosis and haemostasis, are important mediators affecting a broad spectrum of (patho)physiological conditions. These biologically active proteins are released from α-granules upon platelet activation, most probably even during physiological conditions. In this review, we give a concise overview and an update on the current understanding of platelet-derived chemokines in a context of health and disease.Note: The review process for this manuscript was fully handled by G. Y. H. Lip, Editor in Chief.
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22
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Guo F, Ru Q, Zhang J, He S, Yu J, Zheng S, Wang J. Inflammation factors in hepatoblastoma and their clinical significance as diagnostic and prognostic biomarkers. J Pediatr Surg 2017; 52:1496-1502. [PMID: 28188039 DOI: 10.1016/j.jpedsurg.2017.01.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/18/2017] [Accepted: 01/21/2017] [Indexed: 01/17/2023]
Abstract
PURPOSE The aims of this study were to identify inflammation factors in hepatoblastoma tissue that correlated with different clinical characteristics, and to explore the probability as predictive biomarkers for diagnosis and prognosis. METHODS SELDI-TOF-MS was performed to screen protein peaks that were significantly highly expressed in tumor tissue compared with adjacent liver tissue. After removing proteins larger than 30kDa, the targeted peaks were separated by solid phase extraction and tricine-SDS-PAGE. Protein fragments produced by in-gel digestion were identified by LC-MS/MS. Immunohistochemical assays further confirmed these results. Overall survival curves were graphed by Kaplan-Meier method and multivariate analysis was performed by Cox proportional hazards regression model. RESULTS Three protein peaks (m/z 12,138, m/z 13,462, and m/z 15,120) that were significantly upregulated in the tumor tissue were identified as macrophage migration inhibitory factor (MIF), chemokine (C-X-C motif) ligand 7 (CXCL7), and interleukin 25 (IL-25). These factors were closely related to clinical stage, lymph node metastasis, vascular invasion and serum AFP level. High expression of each inflammatory marker indicated poor prognosis. Multivariate analysis suggested that MIF, CXCL7, and IL-25 were prognostic factors independent of patient sex, age and tumor histological type. CONCLUSIONS MIF, CXCL7, and IL-25 might be considered as effective inflammation factors for diagnosis and prognosis of hepatoblastoma and as potential novel treatment targets through inhibition of inflammatory function. TYPE OF STUDY Prognosis study LEVEL OF EVIDENCE: Level I.
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Affiliation(s)
- Fei Guo
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Qin Ru
- Record Room, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453000, Henan, PR China
| | - Junjie Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Shen He
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Jiekai Yu
- Institute of Cancer, the Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, Zhejiang, PR China
| | - Shu Zheng
- Institute of Cancer, the Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, Zhejiang, PR China
| | - Jiaxiang Wang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China.
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23
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Silva-Cardoso SC, Affandi AJ, Spel L, Cossu M, van Roon JAG, Boes M, Radstake TRDJ. CXCL4 Exposure Potentiates TLR-Driven Polarization of Human Monocyte-Derived Dendritic Cells and Increases Stimulation of T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:253-262. [PMID: 28515281 DOI: 10.4049/jimmunol.1602020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/17/2017] [Indexed: 12/11/2022]
Abstract
Chemokines have been shown to play immune-modulatory functions unrelated to steering cell migration. CXCL4 is a chemokine abundantly produced by activated platelets and immune cells. Increased levels of circulating CXCL4 are associated with immune-mediated conditions, including systemic sclerosis. Considering the central role of dendritic cells (DCs) in immune activation, in this article we addressed the effect of CXCL4 on the phenotype and function of monocyte-derived DCs (moDCs). To this end, we compared innate and adaptive immune responses of moDCs with those that were differentiated in the presence of CXCL4. Already prior to TLR- or Ag-specific stimulation, CXCL4-moDCs displayed a more matured phenotype. We found that CXCL4 exposure can sensitize moDCs for TLR-ligand responsiveness, as illustrated by a dramatic upregulation of CD83, CD86, and MHC class I in response to TLR3 and TLR7/8-agonists. Also, we observed a markedly increased secretion of IL-12 and TNF-α by CXCL4-moDCs exclusively upon stimulation with polyinosinic-polycytidylic acid, R848, and CL075 ligands. Next, we analyzed the effect of CXCL4 in modulating DC-mediated T cell activation. CXCL4-moDCs strongly potentiated proliferation of autologous CD4+ T cells and CD8+ T cells and production of IFN-γ and IL-4, in an Ag-independent manner. Although the internalization of Ag was comparable to that of moDCs, Ag processing by CXCL4-moDCs was impaired. Yet, these cells were more potent at stimulating Ag-specific CD8+ T cell responses. Together our data support that increased levels of circulating CXCL4 may contribute to immune dysregulation through the modulation of DC differentiation.
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Affiliation(s)
- Sandra C Silva-Cardoso
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; and
| | - Alsya J Affandi
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; and
| | - Lotte Spel
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
- Department of Pediatrics, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
| | - Marta Cossu
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; and
| | - Joel A G van Roon
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; and
| | - Marianne Boes
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands;
- Department of Pediatrics, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands
| | - Timothy R D J Radstake
- Laboratory of Translational Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands;
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; and
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24
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Reichert M. Proteome analysis of sheep B lymphocytes in the course of bovine leukemia virus-induced leukemia. Exp Biol Med (Maywood) 2017; 242:1363-1375. [PMID: 28436273 DOI: 10.1177/1535370217705864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Presented are the results of a study of the expression pattern of different proteins in the course of bovine leukemia virus-induced leukemia in experimental sheep and I discuss how the obtained data may be useful in gaining a better understanding of the pathogenesis of the disease, diagnosis, and for the selection of possible therapeutic targets. In cattle, the disease is characterized by life-long persistent lymphocytosis leading to leukemia/lymphoma in about 5% of infected animals. In sheep, as opposed to cattle, the course of the disease is always fatal and clinical symptoms usually occur within a three-year period after infection. For this reason, sheep are an excellent experimental model of retrovirus-induced leukemia. This model can be useful for human pathology, as bovine leukemia virus is closely related to human T-lymphotropic virus type 1. The data presented here provide novel insights into the molecular mechanisms of the bovine leukemia virus-induced tumorigenic process and indicate the potential marker proteins both for monitoring progression of the disease and as possible targets of pharmacological intervention. A study of the proteome of B lymphocytes from four leukemic sheep revealed 11 proteins with altered expression. Among them, cytoskeleton and intermediate filament proteins were the most abundant, although proteins belonging to the other functional groups, i.e. enzymes, regulatory proteins, and transcription factors, were also present. It was found that trypsin inhibitor, platelet factor 4, thrombospondin 1, vasodilator-stimulated phosphoprotein, fibrinogen alpha chain, zyxin, filamin-A, and vitamin D-binding protein were downregulated, whereas cleavage and polyadenylation specificity factor subunit 5, non-POU domain-containing octamer-binding protein and small glutamine-rich tetratricopeptide repeat-containing protein alpha were upregulated. Discussed are the possible mechanisms of their altered expression and its significance in the bovine leukemia virus-induced leukemogenic process. Impact statement The submitted manuscript provides new data on the molecular mechanisms of BLV-induced tumorigenic process indicating the potential marker proteins both for monitoring the progression of the disease and as possible targets of pharmacological intervention. This is to my knowledge the first study of the proteome of the transformed lymphocytes in the course of bovine leukemia virus-induced leukemia in susceptible animals. BLV can be considered as useful model for related human pathogen - HTLV-1, another member of the deltaretrovirus genus evolutionary closely related to BLV. Information gathered in this study can be useful to speculate on possible shared mechanisms of deltaretrovirus-induced carcinogenesis.
