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Skelton WP, Masur J, Thomas J, Fallah P, Jain RK, Ravi P, Mantia C, McGregor BA, Nuzzo PV, Adib E, Zarif TE, Preston MA, Clinton TN, Li R, Steele GS, Kassouf W, Freeman D, Pond GR, Jain RK, Sonpavde GP. Impact of Angiotensin Converting Enzyme Inhibitors on Pathologic Complete Response With Neoadjuvant Chemotherapy for Muscle Invasive Bladder Cancer. Clin Genitourin Cancer 2024; 22:102143. [PMID: 39032202 DOI: 10.1016/j.clgc.2024.102143] [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: 04/29/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 07/22/2024]
Abstract
INTRODUCTION The renin-angiotensin system (RAS) has been demonstrated to modulate cell proliferation, desmoplasia, angiogenesis and immunosuppression. We examined the association of RAS inhibitors (RASi)-namely angiotensin converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARB)-with neoadjuvant chemotherapy (NAC) for muscle-invasive bladder cancer (MIBC) preceding radical cystectomy (RC). PATIENTS AND METHODS We retrospectively investigated concurrent RASi use with NAC prior to RC in 302 patients with MIBC from 3 academic institutions. Outcomes included pathologic complete response (pCR) and overall survival (OS). Pathologic features, performance status (PS), clinical stage, type/number of cycles of NAC, and toxicities were collected. RESULTS Overall pCR rate was 26.2% and 5-year OS was 62%. Concurrent ACEi intake with NAC approached significance for association with pCR (odds ratio [OR] = 1.71; 95% CI, 0.94-3.11; P = .077). Patients with cT3/4N0-N1 disease receiving ACEi had higher pCR rates (30.8% vs. 17.7%, P = .056) than those not on ACEi. Female sex had a statistically significant favorable interaction for pCR with ACEi intake (P = .044). ACEi intake was not associated with OS, while pCR, PS and lower clinical stage were significantly associated with improved OS. CONCLUSION ACEi intake is potentially associated with increased pCR in patients with MIBC receiving NAC prior to RC, and this association is more pronounced in patients with higher clinical stage of disease at the initiation of therapy and female sex. Our data suggest the potential relevance of the RAS as a therapeutic target in aggressive MIBC.
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Affiliation(s)
- William Paul Skelton
- University of Virginia Comprehensive Cancer Center, Department of Oncology, Charlottesville, VA; H. Lee Moffitt Cancer Center and Research Institute, Department of Oncology, Tampa, FL
| | - Jack Masur
- University of Virginia Comprehensive Cancer Center, Department of Oncology, Charlottesville, VA
| | - Jonathan Thomas
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA
| | - Parvaneh Fallah
- McGill University, Department of Oncology, Montreal, Quebec, Canada
| | - Rohit K Jain
- H. Lee Moffitt Cancer Center and Research Institute, Department of Oncology, Tampa, FL
| | - Praful Ravi
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA
| | - Charlene Mantia
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA
| | | | | | - Elio Adib
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA
| | - Talal El Zarif
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA
| | - Mark A Preston
- Brigham and Women's Hospital, Department of Oncology, Boston, MA
| | | | - Roger Li
- H. Lee Moffitt Cancer Center and Research Institute, Department of Oncology, Tampa, FL
| | - Graeme S Steele
- Brigham and Women's Hospital, Department of Oncology, Boston, MA
| | - Wassim Kassouf
- McGill University, Department of Oncology, Montreal, Quebec, Canada
| | - Dory Freeman
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA
| | | | - Rakesh K Jain
- Massachusetts General Hospital, Department of Oncology, Boston, MA
| | - Guru P Sonpavde
- Dana-Farber Cancer Institute, Department of Oncology, Boston, MA; AdventHealth Cancer Institute and the University of Central Florida, Department of Oncology, Orlando, FL.
