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Yang K, Li X, Xie K. Senescence program and its reprogramming in pancreatic premalignancy. Cell Death Dis 2023; 14:528. [PMID: 37591827 PMCID: PMC10435572 DOI: 10.1038/s41419-023-06040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Tumor is a representative of cell immortalization, while senescence irreversibly arrests cell proliferation. Although tumorigenesis and senescence seem contrary to each other, they have similar mechanisms in many aspects. Pancreatic ductal adenocarcinoma (PDA) is highly lethal disease, which occurs and progresses through a multi-step process. Senescence is prevalent in pancreatic premalignancy, as manifested by decreased cell proliferation and increased clearance of pre-malignant cells by immune system. However, the senescent microenvironment cooperates with multiple factors and significantly contributes to tumorigenesis. Evidently, PDA progression requires to evade the effects of cellular senescence. This review will focus on dual roles that senescence plays in PDA development and progression, the signaling effectors that critically regulate senescence in PDA, the identification and reactivation of molecular targets that control senescence program for the treatment of PDA.
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Affiliation(s)
- Kailing Yang
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
| | - Xiaojia Li
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China.
- The South China University of Technology Comprehensive Cancer Center, Guangdong, China.
- The Second Affiliated Hospital and Guangzhou First People's Hospital, South China University of Technology School of Medicine, Guangdong, China.
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2
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Baldan-Martin M, Chaparro M, Gisbert JP. Systematic Review: Urine Biomarker Discovery for Inflammatory Bowel Disease Diagnosis. Int J Mol Sci 2023; 24:10159. [PMID: 37373307 DOI: 10.3390/ijms241210159] [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: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic, heterogeneous, and inflammatory conditions mainly affecting the gastrointestinal tract. Currently, endoscopy is the gold standard test for assessing mucosal activity and healing in clinical practice; however, it is a costly, time-consuming, invasive, and uncomfortable procedure for the patients. Therefore, there is an urgent need for sensitive, specific, fast and non-invasive biomarkers for the diagnosis of IBD in medical research. Urine is an excellent biofluid for discovering biomarkers because it is non-invasive to sample. In this review, we aimed to summarize proteomics and metabolomics studies performed in both animal models of IBD and humans that identify urinary biomarkers for IBD diagnosis. Future large-scale multi-omics studies should be conducted in collaboration with clinicians, researchers, and industry to make progress toward the development of sensitive and specific diagnostic biomarkers, thereby making personalized medicine possible.
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Affiliation(s)
- Montse Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
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3
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Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study. Cancers (Basel) 2022; 14:cancers14082001. [PMID: 35454907 PMCID: PMC9031064 DOI: 10.3390/cancers14082001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is one of the most common cancers. Due to the limited and invasive approaches for PCa diagnosis, it is crucial to identify more accurate and non-invasive biomarkers for its detection. The aim of our study was to non-invasively uncover new protein targets for detecting PCa using a proteomics and proteogenomics approach. This work identified several dysregulated mutant protein isoforms in urine from PCa patients, some of them predicted to have a protective or an adverse role in these patients. These results are promising given urine’s non-invasive nature and offers an auspicious opportunity for research and development of PCa biomarkers. Abstract To identify new protein targets for PCa detection, first, a shotgun discovery experiment was performed to characterize the urinary proteome of PCa patients. This revealed 18 differentially abundant urinary proteins in PCa patients. Second, selected targets were clinically tested by immunoblot, and the soluble E-cadherin fragment was detected for the first time in the urine of PCa patients. Third, the proteogenome landscape of these PCa patients was characterized, revealing 1665 mutant protein isoforms. Statistical analysis revealed 6 differentially abundant mutant protein isoforms in PCa patients. Analysis of the likely effects of mutations on protein function and PPIs involving the dysregulated mutant protein isoforms suggests a protective role of mutations HSPG2*Q1062H and VASN*R161Q and an adverse role of AMBP*A286G and CD55*S162L in PCa patients. This work originally characterized the urinary proteome, focusing on the proteogenome profile of PCa patients, which is usually overlooked in the analysis of PCa and body fluids. Combined analysis of mass spectrometry data using two different software packages was performed for the first time in the context of PCa, which increased the robustness of the data analysis. The application of proteogenomics to urine proteomic analysis can be very enriching in mutation-related diseases such as cancer.