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Affiliation(s)
- Michal Reichert
- Department of Pathology, National Veterinary Research Institute, Pulawy 24-100, Poland
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Abstract
Platelets have various roles in vascular biology and homeostasis. They are the first actor in primary haemostasis and play important roles in thrombosis pathogenesis, but they are also part of innate immunity, which initiates and accelerate many inflammatory conditions. In some contexts, their immune functions are protective, while in others they contribute to adverse inflammatory outcomes. Platelets express numerous receptors and contain hundreds of secretory molecules that are crucial for platelet functional responses. The capacity of platelets to produce and secrete cytokines, chemokines and related molecules, under the control of specific intracellular pathways, is intimately related to their key role in inflammation. They are also able to intervene in tissue regeneration and repair because they produce pro-angiogenic mediators. Due to this characteristic platelets are involved in cancer progression and spreading. In this review we discuss the complex role of platelets, which bridges haemostasis, inflammation and immune response both in physiological and pathological conditions.
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Affiliation(s)
- Maria Elisa Mancuso
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Centre, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Elena Santagostino
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Centre, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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Norozi F, Shahrabi S, Hajizamani S, Saki N. Regulatory role of Megakaryocytes on Hematopoietic Stem Cells Quiescence by CXCL4/PF4 in Bone Marrow Niche. Leuk Res 2016; 48:107-12. [DOI: 10.1016/j.leukres.2015.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/26/2015] [Accepted: 12/28/2015] [Indexed: 01/20/2023]
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Plasma Protein Biomarker Candidates for Myelodysplastic Syndrome Subgroups. BIOMED RESEARCH INTERNATIONAL 2015; 2015:209745. [PMID: 26448929 PMCID: PMC4584066 DOI: 10.1155/2015/209745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/19/2014] [Accepted: 01/13/2015] [Indexed: 01/13/2023]
Abstract
In recent years the plasma proteomes of several different myelodysplastic syndrome (MDS) subgroups have been investigated and compared with those of healthy donors. However, the resulting data do not facilitate a direct and statistical comparison of the changes among the different MDS subgroups that would be useful for the selection and proposal of diagnostic biomarker candidates. The aim of this work was to identify plasma protein biomarker candidates for different MDS subgroups by reanalyzing the proteomic data of four MDS subgroups: refractory cytopenia with multilineage dysplasia (RCMD), refractory anemia or refractory anemia with ringed sideroblasts (RA-RARS), refractory anemia with excess blasts subtype 1 (RAEB-1), and refractory anemia with excess blasts subtype 2 (RAEB-2). Reanalysis of a total of 47 MDS patients revealed biomarker candidates, with alpha-2-HS-glycoprotein and leucine-rich alpha-2-glycoprotein as the most promising candidates.
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28
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Fröbel J, Hartwig S, Jourdain S, Fischer JC, Zilkens C, Kündgen A, Suckau D, Germing U, Czibere A, Lehr S. Deep serum discoveries: SDF-1α and HSA fragments in myelodysplastic syndromes. Am J Hematol 2015; 90:E185-7. [PMID: 26010554 DOI: 10.1002/ajh.24070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Julia Fröbel
- Department of Clinical Biochemistry and Pathobiochemistry; Leibniz Center for Diabetes Research, Heinrich-Heine-University; 40225 Düsseldorf Germany
- Department of Hematology, Oncology and Clinical Immunology; Heinrich-Heine-University; 40225 Düsseldorf Germany
- Department of Orthopedic Surgery; Heinrich-Heine-University; 40225 Düsseldorf Germany
| | - Sonja Hartwig
- Department of Clinical Biochemistry and Pathobiochemistry; Leibniz Center for Diabetes Research, Heinrich-Heine-University; 40225 Düsseldorf Germany
| | | | - Johannes C. Fischer
- Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine-University; 40225 Düsseldorf Germany
| | - Christoph Zilkens
- Department of Orthopedic Surgery; Heinrich-Heine-University; 40225 Düsseldorf Germany
| | - Andrea Kündgen
- Department of Hematology, Oncology and Clinical Immunology; Heinrich-Heine-University; 40225 Düsseldorf Germany
| | | | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology; Heinrich-Heine-University; 40225 Düsseldorf Germany
| | - Akos Czibere
- Department of Hematology, Oncology and Clinical Immunology; Heinrich-Heine-University; 40225 Düsseldorf Germany
| | - Stefan Lehr
- Department of Clinical Biochemistry and Pathobiochemistry; Leibniz Center for Diabetes Research, Heinrich-Heine-University; 40225 Düsseldorf Germany
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Unver N, Esendagli G, Yilmaz G, Guc D. CXCL7-induced macrophage infiltration in lung tumor is independent of CXCR2 expression: CXCL7-induced macrophage chemotaxis in LLC tumors. Cytokine 2015; 75:330-7. [PMID: 26233476 DOI: 10.1016/j.cyto.2015.07.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
Chemokines play diverse roles in modulating the immune response during tumor development. Levels of CXC chemokine ligand 7 (CXCL7) protein vary during tumorigenesis, and the evidence suggests that this chemokine serves as a novel biomarker of early-stage lung cancer. We investigated the effect of CXCL7 gene expression on the infiltration of myeloid cells into the tumor microenvironment in Lewis lung carcinoma (LLC). Tumors established from LLC cells overexpressing CXCL7 (CXCL7-LLC tumors) increased the infiltration of CD206(+) M2 macrophages at the early stages of tumorigenesis. This infiltration was independent of CXCR2 expression on either tumor cells or macrophages. CXCL7-LLC tumors developed faster than control-LLC tumors (IRES-LLC tumor) did. The extent of CD4(+) T cell, CD8(+) T cell, and natural killer T cell infiltration was similar between the two tumor groups. Our findings suggest that CXCL7 attracts macrophages especially at the tumor site and may accelerate lung tumor development in the early stages.