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Li Z, Chen J, Xu B, Zhao W, Zha H, Han Y, Shen W, Dong Y, Zhao N, Zhang M, He K, Li Z, Liu X. Correlation between small-cell lung cancer serum protein/peptides determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and chemotherapy efficacy. Clin Proteomics 2024; 21:35. [PMID: 38764042 PMCID: PMC11103996 DOI: 10.1186/s12014-024-09483-8] [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: 12/13/2023] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Currently, no effective measures are available to predict the curative efficacy of small-cell lung cancer (SCLC) chemotherapy. We expect to develop a method for effectively predicting the SCLC chemotherapy efficacy and prognosis in clinical practice in order to offer more pertinent therapeutic protocols for individual patients. METHODS We adopted matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and ClinPro Tools system to detect serum samples from 154 SCLC patients with different curative efficacy of standard chemotherapy and analyze the different peptides/proteins of SCLC patients to discover predictive tumor markers related to chemotherapy efficacy. Ten peptide/protein peaks were significantly different in the two groups. RESULTS A genetic algorithm model consisting of four peptides/proteins was developed from the training group to separate patients with different chemotherapy efficacies. Among them, three peptides/proteins (m/z 3323.35, 6649.03 and 6451.08) showed high expression in the disease progression group, whereas the peptide/protein at m/z 4283.18 was highly expressed in the disease response group. The classifier exhibited an accuracy of 91.4% (53/58) in the validation group. The survival analysis showed that the median progression-free survival (PFS) of 30 SCLC patients in disease response group was 9.0 months; in 28 cases in disease progression group, the median PFS was 3.0 months, a statistically significant difference (χ2 = 46.98, P < 0.001). The median overall survival (OS) of the two groups was 13.0 months and 7.0 months, a statistically significant difference (χ2 = 40.64, P < 0.001). CONCLUSIONS These peptides/proteins may be used as potential biological markers for prediction of the curative efficacy and prognosis for SCLC patients treated with standard regimen chemotherapy.
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Affiliation(s)
- Zhihua Li
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Junnan Chen
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Bin Xu
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Wei Zhao
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Haoran Zha
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Yalin Han
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Wennan Shen
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Yuemei Dong
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Nan Zhao
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Manze Zhang
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China
| | - Kun He
- National Center of Biomedical Analysis, Beijing, 100850, China
| | - Zhaoxia Li
- Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing, 100088, China.
| | - Xiaoqing Liu
- Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, 100071, China.
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A Circulating Risk Score, Based on Combined Expression of Exo-miR-130a-3p and Fibrinopeptide A, as Predictive Biomarker of Relapse in Resectable Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2022; 14:cancers14143412. [PMID: 35884472 PMCID: PMC9317031 DOI: 10.3390/cancers14143412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary To date, the five-year survival rate of early stages of non-small cell lung cancer (NSCLC) is still disappointing and reliable prognostic factors are mandatory. Here, we performed in-depth high-throughput analyses of plasma circulating markers, including exosomal microRNAs and peptidome to identify a prognostic score. The miRnome profile selected the Exo-miR-130a-3p as the most overexpressed in relapsed patients. Peptidome analysis identified four progressively more degraded forms of fibrinopeptide A (FpA), which were depleted in relapse patients. Notably, a stepwise algorithm selected Exo-miR-130a-3p and the greatest FpA (2–16) to build a prognostic score, where high-risk patients had 18 months of median disease-free survival. Overexpression of miR-130a-3p cells led to a deregulation of pathways such as angiogenesis as well as the coagulation and metalloprotease, which might be linked to FpA reduction. The risk score integrating circulating markers may help clinicians predict early-stage NSCLC patients who are more likely to relapse after surgery. Abstract To date, the 5-year overall survival rate of 60% for early-stage non-small cell lung cancer (NSCLC) is still unsatisfactory. Therefore, reliable prognostic factors are needed. Growing evidence shows that cancer progression may depend on an interconnection between cancer cells and the surrounding tumor microenvironment; hence, circulating molecules may represent promising markers of cancer recurrence. In order to identify a prognostic score, we performed in-depth high-throughput analyses of plasma circulating markers, including exosomal microRNAs (Exo-miR) and peptides, in 67 radically resected NSCLCs. The miRnome profile selected the Exo-miR-130a-3p as the most overexpressed in relapsed patients. Peptidome analysis identified four progressively more degraded forms of fibrinopeptide A (FpA), which were depleted in progressing patients. Notably, stepwise Cox regression analysis selected Exo-miR-130a-3p and the greatest FpA (2-16) to build a score predictive of recurrence, where high-risk patients had 18 months of median disease-free survival. Moreover, in vitro transfections showed that higher levels of miR-130a-3p lead to a deregulation of pathways involved in metastasis and angiogenesis, including the coagulation process and metalloprotease increase which might be linked to FpA reduction. In conclusion, by integrating circulating markers, the identified risk score may help clinicians predict early-stage NSCLC patients who are more likely to relapse after primary surgery.