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Roy R, Morad G, Jedinak A, Moses MA. Metalloproteinases and their roles in human cancer. Anat Rec (Hoboken) 2019; 303:1557-1572. [PMID: 31168956 DOI: 10.1002/ar.24188] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/27/2018] [Accepted: 03/04/2019] [Indexed: 02/06/2023]
Abstract
It is now widely appreciated that members of the matrix metalloproteinase (MMP) family of enzymes play a key role in cancer development and progression along with many of the hallmarks associated with them. The activity of these enzymes has been directly implicated in extracellular matrix remodeling, the processing of growth factors and receptors, the modulation of cell migration, proliferation, and invasion, the epithelial to mesenchymal transition, the regulation of immune responses, and the control of angiogenesis. Certain MMP family members have been validated as biomarkers of a variety of human cancers including those of the breast, brain, pancreas, prostate, ovary, and others. The related metalloproteinases, the A disintegrin and metalloproteinases (ADAMs), share a number of these functions as well. Here, we explore these essential metalloproteinases and some of their disease-associated activities in detail as well as some of their complementary translational potential. Anat Rec, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Roopali Roy
- The Vascular Biology Program, Boston Children's Hospital and the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Golnaz Morad
- The Vascular Biology Program, Boston Children's Hospital and the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Andrej Jedinak
- The Vascular Biology Program, Boston Children's Hospital and the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Marsha A Moses
- The Vascular Biology Program, Boston Children's Hospital and the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
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5
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Schunkert EM, Zhao W, Zänker K. Breast Cancer Recurrence Risk Assessment: Is Non-Invasive Monitoring an Option? Biomed Hub 2018; 3:1-17. [PMID: 31988964 PMCID: PMC6945973 DOI: 10.1159/000492929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metastatic breast cancer (MBC) represents a life-threatening disease with a median survival time of 18-24 months that often can only be treated palliatively. The majority of women suffering from MBC are those who had been previously diagnosed with locally advanced disease and subsequently experienced cancer recurrence in the form of metastasis. However, according to guidelines, no systemic follow-up for monitoring purposes is recommended for these women. The purpose of this article is to review current methods of recurrent risk assessment as well as non-invasive monitoring options for women at risk for distant disease relapse and metastasis formation. METHODS We used PubMed and national guidelines, such as the National Comprehensive Cancer Network (NCCN), to find recently published studies on breast cancer recurrence risk assessment and systemic monitoring of breast cancer patients through non-invasive means. RESULTS The options for recurrence risk assessment of locally invasive breast cancer has improved due to diverse genetic tests, such as Oncotype DX, MammaPrint, the PAM50 (now known as the "Prosigna Test") assay, EndoPredict (EP), and the Breast Cancer Index (BCI), which evaluate a women's risk of relapse according to certain cancer-gene expression patterns. Different promising non-invasive urinary protein-based biomarkers with metastasis surveillance potential that have been identified are MMP-2, MMP-9, NGAL, and ADAM12. In particular, ααCTX, ββCTX, and NTX could help to monitor bone metastasis. CONCLUSION In times of improved recurrence risk assessment of women with breast cancer, non-invasive biomarkers are urgently needed as potential monitoring options for women who have an increased risk of recurrence. Urine as a bioliquid of choice provides several advantages - it is non-invasive, can be obtained easily and frequently, and is economical. Promising biomarkers that could help to follow up women with increased recurrence risk have been identified. In order for them to be implemented in clinical usage and national guideline recommendations, further validation in larger independent cohorts will be needed.
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Affiliation(s)
- Elisa M. Schunkert
- Institute of Immunology, Faculty of Health Science, Department of Medicine and School of Life Sciences (ZBAF), University of Witten-Herdecke, Witten, Germany
| | - Wanzhou Zhao
- Nanjing Han and Zaenker Cancer Institute, Nanjing, China
| | - Kurt Zänker
- Institute of Immunology, Faculty of Health Science, Department of Medicine and School of Life Sciences (ZBAF), University of Witten-Herdecke, Witten, Germany
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Jedinak A, Loughlin KR, Moses MA. Approaches to the discovery of non-invasive urinary biomarkers of prostate cancer. Oncotarget 2018; 9:32534-32550. [PMID: 30197761 PMCID: PMC6126692 DOI: 10.18632/oncotarget.25946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) continues to be one of the most common cancers in men worldwide. Prostate specific antigen (PSA) measured in blood has been used for decades as an aid for physicians to detect the presence of prostate cancer. However, the PSA test has limited sensitivity and specificity, leading to unnecessary biopsies, overdiagnosis and overtreatment of patients. For these reasons, there is an urgent need for more accurate PCa biomarkers that can detect PCa with high sensitivity and specificity. Urine is a unique source of potential protein biomarkers that can be measured in a non-invasive way. This review comprehensively summarizes state of the art approaches used in the discovery and validation of urinary biomarkers for PCa. Numerous strategies are currently being used in the discovery of urinary biomarkers for prostate cancer including gel-based separation techniques, mass spectrometry, activity-based proteomic assays and software approaches. Antibody-based approaches remain preferred method for validation of candidate biomarkers with rapidly advancing multiplex immunoassays and MS-based targeted approaches. In the last decade, there has been a dramatic acceleration in the development of new techniques and approaches in the discovery of protein biomarkers for prostate cancer including computational, statistical and data mining methods. Many urinary-based protein biomarkers have been identified and have shown significant promise in initial studies. Examples of these potential biomarkers and the methods utilized in their discovery are also discussed in this review.