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Affiliation(s)
- Nese Unver
- Department of Basic Oncology, Cancer Institute, Hacettepe University, Ankara, Turkey.
| | - Gunes Esendagli
- Department of Basic Oncology, Cancer Institute, Hacettepe University, Ankara, Turkey
| | - Guldal Yilmaz
- Department of Pathology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Dicle Guc
- Department of Basic Oncology, Cancer Institute, Hacettepe University, Ankara, Turkey
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Peripheral blood mononuclear cell proteome changes in patients with myelodysplastic syndrome. BIOMED RESEARCH INTERNATIONAL 2015; 2015:872983. [PMID: 25969835 PMCID: PMC4415457 DOI: 10.1155/2015/872983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/31/2015] [Indexed: 12/13/2022]
Abstract
Our aim was to search for proteome changes in peripheral blood mononuclear cells (PBMCs) of MDS patients with refractory cytopenia with multilineage dysplasia. PBMCs were isolated from a total of 12 blood samples using a Histopaque-1077 solution. The proteins were fractioned, separated by 2D SDS-PAGE (pI 4–7), and double-stained. The proteomes were compared and statistically processed with Progenesis SameSpots; then proteins were identified by nano-LC-MS/MS. Protein functional association and expression profiles were analyzed using the EnrichNet application and Progenesis SameSpots hierarchical clustering software, respectively. By comparing the cytosolic, membrane, and nuclear fractions of the two groups, 178 significantly (P < 0.05, ANOVA) differing spots were found, corresponding to 139 unique proteins. Data mining of the Reactome and KEGG databases using EnrichNet highlighted the possible involvement of the identified protein alterations in apoptosis, proteasome protein degradation, heat shock protein action, and signal transduction. Western blot analysis revealed underexpression of vinculin and advanced fragmentation of fermitin-3 in MDS patients. To the best of our knowledge, this is the first time that proteome changes have been identified in the mononuclear cells of MDS patients. Vinculin and fermitin-3, the proteins involved in cell adhesion and integrin signaling, have been shown to be dysregulated in MDS.
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Meldi K, Qin T, Buchi F, Droin N, Sotzen J, Micol JB, Selimoglu-Buet D, Masala E, Allione B, Gioia D, Poloni A, Lunghi M, Solary E, Abdel-Wahab O, Santini V, Figueroa ME. Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia. J Clin Invest 2015; 125:1857-72. [PMID: 25822018 DOI: 10.1172/jci78752] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/09/2015] [Indexed: 12/22/2022] Open
Abstract
Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in genes encoding epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable, with few means to predict which patients will benefit. Here, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients who were responsive or resistant to decitabine (DAC) in order to develop a molecular means of predicting response at diagnosis. While somatic mutations did not differentiate responders from nonresponders, we identified 167 differentially methylated regions (DMRs) of DNA at baseline that distinguished responders from nonresponders using next-generation sequencing. These DMRs were primarily localized to nonpromoter regions and overlapped with distal regulatory enhancers. Using the methylation profiles, we developed an epigenetic classifier that accurately predicted DAC response at the time of diagnosis. Transcriptional analysis revealed differences in gene expression at diagnosis between responders and nonresponders. In responders, the upregulated genes included those that are associated with the cell cycle, potentially contributing to effective DAC incorporation. Treatment with CXCL4 and CXCL7, which were overexpressed in nonresponders, blocked DAC effects in isolated normal CD34+ and primary CMML cells, suggesting that their upregulation contributes to primary DAC resistance.
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MESH Headings
- Aged
- Aged, 80 and over
- Antimetabolites, Antineoplastic/pharmacology
- Antimetabolites, Antineoplastic/therapeutic use
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Azacitidine/therapeutic use
- Bone Marrow/pathology
- DNA Methylation/drug effects
- DNA Mutational Analysis
- DNA, Intergenic/genetics
- Decitabine
- Drug Resistance, Neoplasm/genetics
- Enhancer Elements, Genetic/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/genetics
- Genes, Neoplasm
- Humans
- Leukemia, Myelomonocytic, Chronic/drug therapy
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/metabolism
- Male
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Platelet Factor 4/biosynthesis
- Platelet Factor 4/genetics
- Platelet Factor 4/physiology
- Treatment Outcome
- beta-Thromboglobulin/biosynthesis
- beta-Thromboglobulin/genetics
- beta-Thromboglobulin/physiology
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32
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Germing U, Kobbe G, Haas R, Gattermann N. Myelodysplastic syndromes: diagnosis, prognosis, and treatment. DEUTSCHES ARZTEBLATT INTERNATIONAL 2015; 110:783-90. [PMID: 24300826 DOI: 10.3238/arztebl.2013.0783] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) are malignant stem-cell diseases that are usually diagnosed in elderly patients who present with anemia or, less commonly, bi- or pancytopenia. Their incidence in persons over age 80 is above 50 new cases per 100,000 persons per year. Their clinical course is highly variable. About one-quarter of all patients with MDS develop acute leukemia. The median survival time from the moment of diagnosis is about 30 months. METHOD We selectively searched the PubMed database for pertinent articles and guidelines from the years 2000-2013. We used the search term "myelodysplastic syndromes." RESULTS MDS are diagnosed by cytology, with consideration of the degree of dysplasia and the percentage of blast cells in the blood and bone marrow, and on a cytogenetic basis, as recommended in the WHO classification. In particular, chromosomal analysis is necessary for prognostication. The Revised International Prognosis Scoring System (IPSS-R) enables more accurate prediction of the course of disease by dividing patients into a number of low- and high-risk groups. The median survival time ranges from a few months to many years. The approved treatments, aside from transfusion therapy, include iron depletion therapy for low-risk patients, lenalidomide for low-risk patients with a deletion on the long arm of chromosome 5, and 5-azacytidine for high-risk patients. High-risk patients up to age 70 who have no major accompanying illnesses should be offered allogenic stem-cell transplantation with curative intent. The cure rates range from 30% to 50%. Mucositis, hemorrhages, infections, and graft-versus-host diseases are the most common complications of this form of treatment. CONCLUSION Myelodysplastic syndromes are treated on an individualized, risk-adapted basis after precise diagnostic evaluation and after assessment of the prognosis. More studies are needed so that stage-adapted treatment can be improved still further.