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Breast cancer in the era of integrating “Omics” approaches. Oncogenesis 2022; 11:17. [PMID: 35422484 PMCID: PMC9010455 DOI: 10.1038/s41389-022-00393-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Worldwide, breast cancer is the leading cause of cancer-related deaths in women. Breast cancer is a heterogeneous disease characterized by different clinical outcomes in terms of pathological features, response to therapies, and long-term patient survival. Thus, the heterogeneity found in this cancer led to the concept that breast cancer is not a single disease, being very heterogeneous both at the molecular and clinical level, and rather represents a group of distinct neoplastic diseases of the breast and its cells. Indubitably, in the past decades we witnessed a significant development of innovative therapeutic approaches, including targeted and immunotherapies, leading to impressive results in terms of increased survival for breast cancer patients. However, these multimodal treatments fail to prevent recurrence and metastasis. Therefore, it is urgent to improve our understanding of breast tumor and metastasis biology. Over the past few years, high-throughput “omics” technologies through the identification of novel biomarkers and molecular profiling have shown their great potential in generating new insights in the study of breast cancer, also improving diagnosis, prognosis and prediction of response to treatment. In this review, we discuss how the implementation of “omics” strategies and their integration may lead to a better comprehension of the mechanisms underlying breast cancer. In particular, with the aim to investigate the correlation between different “omics” datasets and to define the new important key pathway and upstream regulators in breast cancer, we applied a new integrative meta-analysis method to combine the results obtained from genomics, proteomics and metabolomics approaches in different revised studies.
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Lo CWS, Tsui TKC, Ma RCW, Chan MHM, Ho CS. Quantitation of plasma angiotensin II in healthy Chinese subjects by a validated liquid chromatography tandem mass spectrometry method. Biomed Chromatogr 2022; 36:e5318. [PMID: 34981551 DOI: 10.1002/bmc.5318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/06/2022]
Abstract
INTRODUCTION Quantitation of plasma angiotensin (Ang) II, the active mediator of the renin-angiotensin system (RAS), is challenging due to its low physiological concentration. We report a validated liquid chromatography-mass spectrometry (LCMS) method to overcome this challenge. METHOD Ang II was extracted from EDTA plasma by an offline solid-phase extraction procedure with Waters MAX μElution plate. LCMS quantitation was performed on the Waters TQS system, monitoring the 3+ ions of the peptide. The analytical performance of the LCMS method was validated. The stability of Ang II was studied with or without the presence of a protease inhibitor. Local reference intervals were established from 143 healthy normotensive subjects (57% female, 21-60 years old). RESULTS The Ang II LCMS method had a measurable range of 3.3 - 700 pmol/L. Between batch precision coefficient of variation was <7% over the Ang II concentrations of 8.6 - 110 pmol/L. No significant matrix interference and carryover was observed. There was no significant difference in Ang II concentration in EDTA blood and plasma for at least 2 hours and 1 hour at room temperature, respectively. Ang II was stable for at least one year when stored at -80 o C, with or without the protease inhibitor. Age-dependent Ang II reference intervals were established: 4.4-17.7 pmol/L (21-30 years) and 3.9-12.8 pmol/L (31-60 years). CONCLUSION The present LCMS method is suitable for quantitation of Ang II to study the RAS system. Ang II collected at room temperature into EDTA bottles was stable at -80 o C for at least 1 year. The first age-dependent reference intervals of plasma Ang II were established for a healthy normotensive Chinese population.
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Affiliation(s)
- Clara Wai-Shan Lo
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Statin, NT, Hong Kong
| | - Teresa Kam-Chi Tsui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Statin, NT, Hong Kong
| | - Ronald Ching-Wan Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong
| | - Michael Ho-Ming Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Statin, NT, Hong Kong
| | - Chung-Shun Ho
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Statin, NT, Hong Kong
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Del Prete E, Facchiano A, Profumo A, Angelini C, Romano P. GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis. Front Genet 2021; 12:635814. [PMID: 33854526 PMCID: PMC8039533 DOI: 10.3389/fgene.2021.635814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such as the identification of cancer biomarkers, the detection of food frauds, the identification of doping substances in athletes’ fluids, and so on. The massive quantity of data, in the form of mass spectra, are often biased and altered by different sources of noise. Therefore, extracting the most relevant features that characterize the samples is often challenging and requires combining several computational methods. Here, we present GeenaR, a novel web tool that provides a complete workflow for pre-processing, analyzing, visualizing, and comparing MALDI-TOF mass spectra. GeenaR is user-friendly, provides many different functionalities for the analysis of the mass spectra, and supports reproducible research since it produces a human-readable report that contains function parameters, results, and the code used for processing the mass spectra. First, we illustrate the features available in GeenaR. Then, we describe its internal structure. Finally, we prove its capabilities in analyzing oncological datasets by presenting two case studies related to ovarian cancer and colorectal cancer. GeenaR is available at http://proteomics.hsanmartino.it/geenar/.