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Affiliation(s)
- Andrej Jedinak
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kevin R Loughlin
- Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marsha A Moses
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
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Shimura T, Ebi M, Yamada T, Yamada T, Katano T, Nojiri Y, Iwasaki H, Nomura S, Hayashi N, Mori Y, Kataoka H, Moses MA, Joh T. Urinary kallikrein 10 predicts the incurability of gastric cancer. Oncotarget 2018; 8:29247-29257. [PMID: 28418926 PMCID: PMC5438727 DOI: 10.18632/oncotarget.16453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/22/2017] [Indexed: 01/06/2023] Open
Abstract
The current imaging modalities are not sufficient to identify inoperable tumor factors, including distant metastasis and local invasion. Hence, we conducted this study using urine samples to discover non-invasive biomarkers for the incurability of gastric cancer (GC). Urine samples from 111 GC patients were analyzed in this study. The GC cohort was categorized and analyzed according to disease stage and operability. In the discovery phase, protease protein array analysis identified 3 potential candidate proteins that were elevated in the urine of advanced GC patients compared to early GC patients. Among them, urinary kallikrein 10 (KLK10) was positively associated with tumor stage progression. Moreover, the urinary level of KLK10 (uKLK10) was significantly elevated in the urine of patients with inoperable GC compared to operable GC patients (median, 118 vs. 229; P=0.014). The combination of uKLK10, tumor location and tumor size distinguished operability of GC with an area under the curve of 0.859, 82.4% sensitivity and 86.2% specificity. Disease-free survival (DFS) was significantly shorter in GC patients with high uKLK10 compared to those with low uKLK10 (hazard ratio: 3.30 [95% confidence interval, 1.58-6.90] P<0.001). Immunohistochemical analyses also demonstrated a positive correlation between tumor stage and KLK10 expression in GC tissues (r=0.426, P<0.001). In addition, GC patients with high expression of pathological KLK10 (pKLK10) showed a significantly shorter DFS compared to those with low pKLK10 (hazard ratio: 3.79 [95% confidence interval, 1.27-11.24] P=0.010). uKLK10 is a promising non-invasive biomarker for the inoperability and incurability of GC.
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Affiliation(s)
- Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masahide Ebi
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.,Department of Gastroenterology, Aichi Medical University, Nagakute, Japan
| | - Tomonori Yamada
- Department of Gastroenterology, Japanese Red Cross Nagoya Daini Hospital, Nagoya, Japan
| | | | - Takahito Katano
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yu Nojiri
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.,Department of Gastroenterology, Japanese Red Cross Nagoya Daini Hospital, Nagoya, Japan
| | - Hiroyasu Iwasaki
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.,Department of Gastroenterology, Japanese Red Cross Nagoya Daini Hospital, Nagoya, Japan
| | - Satoshi Nomura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Noriyuki Hayashi
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yoshinori Mori
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hiromi Kataoka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Marsha A Moses
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA, USA
| | - Takashi Joh
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Di Venere M, Viglio S, Sassera D, Fumagalli M, Bardoni A, Salvini R, Cagnone M, Iadarola P. Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade. Electrophoresis 2017; 38:1538-1550. [PMID: 28130906 DOI: 10.1002/elps.201600504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 12/21/2022]
Abstract
This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches can be a strategy to enrich the extent of proteomic information achieved from a sample. The coupling of "top-down" and "bottom-up" proteomics may result in the generation of a hybrid analytical tool, very efficient not only for large-scale profiling of complex proteomes but also for studying specific subproteomes. The range of applications described, while evidencing a continuous boost in the imagination of researchers for developing new combinations of methods for protein separation, also underlines the adaptability of these techniques to a wide variety of samples. This report points out the general usefulness of combining different procedures for proteomic analysis, an approach that allows researchers to go deeper in the proteome of samples under investigation.
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Affiliation(s)
- Monica Di Venere
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
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Guzman NA, Guzman DE. An emerging micro-scale immuno-analytical diagnostic tool to see the unseen. Holding promise for precision medicine and P4 medicine. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:14-29. [DOI: 10.1016/j.jchromb.2015.11.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/15/2015] [Accepted: 11/17/2015] [Indexed: 01/10/2023]
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10
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Chen Z, Kim J. Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. BMC Urol 2016; 16:11. [PMID: 27000794 PMCID: PMC4802825 DOI: 10.1186/s12894-016-0129-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
Background Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism. Discussion We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition. Conclusion Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.
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Affiliation(s)
- Zhaohui Chen
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Medicine, University of California, Los Angeles, CA, USA.
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