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Affiliation(s)
- Ulrich Germing
- Department of Haematology, Oncology and Clinical Immunology, Düsseldorf University Hospital
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Bruns I, Lucas D, Pinho S, Ahmed J, Lambert MP, Kunisaki Y, Scheiermann C, Schiff L, Poncz M, Bergman A, Frenette PS. Megakaryocytes regulate hematopoietic stem cell quiescence through CXCL4 secretion. Nat Med 2014; 20:1315-20. [PMID: 25326802 PMCID: PMC4258871 DOI: 10.1038/nm.3707] [Citation(s) in RCA: 417] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/28/2014] [Indexed: 12/14/2022]
Abstract
In the bone marrow (BM), hematopoietic stem cells (HSCs) lodge in specialized microenvironments that tightly control their proliferative state to adapt to the varying needs for replenishment of blood cells while also preventing exhaustion1. All putative niche cells suggested thus far have a non-hematopoietic origin2-8. Thus, it remains unclear how feedback from mature cells is conveyed to HSCs to adjust proliferation. Here we show that megakaryocytes (Mk) can directly regulate HSC pool size. Three-dimensional whole-mount imaging revealed that endogenous HSCs are frequently located adjacent to Mk in a non-random fashion. Selective in vivo depletion of Mk resulted in specific loss of HSC quiescence and led to a marked expansion of functional HSCs. Gene expression analyses revealed that Mk were the source of chemokine C-X-C motif ligand 4 (Cxcl4, also named platelet factor 4, Pf4) in the BM and Cxcl4 injection reduced HSC numbers via increased quiescence. By contrast, Cxcl4−/− mice exhibited increased HSC numbers and proliferation. Combined use of whole-mount imaging and computational modelling was highly suggestive of a megakaryocytic niche capable of influencing independently HSC maintenance by regulating quiescence. Thus, these results indicate that a terminally differentiated HSC progeny contributes to niche activity by directly regulating HSC behavior.
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Affiliation(s)
- Ingmar Bruns
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University, Düsseldorf, Germany. [3] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Daniel Lucas
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sandra Pinho
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jalal Ahmed
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA. [3] Mount Sinai School of Medicine, New York, New York, USA
| | - Michele P Lambert
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuya Kunisaki
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Christoph Scheiermann
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Lauren Schiff
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Mortimer Poncz
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Paul S Frenette
- 1] Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA. [3] Mount Sinai School of Medicine, New York, New York, USA. [4] Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
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Bai J, He A, Huang C, Yang J, Zhang W, Wang J, Yang Y, Zhang P, Zhang Y, Zhou F. Serum peptidome based biomarkers searching for monitoring minimal residual disease in adult acute lymphocytic leukemia. Proteome Sci 2014; 12:49. [PMID: 25317080 PMCID: PMC4195909 DOI: 10.1186/s12953-014-0049-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 09/08/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The persistence of minimal residual disease (MRD) during therapy is the strongest adverse prognostic factor in acute lymphocytic leukemia (ALL). This study was to identify serum candidate peptides for monitoring MRD in adult ALL. RESULTS A total of 33 peptides in the molecular weight range of 1000-10000 Da were detected using ClinProt system and statistically different between adult patients with ALL and healthy controls. Quick classifier (QC) algorithm was used to obtain a diagnostic model consisting of five peptides that could discriminate patients with ALL from controls with a high sensitivity (100%) and specificity (96.67%). The peptides in the QC model were identified as fibrinogen alpha chain (FGA), glutathione S-transferase P1 (GSTP1), isoform 1 of fibrinogen alpha chain precursor, platelet factor 4 (PF4) by high pressure/performance liquid chromatography mass spectrometry/mass spectrometry. Relative intensities of the five peptides were compared among ALL different groups for the potential importance of MRD evaluation in ALL. The peptides with increased relative intensities in newly diagnosed (ND) ALL patients were found to be decreased in their relative intensities after complete remission (CR) of adult ALL. When ALL patients were refractory & relapsed (RR), relative intensities of the peptides were elevated again. Peptides with decreased relative intensities in ND and RR ALL patients were found to be increased in their relative intensities when ALL patients achieved CR. The findings were validated by ELISA and western blot. Further linear regression analyses were performed to eliminate the influence of platelet and white blood cell counts on serum protein contents and indicated that there were no correlations between the contents of all four proteins (PF4, connective tissue active peptide III, FGA and GSTP1) and white blood cell or platelet counts in ALL different groups and healthy control. CONCLUSIONS We speculate the five peptides, FGA, isoform 1 of fibrinogen alpha chain precursor, GSTP1, PF4 and connective tissue active peptide III would be potential biomarkers for forecasting relapse, monitoring MRD and evaluating therapeutic response in adult ALL.
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Affiliation(s)
- Ju Bai
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Aili He
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Chen Huang
- />Department of Genetics and Molecular Biology, Medical school of Xi’an Jiaotong University/Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi’an, 710061 Shaanxi China
| | - Juan Yang
- />Department of Genetics and Molecular Biology, Medical school of Xi’an Jiaotong University/Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi’an, 710061 Shaanxi China
| | - Wanggang Zhang
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Jianli Wang
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Yun Yang
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Pengyu Zhang
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Yang Zhang
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
| | - Fuling Zhou
- />Department of Hematology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong University, Xi’an, 710004 Shaanxi Province China
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Grépin R, Guyot M, Giuliano S, Boncompagni M, Ambrosetti D, Chamorey E, Scoazec JY, Negrier S, Simonnet H, Pagès G. The CXCL7/CXCR1/2 axis is a key driver in the growth of clear cell renal cell carcinoma. Cancer Res 2013; 74:873-83. [PMID: 24335961 DOI: 10.1158/0008-5472.can-13-1267] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutations in the von Hippel-Lindau gene upregulate expression of the central angiogenic factor VEGF, which drives abnormal angiogenesis in clear cell renal cell carcinomas (ccRCC). However, the overexpression of VEGF in these tumors was not found to correlate with overall survival. Here, we show that the proangiogenic, proinflammatory cytokine CXCL7 is an independent prognostic factor for overall survival in this setting. CXCL7 antibodies strongly reduced the growth of ccRCC tumors in nude mice. Conversely, conditional overexpression of CXCL7 accelerated ccRCC development. CXCL7 promoted cell proliferation in vivo and in vitro, in which expression of CXCL7 was induced by the central proinflammatory cytokine interleukin (IL)-1β. ccRCC cells normally secrete low amounts of CXCL7; it was more highly expressed in tumors due to high levels of IL-1β there. We found that a pharmacological inhibitor of the CXCL7 receptors CXCR1 and CXCR2 (SB225002) was sufficient to inhibit endothelial cell proliferation and ccRCC growth. Because CXCR1 and CXCR2 are present on both endothelial and ccRCC cells, their inhibition affected both the tumor vasculature and the proliferation of tumor cells. Our results highlight the CXCL7/CXCR1/CXCR2 axis as a pertinent target for the treatment of ccRCC.