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Affiliation(s)
- Eugenio Del Prete
- Institute for Applied Mathematics, National Research Council, Naples, Italy
| | - Angelo Facchiano
- Institute of Food Sciences, National Research Council, Avellino, Italy
| | - Aldo Profumo
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino IST, Genova, Italy
| | - Claudia Angelini
- Institute for Applied Mathematics, National Research Council, Naples, Italy
| | - Paolo Romano
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino IST, Genova, Italy
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Almutlaq M, Alamro AA, Alamri HS, Alghamdi AA, Barhoumi T. The Effect of Local Renin Angiotensin System in the Common Types of Cancer. Front Endocrinol (Lausanne) 2021; 12:736361. [PMID: 34539580 PMCID: PMC8446618 DOI: 10.3389/fendo.2021.736361] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
The Renin Angiotensin System (RAS) is a hormonal system that is responsible for blood pressure hemostasis and electrolyte balance. It is implicated in cancer hallmarks because it is expressed locally in almost all of the body's tissues. In this review, current knowledge on the effect of local RAS in the common types of cancer such as breast, lung, liver, prostate and skin cancer is summarised. The mechanisms by which RAS components could increase or decrease cancer activity are also discussed. In addition to the former, this review explores how the administration of AT1R blockers and ACE inhibitors drugs intervene with cancer therapy and contribute to the outcomes of cancer.
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Affiliation(s)
- Moudhi Almutlaq
- King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- *Correspondence: Moudhi Almutlaq, ; Tlili Barhoumi,
| | - Abir Abdullah Alamro
- Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hassan S. Alamri
- King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Medical Research Core Facility and Platforms, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Amani Ahmed Alghamdi
- Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Tlili Barhoumi
- King Abdullah International Medical Research Centre, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Medical Research Core Facility and Platforms, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- *Correspondence: Moudhi Almutlaq, ; Tlili Barhoumi,
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The Activation of Prothrombin Seems to Play an Earlier Role than the Complement System in the Progression of Colorectal Cancer: A Mass Spectrometry Evaluation. Diagnostics (Basel) 2020; 10:diagnostics10121077. [PMID: 33322644 PMCID: PMC7763171 DOI: 10.3390/diagnostics10121077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/13/2023] Open
Abstract
Colorectal cancer (CRC) is the second cause of death in men and the third in women. This work deals with the study of the low molecular weight protein fraction of sera from patients who underwent surgery for CRC and who were followed for several years thereafter. MALDI-TOF MS was used to identify serum peptidome profiles of healthy controls, non-metastatic CRC patients and metastatic CRC patients. A multiple regression model was applied to signals preliminarily selected by SAM analysis to take into account the age and gender differences between the groups. We found that, while a signal m/z 2021.08, corresponding to the C3f fragment of the complement system, appears significantly increased only in serum from metastatic CRC patients, a m/z 1561.72 signal, identified as a prothrombin fragment, has a significantly increased abundance in serum from non-metastatic patients as well. The findings were also validated by a bootstrap resampling procedure. The present results provide the basis for further studies on large cohorts of patients in order to confirm C3f and prothrombin as potential serum biomarkers. Thus, new and non-invasive tests might be developed to improve the classification of colorectal cancer.