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MESH Headings
- Animals
- Antibodies, Monoclonal/pharmacology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/mortality
- Carcinoma, Renal Cell/pathology
- Cell Proliferation/drug effects
- Disease Models, Animal
- Female
- Gene Expression
- Gene Expression Regulation, Neoplastic
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Mice
- Neoplasm Grading
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Phenylurea Compounds/administration & dosage
- Phenylurea Compounds/pharmacology
- Prognosis
- Receptors, Interleukin-8A/antagonists & inhibitors
- Receptors, Interleukin-8A/genetics
- Receptors, Interleukin-8A/metabolism
- Receptors, Interleukin-8B/antagonists & inhibitors
- Receptors, Interleukin-8B/genetics
- Receptors, Interleukin-8B/metabolism
- Tumor Burden/drug effects
- Xenograft Model Antitumor Assays
- beta-Thromboglobulin/antagonists & inhibitors
- beta-Thromboglobulin/genetics
- beta-Thromboglobulin/metabolism
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Affiliation(s)
- Renaud Grépin
- Authors' Affiliations: University of Nice Sophia Antipolis, UMR CNRS 7284/U INSERM 1081; Department of Anatomo Pathology, Nice University Hospital, University of Nice Sophia Antipolis; Department of Statistics, Centre Antoine Lacassagne, Nice; University Lyon 1, Centre de Recherche en Cancérologie de Lyon, UMR CNRS 5286/U INSERM 1052, Lyon, France; and Centre Scientifique de Monaco, Monaco
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Bai J, He A, Zhang W, Huang C, Yang J, Yang Y, Wang J, Zhang Y. Potential biomarkers for adult acute myeloid leukemia minimal residual disease assessment searched by serum peptidome profiling. Proteome Sci 2013; 11:39. [PMID: 23915341 PMCID: PMC3751134 DOI: 10.1186/1477-5956-11-39] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/01/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Post treatment minimal residual disease (MRD) determination contributes to impending relapse prediction, chemotherapy response and clinical outcomes assessment, guiding clinicians to develop reasonable and effective individual chemotherapy options after induction/consolidation. This study was to identify serum candidate peptides for monitoring adult acute myeloid leukemia (AML) MRD. RESULTS 47 statistically different expressed peptide peaks were obtained in the molecular weight range of 700-10000 Da. Quick classifier (QC) model had optimal distinction efficiency, in the training set with a sensitivity of 90% and a specificity of 93.33%. Peptides were identified as ubiquitin-like modifier activating enzyme 1(UBA1), isoform 1 of fibrinogen alpha chain precursor and platelet factor 4(PF4). The peptide up-regulated in newly diagnosed AML patients were decreased to the normal level after CR. When refractory & relapsed, relative intensity was elevated again. Results were contrary to down-regulated peptide peaks. Western blot demonstrated that levels of the UBA1 protein did not differ between the leukemia and normal cells. Levels of isoform 1 of fibrinogen alpha chain precursor protein and PF4 protein were both decreased in leukemia cells comparing with normal cells. The serum levels of the PF4 in the newly diagnosed AML patients and healthy controls were significantly different. Further correlation analysis did not indicate the correlated relation between platelet counts and PF4 content, the correlation coefficient was 0.097. Kaplan-Meier analyses of overall survival showed that relative intensity of peptides was correlated with patient's clinical outcome. CONCLUSIONS We speculate the peptides can be used as potential markers for monitoring minimal residual disease and clinical outcome assessment.
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Affiliation(s)
- Ju Bai
- Department of Hematology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, PR China
| | - Aili He
- Department of Hematology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, PR China
| | - Wanggang Zhang
- Department of Hematology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, PR China
| | - Chen Huang
- Department of Genetics and Molecular Biology, Medical school of Xi'an Jiaotong University/Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, 76 Western Yanta Road, Xi'an, Shaanxi 710061, PR China
| | - Juan Yang
- Department of Genetics and Molecular Biology, Medical school of Xi'an Jiaotong University/Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, 76 Western Yanta Road, Xi'an, Shaanxi 710061, PR China
| | - Yun Yang
- Department of Hematology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, PR China
| | - Jianli Wang
- Department of Hematology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, PR China
| | - Yang Zhang
- Department of Hematology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, PR China
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Serum proteomics in biomedical research: a systematic review. Appl Biochem Biotechnol 2013; 170:774-86. [PMID: 23609910 DOI: 10.1007/s12010-013-0238-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 04/11/2013] [Indexed: 12/22/2022]
Abstract
Proteins that are important indicators of physiological or pathological states may contribute to the early diagnosis of disease, which may provide a basis for identifying the underlying mechanism of disease development. Serum, contains an abundance of proteins, offers an easy and inexpensive approach for disease detection and possesses a high potential to revolutionize the diagnostics. These differentially expressed proteins in serum have become an important role to monitoring the state for disease. Availability of emerging proteomic techniques gives optimism that serum can eventually be placed as a biomedium for clinical diagnostics. Advancements have benefited biomarker research to the point where serum is now recognized as an excellent diagnostic medium for the detection of disease. Comprehensive proteome of human serum fluid with high accuracy and availability has the potential to open new doors for disease biomarker discovery and for disease diagnostics, providing insights useful for future study. Thus, this review presents an overview of the value of serum as a credible diagnostic tool, and we aim to summarize the proteomic technologies currently used for global analysis of serum proteins and to elaborate on the application of serum proteomics to the discovery of disease biomarkers, and discuss some of the critical challenges and perspectives for this emerging field.
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38
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Májek P, Riedelová-Reicheltová Z, Suttnar J, Pečánková K, Cermák J, Dyr JE. Plasma proteome changes associated with refractory anemia and refractory anemia with ringed sideroblasts in patients with myelodysplastic syndrome. Proteome Sci 2013; 11:14. [PMID: 23566303 PMCID: PMC3635902 DOI: 10.1186/1477-5956-11-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 04/04/2013] [Indexed: 11/17/2022] Open
Abstract
Background Refractory anemia and refractory anemia with ringed sideroblasts are two myelodysplastic syndrome (MDS) subgroups linked with anemia. MDS is a group of heterogeneous oncohematological bone marrow disorders characterized by ineffective hematopoiesis, blood cytopenias, and progression of the disease toward acute myeloid leukemia. The aim of this study was to search for plasma proteome changes in MDS patients with refractory anemia and refractory anemia with ringed sideroblasts. Results A total of 26 patient and healthy donor plasma samples were depleted of fourteen high-abundant plasma proteins, separated with 2D electrophoresis, and statistically processed with Progenesis SameSpots software. 55 significantly differing spots were observed and corresponded to 39 different proteins identified by nanoLC-MS/MS. Changes in the fragments of the inter-alpha-trypsin inhibitor heavy chain H4 protein were observed. Using mass spectrometry-based relative label-free quantification of tryptic peptides, there were differences in alpha-2-HS-glycoprotein peptides, while no differences were observed between the control and patient sample groups for retinol-binding protein 4 peptides. Conclusions This study describes plasma proteome changes associated with MDS patients with refractory anemia and refractory anemia with ringed sideroblasts. Changes observed in the inter-alpha-trypsin inhibitor heavy chain H4 fragments were in agreement with our previous studies of other MDS subgroups: refractory cytopenia with multilineage dysplasia and refractory anemia with excess blasts subtype 1. Mass spectrometry-based relative quantification of retinol-binding protein 4 peptides has shown that there are differences in the modification of this protein between refractory anemia with excess blasts subtype 1 patients and MDS patients with refractory anemia and refractory anemia with ringed sideroblasts. Alpha-2-HS-glycoprotein seems to be a new potential MDS biomarker candidate.
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Affiliation(s)
- Pavel Májek
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, Prague 2, 128 20, Czech Republic.
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Li Y, Wu J, Zhang W, Zhang N, Guo H. Identification of serum CCL15 in hepatocellular carcinoma. Br J Cancer 2013; 108:99-106. [PMID: 23321514 PMCID: PMC3553511 DOI: 10.1038/bjc.2012.494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background: Early serum detection is of critical importance to improve the therapy for hepatocellular carcinoma (HCC), one of the most deadly cancers. Hepatitis infection is a leading cause of HCC. Methods: In the present study, we collected total serum samples with informed consent from 80 HCC patients with HBV (+)/cirrhosis (+), 80 patients with benign diseases (50 liver cirrhosis patients and 30 HBV-infected patients) and 60 healthy controls. Analysis was by using surface-enhanced laser desorption/ionisation-time-of-flight mass spectroscopy (SELDI-TOF-MS) to find new serum markers of HCC. SELDI peaks were isolated by SDS–PAGE, identified by LC-MS/MS and validated by immunohistochemistry (IHC) in liver tissues. Migration and invasion assay were performed to test the ability of cell migration and invasion in vitro. Results: SELDI-TOF-MS revealed a band at 7777 M/Z in the serum samples from HCC patients but not from healthy controls or patients with benign diseases. The protein (7777.27 M/Z) in the proteomic signature was identified as C-C motif chemokine 15 (CCL15) by peptide mass fingerprinting. A significant increase in serum CCL15 was detected in HCC patients. Functional analysis showed that HCC cell expressed CCL15, which in turn promoted HCC cell migration and invasion. Conclusion: CCL15 may be a specific proteomic biomarker of HCC, which has an important role in tumorigenesis and tumour invasion.
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Affiliation(s)
- Y Li
- Clinical laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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40
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Reikvam H, Fredly H, Kittang AO, Bruserud Ø. The possible diagnostic and prognostic use of systemic chemokine profiles in clinical medicine—the experience in acute myeloid leukemia from disease development and diagnosis via conventional chemotherapy to allogeneic stem cell transplantation. Toxins (Basel) 2013; 5:336-62. [PMID: 23430540 PMCID: PMC3640539 DOI: 10.3390/toxins5020336] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/05/2013] [Accepted: 02/06/2013] [Indexed: 12/29/2022] Open
Abstract
Chemokines are important regulators of many different biological processes, including (i) inflammation with activation and local recruitment of immunocompetent cells; (ii) angiogenesis as a part of inflammation or carcinogenesis; and (iii) as a bridge between the coagulation system and inflammation/immune activation. The systemic levels of various chemokines may therefore reflect local disease processes, and such variations may thereby be used in the routine clinical handling of patients. The experience from patients with myeloproliferative diseases, and especially patients with acute myeloid leukemia (AML), suggests that systemic plasma/serum cytokine profiles can be useful, both as a diagnostic tool and for prognostication of patients. However, cytokines/chemokines are released by a wide range of cells and are involved in a wide range of biological processes; the altered levels may therefore mainly reflect the strength and nature of the biological processes, and the optimal clinical use of chemokine/cytokine analyses may therefore require combination with organ-specific biomarkers. Chemokine levels are also altered by clinical procedures, therapeutic interventions and the general status of the patients. A careful standardization of sample collection is therefore important, and the interpretation of the observations will require that the overall clinical context is considered. Despite these limitations, we conclude that analysis of systemic chemokine/cytokine profiles can reflect important clinical characteristics and, therefore, is an important scientific tool that can be used as a part of future clinical studies to identify clinically relevant biomarkers.
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Affiliation(s)
- Håkon Reikvam
- Section for Hematology, Department of Medicine, Haukeland University Hospital, Bergen N-5021, Norway; E-Mails: (H.R.); (H.F.)
- Institute of Medicine, University of Bergen, Bergen N-5021, Norway; E-Mail:
| | - Hanne Fredly
- Section for Hematology, Department of Medicine, Haukeland University Hospital, Bergen N-5021, Norway; E-Mails: (H.R.); (H.F.)
- Institute of Medicine, University of Bergen, Bergen N-5021, Norway; E-Mail:
| | | | - Øystein Bruserud
- Section for Hematology, Department of Medicine, Haukeland University Hospital, Bergen N-5021, Norway; E-Mails: (H.R.); (H.F.)
- Institute of Medicine, University of Bergen, Bergen N-5021, Norway; E-Mail:
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Germing U, Kündgen A. Prognostic scoring systems in MDS. Leuk Res 2012; 36:1463-9. [PMID: 22980036 DOI: 10.1016/j.leukres.2012.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 07/30/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
Abstract
Prognostic scoring systems in myelodysplastic syndromes are useful tools in order to get in idea on the expected course of the disease and offer patients a risk adapted treatment. Several good scores have been developed, the international prognostic scoring system (IPSS) being the gold standard for 15 years, now validated and refined. As more and more patients receive therapy and drugs are approved, the major goal for future projects must be the identification of predictive parameters and scoring systems in order to predict the response and outcome after specific treatments.
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Affiliation(s)
- Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine-University of Duesseldorf, Duesseldorf, Germany.