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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Romano P, Profumo A, Facchiano A. Pre-Processing MALDI/TOF Mass Spectra by Using Geena 2. ACTA ACUST UNITED AC 2018; 64:e59. [PMID: 30422396 DOI: 10.1002/cpbi.59] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Geena 2 is a tool for filtering, averaging, and aligning MALDI/TOF mass spectra, designed to assist scientists in the analysis of high volumes of data and support them for comparative studies. Three web interfaces are available with different levels of complexity. In this manuscript, we explain how to use Geena 2 with these three interfaces to perform analyses of one's own data. Two support protocols showing how to check the example input file and how to create an input file with own data are also presented. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- P Romano
- Ospedale Policlinico San Martino, Ospedale Policlinico San Martino, Genoa, Italy
| | - A Profumo
- Ospedale Policlinico San Martino, Ospedale Policlinico San Martino, Genoa, Italy
| | - A Facchiano
- CNR-Istituto di Scienze dell'Alimentazione, Avellino, Italy
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Romano P, Beitia San Vicente M, Profumo A. A mass spectrometry based method and a software tool to assess degradation status of serum samples to be used in proteomics for biomarker discovery. J Proteomics 2017; 173:99-106. [PMID: 29242081 DOI: 10.1016/j.jprot.2017.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/09/2017] [Accepted: 12/05/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Paolo Romano
- Biopolymers and Proteomics Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | | | - Aldo Profumo
- Biopolymers and Proteomics Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Chen WY, Zhang XY, Liu T, Liu Y, Zhao YS, Pang D. Chromobox homolog 2 protein: A novel biomarker for predicting prognosis and Taxol sensitivity in patients with breast cancer. Oncol Lett 2016; 13:1149-1156. [PMID: 28454227 PMCID: PMC5403172 DOI: 10.3892/ol.2016.5529] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Polycomb group (PcG) complexes modify histones to silence tumor suppressor genes, which exhibit an important function in tumorigenesis and progression. The chromobox (Cbx) protein family is a critical component of PcG-mediated repression. Cbx2, a member of the Cbx protein family, is hypothesized to exhibit a vital role in breast cancer. In the present study, immunohistochemical analysis using tissue microarrays was performed to determine the levels of Cbx2 protein expression in breast cancer. The association between Cbx2 expression and the clinical features and prognosis of 455 breast cancer patients was analyzed. In addition, the efficacy of Taxol was evaluated by comparing the survival of patients with high or low Cbx2 expression. The results revealed that Cbx2 expression was higher in cancer tissues compared with adjacent normal tissues. Furthermore, high Cbx2 expression was significantly associated with large tumor size, lymph node metastasis, high TNM stage and positive human epidermal growth factor receptor-2 (HER-2) status. Patients with high Cbx2 expression also exhibited a shorter mean overall survival (OS) time (74.37 months) compared with patients with low Cbx2 expression (77.37 months). Univariate analysis indicated that high Cbx2 expression increased the risk of mortality by 1.826-fold compared with low Cbx2 expression [hazard ratio (HR), 1.826; 95% confidence interval (CI), 1.069–3.116; P=0.027]. Among patients with high Cbx2 expression, the mean OS time of individuals treated with Taxol (71.01 months) was lower compared with patients that had not received Taxol treatment (78.43 months; log-rank test statistic, 13.03; P<0.001). However, no significant difference in OS time was identified in the low expression group. The results of the current study revealed that Cbx2 may present a novel biomarker for predicting the prognosis of breast cancer patients. Cbx2 may also represent a potential target for treatment due to its important function in Taxol treatment responses.
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Affiliation(s)
- Wang Yang Chen
- Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150044, P.R. China.,Department of Cancer Epidemiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xian Yu Zhang
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Tong Liu
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yang Liu
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Ya Shuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Da Pang
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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HONG XY, LI SM, WANG Y. Analysis of Urine Peptidome and Post-translation Modifications by Nano Liquid Chromatography-High Resolution Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60931-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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14
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Challenges in biomarker discovery with MALDI-TOF MS. Clin Chim Acta 2016; 458:84-98. [PMID: 27134187 DOI: 10.1016/j.cca.2016.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Abstract
MALDI-TOF MS technique is commonly used in system biology and clinical studies to search for new potential markers associated with pathological conditions. Despite numerous concerns regarding a sample preparation or processing of complex data, this strategy is still recognized as a popular tool and its awareness has risen in the proteomic community over the last decade. In this review, we present comprehensive application of MALDI mass spectrometry with special focus on profiling research. We also discuss major advantages and disadvantages of universal sample preparation methods such as micro-SPE columns, immunodepletion or magnetic beads, and we show the potential of nanostructured materials in capturing low molecular weight subproteomes. Furthermore, as the general protocol considerably affects spectra quality and interpretation, an alternative solution for improved ion detection, including hydrophobic constituents, data processing and statistical analysis is being considered in up-to-date profiling pattern. In conclusion, many reports involving MALDI-TOF MS indicated highly abundant proteins as valuable indicators, and at the same time showed the inaccuracy of available methods in the detection of low abundant proteome that is the most interesting from the clinical perspective. Therefore, the analytical aspects of sample preparation methods should be standardized to provide a reproducible, low sample handling and credible procedure.
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Romano P, Profumo A, Rocco M, Mangerini R, Ferri F, Facchiano A. Geena 2, improved automated analysis of MALDI/TOF mass spectra. BMC Bioinformatics 2016; 17 Suppl 4:61. [PMID: 26961516 PMCID: PMC4896264 DOI: 10.1186/s12859-016-0911-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Results Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Conclusions Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0911-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Fabio Ferri
- Dipartimento di Scienza e Alta Tecnologia and To.Sca.Lab, Università dell'Insubria, Como, Italy.
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