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42
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MALDI-MS-Based Profiling of Serum Proteome: Detection of Changes Related to Progression of Cancer and Response to Anticancer Treatment. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:926427. [PMID: 22900176 PMCID: PMC3413974 DOI: 10.1155/2012/926427] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 06/12/2012] [Accepted: 06/12/2012] [Indexed: 01/25/2023]
Abstract
Mass spectrometry-based analyses of the low-molecular-weight fraction of serum proteome allow identifying proteome profiles (signatures) that are potentially useful in detection and classification of cancer. Several published studies have shown that multipeptide signatures selected in numerical tests have potential values for diagnostics of different types of cancer. However due to apparent problems with standardization of methodological details, both experimental and computational, none of the proposed peptide signatures analyzed directly by MALDI/SELDI-ToF spectrometry has been approved for routine diagnostics. Noteworthy, several components of proposed cancer signatures, especially those characteristic for advanced cancer, were identified as fragments of blood proteins involved in the acute phase and inflammatory response. This indicated that among cancer biomarker candidates to be possibly identified by serum proteome profiling were rather those reflecting overall influence of a disease (and the therapy) upon the human organism, than products of cancer-specific genes. Current paper focuses on changes in serum proteome that are related to response of patient's organism to progressing malignancy and toxicity of anticancer treatment. In addition, several methodological issues that affect robustness and interlaboratory reproducibility of MS-based serum proteome profiling are discussed.
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Luczak M, Kaźmierczak M, Handschuh L, Lewandowski K, Komarnicki M, Figlerowicz M. Comparative proteome analysis of acute myeloid leukemia with and without maturation. J Proteomics 2012; 75:5734-48. [PMID: 22850270 DOI: 10.1016/j.jprot.2012.07.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/02/2012] [Accepted: 07/20/2012] [Indexed: 01/18/2023]
Abstract
Acute myeloid leukemia (AML) is a severe, rapidly progressing disease triggered by blocking granulocyte or monocyte differentiation and maturation. Because of its heterogeneity, AML is divided into a number of subtypes. Unfortunately, so far very few correlations have been found between AML classification and its clinical course or patient response to treatment. In addition, as yet only a few subtype-specific AML biomarkers have been discovered. To solve these problems here, we focused on two AML subtypes M1 and M2 that are especially difficult to differentiate. Using 2D electrophoresis and mass spectrometry, we analyzed the protein profiles of peripheral blood (PB) and/or bone marrow (BM) samples collected from 38 AML-M1/M2 patients and 17 healthy volunteers. Comparative analysis of AML-M1/M2 and control PB/BM cells revealed 25 proteins that accumulated differentially. Hierarchical clustering of proteomic results clearly divided the AML samples into 2 groups (M1 and M2). Annexin III, L-plastin and 6-phosphogluconate dehydrogenase were found only in the M2 group. We also observed that the levels of annexin I and actin gamma 1 were correlated with resistance to treatment and the time of relapse. It appears that these five proteins can serve as potential AML biomarkers.
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Affiliation(s)
- Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Metallothionein deficiency in the injured peripheral nerves of complex regional pain syndrome as revealed by proteomics. Pain 2012; 153:532-539. [PMID: 22249007 DOI: 10.1016/j.pain.2011.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 10/05/2011] [Accepted: 11/07/2011] [Indexed: 12/24/2022]
Abstract
Complex regional pain syndrome (CRPS) is characterized by persistent and severe pain after trauma or surgery; however, its molecular mechanisms in the peripheral nervous system are poorly understood. Using proteomics, we investigated whether injured peripheral nerves of CRPS patients have altered protein profiles compared with control nerves. We obtained nerve samples from 3 patients with CRPS-2 who underwent resection of part of an injured peripheral nerve. Sural nerves from fresh cadavers with no history of trauma or neuropathic pain served as controls. Proteomic analysis showed that the number and functional distribution of proteins expressed in CRPS and control nerves was similar. Interestingly, metallothionein was absent in the injured nerves of CRPS-2, although it was readily detected in control nerves. Western blotting further confirmed the absence of metallothionein in CRPS-2 nerves, and immunohistochemistry corroborated the deficiency of metallothionein expression in injured nerves from 5 of 5 CRPS patients and 2 of 2 patients with painful neuromas. In contrast, all control nerves, including 5 sural nerves from fresh cadavers and 41 nerves obtained from surgically resected tumors, expressed MT. Furthermore, expression of S100 as a marker for Schwann cells, and neurofilament M as a marker of axons was comparable in both CRPS-2 and controls. Metallothioneins are zinc-binding proteins that are probably involved in protection against injury and subsequent regeneration after CNS damage. Their absence from the injured peripheral nerves of patients with CRPS-2 suggests a potential pathogenic role in generating pain in the damaged peripheral nerves.
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Comparative proteomics in acute myeloid leukemia. Contemp Oncol (Pozn) 2012; 16:95-103. [PMID: 23788862 PMCID: PMC3687393 DOI: 10.5114/wo.2012.28787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 07/25/2011] [Accepted: 02/13/2012] [Indexed: 01/22/2023] Open
Abstract
The term proteomics was used for the first time in 1995 to describe large-scale protein analyses. At the same time proteomics was distinguished as a new domain of the life sciences. The major object of proteomic studies is the proteome, i.e. the set of all proteins accumulating in a given cell, tissue or organ. During the last years several new methods and techniques have been developed to increase the fidelity and efficacy of proteomic analyses. The most widely used are two-dimensional electrophoresis (2DE) and mass spectrometry (MS). In the past decade proteomic analyses have also been successfully applied in biomedical research. They allow one to determine how various diseases affect the pattern of protein accumulation. In this paper, we attempt to summarize the results of the proteomic analyses of acute myeloid leukemia (AML) cells. They have increased our knowledge on the mechanisms underlying AML development and contributed to progress in AML diagnostics and treatment.
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Li X, LeBlanc J, Truong A, Vuthoori R, Chen SS, Lustgarten JL, Roth B, Allard J, Ippoliti A, Presley LL, Borneman J, Bigbee WL, Gopalakrishnan V, Graeber TG, Elashoff D, Braun J, Goodglick L. A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface. PLoS One 2011; 6:e26542. [PMID: 22132074 PMCID: PMC3221670 DOI: 10.1371/journal.pone.0026542] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 09/28/2011] [Indexed: 01/03/2023] Open
Abstract
Aberrant interactions between the host and the intestinal bacteria are thought to contribute to the pathogenesis of many digestive diseases. However, studying the complex ecosystem at the human mucosal-luminal interface (MLI) is challenging and requires an integrative systems biology approach. Therefore, we developed a novel method integrating lavage sampling of the human mucosal surface, high-throughput proteomics, and a unique suite of bioinformatic and statistical analyses. Shotgun proteomic analysis of secreted proteins recovered from the MLI confirmed the presence of both human and bacterial components. To profile the MLI metaproteome, we collected 205 mucosal lavage samples from 38 healthy subjects, and subjected them to high-throughput proteomics. The spectral data were subjected to a rigorous data processing pipeline to optimize suitability for quantitation and analysis, and then were evaluated using a set of biostatistical tools. Compared to the mucosal transcriptome, the MLI metaproteome was enriched for extracellular proteins involved in response to stimulus and immune system processes. Analysis of the metaproteome revealed significant individual-related as well as anatomic region-related (biogeographic) features. Quantitative shotgun proteomics established the identity and confirmed the biogeographic association of 49 proteins (including 3 functional protein networks) demarcating the proximal and distal colon. This robust and integrated proteomic approach is thus effective for identifying functional features of the human mucosal ecosystem, and a fresh understanding of the basic biology and disease processes at the MLI.
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Affiliation(s)
- Xiaoxiao Li
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - James LeBlanc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Allison Truong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Ravi Vuthoori
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Sharon S. Chen
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Jonathan L. Lustgarten
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bennett Roth
- Department of Medicine, Division of Digestive Disease, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Jeff Allard
- Department of Medicine, Division of Digestive Disease, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Andrew Ippoliti
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Laura L. Presley
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - William L. Bigbee
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Vanathi Gopalakrishnan
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Thomas G. Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - David Elashoff
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
| | - Jonathan Braun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (JB); (LG)
| | - Lee Goodglick
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (JB); (LG)
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Májek P, Reicheltová Z, Suttnar J, Cermák J, Dyr JE. Plasma proteome changes associated with refractory cytopenia with multilineage dysplasia. Proteome Sci 2011; 9:64. [PMID: 21975265 PMCID: PMC3192726 DOI: 10.1186/1477-5956-9-64] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 10/05/2011] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Refractory cytopenia with multilineage dysplasia (RCMD) is a subgroup of myelodysplastic syndrome (MDS), which belongs to oncohematological diseases, occurring particularly in elderly patients, and represents a heterogeneous group of bone marrow diseases. The goal of this study was to look for plasma proteins that changed quantitatively or qualitatively in RCMD patients. RESULTS A total of 46 plasma samples were depleted, proteins were separated by 2D SDS-PAGE (pI 4-7), and proteomes were compared using Progenesis SameSpots statistical software. Proteins were identified by nanoLC-MS/MS. Sixty-one unique, significantly (p < 0.05, ANOVA) different spots were found; proteins in 59 spots were successfully identified and corresponded to 57 different proteins. Protein fragmentation was observed in several proteins: complement C4-A, complement C4-B, inter-alpha-trypsin inhibitor heavy chain H4, and endorepellin. CONCLUSIONS This study describes proteins, which change quantitatively or qualitatively in RCMD patients, and represents the first report on significant alterations in C4-A and C4-B complement proteins and ITIH4 fragments in patients with MDS-RCMD.
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Affiliation(s)
- Pavel Májek
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Castaldi PJ, Dahabreh IJ, Ioannidis JPA. An empirical assessment of validation practices for molecular classifiers. Brief Bioinform 2011; 12:189-202. [PMID: 21300697 PMCID: PMC3088312 DOI: 10.1093/bib/bbq073] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/02/2010] [Indexed: 12/12/2022] Open
Abstract
Proposed molecular classifiers may be overfit to idiosyncrasies of noisy genomic and proteomic data. Cross-validation methods are often used to obtain estimates of classification accuracy, but both simulations and case studies suggest that, when inappropriate methods are used, bias may ensue. Bias can be bypassed and generalizability can be tested by external (independent) validation. We evaluated 35 studies that have reported on external validation of a molecular classifier. We extracted information on study design and methodological features, and compared the performance of molecular classifiers in internal cross-validation versus external validation for 28 studies where both had been performed. We demonstrate that the majority of studies pursued cross-validation practices that are likely to overestimate classifier performance. Most studies were markedly underpowered to detect a 20% decrease in sensitivity or specificity between internal cross-validation and external validation [median power was 36% (IQR, 21-61%) and 29% (IQR, 15-65%), respectively]. The median reported classification performance for sensitivity and specificity was 94% and 98%, respectively, in cross-validation and 88% and 81% for independent validation. The relative diagnostic odds ratio was 3.26 (95% CI 2.04-5.21) for cross-validation versus independent validation. Finally, we reviewed all studies (n = 758) which cited those in our study sample, and identified only one instance of additional subsequent independent validation of these classifiers. In conclusion, these results document that many cross-validation practices employed in the literature are potentially biased and genuine progress in this field will require adoption of routine external validation of molecular classifiers, preferably in much larger studies than in current practice.
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Affiliation(s)
- Peter J Castaldi
- Institute for Clinical Research and Health Policy Studies at Tufts Medical Center, USA
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Matsubara J, Honda K, Ono M, Tanaka Y, Kobayashi M, Jung G, Yanagisawa K, Sakuma T, Nakamori S, Sata N, Nagai H, Ioka T, Okusaka T, Kosuge T, Tsuchida A, Shimahara M, Yasunami Y, Chiba T, Hirohashi S, Yamada T. Reduced plasma level of CXC chemokine ligand 7 in patients with pancreatic cancer. Cancer Epidemiol Biomarkers Prev 2010; 20:160-71. [PMID: 21148121 DOI: 10.1158/1055-9965.epi-10-0397] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Early detection is essential to improve the outcome of patients with pancreatic cancer. A noninvasive and cost-effective diagnostic test using plasma/serum biomarkers would facilitate the detection of pancreatic cancer at the early stage. METHODS Using a novel combination of hollow fiber membrane-based low-molecular-weight protein enrichment and LC-MS-based quantitative shotgun proteomics, we compared the plasma proteome between 24 patients with pancreatic cancer and 21 healthy controls (training cohort). An identified biomarker candidate was then subjected to a large blinded independent validation (n = 237, validation cohort) using a high-density reverse-phase protein microarray. RESULTS Among a total of 53,009 MS peaks, we identified a peptide derived from CXC chemokine ligand 7 (CXCL7) that was significantly reduced in pancreatic cancer patients, showing an area under curve (AUC) value of 0.84 and a P value of 0.00005 (Mann-Whitney U test). Reduction of the CXCL7 protein was consistently observed in pancreatic cancer patients including those with stage I and II disease in the validation cohort (P < 0.0001). The plasma level of CXCL7 was independent from that of CA19-9 (Pearson's r = 0.289), and combination with CXCL7 significantly improved the AUC value of CA19-9 to 0.961 (P = 0.002). CONCLUSIONS We identified a significant decrease of the plasma CXCL7 level in patients with pancreatic cancer, and combination of CA19-9 with CXCL7 improved the discriminatory power of the former for pancreatic cancer. IMPACT The present findings may provide a new diagnostic option for pancreatic cancer and facilitate early detection of the disease.
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Affiliation(s)
- Junichi Matsubara
- Chemotherapy Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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