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Jóźwiak K, Nguyen VH, Sollfrank L, Linn SC, Hauptmann M. Cox proportional hazards regression in small studies of predictive biomarkers. Sci Rep 2024; 14:14232. [PMID: 38902269 PMCID: PMC11190253 DOI: 10.1038/s41598-024-64573-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Predictive biomarkers are essential for personalized medicine since they select the best treatment for a specific patient. However, of all biomarkers that are evaluated, only few are eventually used in clinical practice. Many promising biomarkers may be erroneously abandoned because they are investigated in small studies using standard statistical techniques which can cause small sample bias or lack of power. The standard technique for failure time endpoints is Cox proportional hazards regression with a multiplicative interaction term between binary variables of biomarker and treatment. Properties of this model in small studies have not been evaluated so far, therefore we performed a simulation study to understand its small sample behavior. As a remedy, we applied a Firth correction to the score function of the Cox model and obtained confidence intervals (CI) using a profile likelihood (PL) approach. These methods are generally recommended for small studies of different design. Our results show that a Cox model estimates the biomarker-treatment interaction term and the treatment effect in one of the biomarker subgroups with bias, and overestimates their standard errors. Bias is however reduced and power is increased with Firth correction and PL CIs. Hence, the modified Cox model and PL CI should be used instead of a standard Cox model with Wald based CI in small studies of predictive biomarkers.
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Affiliation(s)
- K Jóźwiak
- Institute of Biostatistics and Registry Research, Brandenburg Medical School Theodor Fontane, Fehrbelliner Straße 39, 16816, Neuruppin, Germany.
| | - V H Nguyen
- Institute of Biostatistics and Registry Research, Brandenburg Medical School Theodor Fontane, Fehrbelliner Straße 39, 16816, Neuruppin, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - L Sollfrank
- Institute of Biostatistics and Registry Research, Brandenburg Medical School Theodor Fontane, Fehrbelliner Straße 39, 16816, Neuruppin, Germany
| | - S C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center, Utrecht, The Netherlands
| | - M Hauptmann
- Institute of Biostatistics and Registry Research, Brandenburg Medical School Theodor Fontane, Fehrbelliner Straße 39, 16816, Neuruppin, Germany
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Ramisetty S, Subbalakshmi AR, Pareek S, Mirzapoiazova T, Do D, Prabhakar D, Pisick E, Shrestha S, Achuthan S, Bhattacharya S, Malhotra J, Mohanty A, Singhal SS, Salgia R, Kulkarni P. Leveraging Cancer Phenotypic Plasticity for Novel Treatment Strategies. J Clin Med 2024; 13:3337. [PMID: 38893049 PMCID: PMC11172618 DOI: 10.3390/jcm13113337] [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: 04/22/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer cells, like all other organisms, are adept at switching their phenotype to adjust to the changes in their environment. Thus, phenotypic plasticity is a quantitative trait that confers a fitness advantage to the cancer cell by altering its phenotype to suit environmental circumstances. Until recently, new traits, especially in cancer, were thought to arise due to genetic factors; however, it is now amply evident that such traits could also emerge non-genetically due to phenotypic plasticity. Furthermore, phenotypic plasticity of cancer cells contributes to phenotypic heterogeneity in the population, which is a major impediment in treating the disease. Finally, plasticity also impacts the group behavior of cancer cells, since competition and cooperation among multiple clonal groups within the population and the interactions they have with the tumor microenvironment also contribute to the evolution of drug resistance. Thus, understanding the mechanisms that cancer cells exploit to tailor their phenotypes at a systems level can aid the development of novel cancer therapeutics and treatment strategies. Here, we present our perspective on a team medicine-based approach to gain a deeper understanding of the phenomenon to develop new therapeutic strategies.
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Affiliation(s)
- Sravani Ramisetty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Ayalur Raghu Subbalakshmi
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Siddhika Pareek
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Dana Do
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Dhivya Prabhakar
- City of Hope Atlanta, 600 Celebrate Life Parkway, Newnan, GA 30265, USA;
| | - Evan Pisick
- City of Hope Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA;
| | - Sagun Shrestha
- City of Hope Phoenix, 14200 West Celebrate Life Way, Goodyear, AZ 85338, USA;
| | - Srisairam Achuthan
- Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Jyoti Malhotra
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Sharad S. Singhal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
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Rayamajhi S, Sipes J, Tetlow AL, Saha S, Bansal A, Godwin AK. Extracellular Vesicles as Liquid Biopsy Biomarkers across the Cancer Journey: From Early Detection to Recurrence. Clin Chem 2024; 70:206-219. [PMID: 38175602 DOI: 10.1093/clinchem/hvad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/26/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer is a dynamic process and thus requires highly informative and reliable biomarkers to help guide patient care. Liquid-based biopsies have emerged as a clinical tool for tracking cancer dynamics. Extracellular vesicles (EVs), lipid bilayer delimited particles secreted by cells, are a new class of liquid-based biomarkers. EVs are rich in selectively sorted biomolecule cargos, which provide a spatiotemporal fingerprint of the cell of origin, including cancer cells. CONTENT This review summarizes the performance characteristics of EV-based biomarkers at different stages of cancer progression, from early malignancy to recurrence, while emphasizing their potential as diagnostic, prognostic, and screening biomarkers. We discuss the characteristics of effective biomarkers, consider challenges associated with the EV biomarker field, and report guidelines based on the biomarker discovery pipeline. SUMMARY Basic science and clinical trial studies have shown the potential of EVs as precision-based biomarkers for tracking cancer status, with promising applications for diagnosing disease, predicting response to therapy, and tracking disease burden. The multi-analyte cargos of EVs enhance the performance characteristics of biomarkers. Recent technological advances in ultrasensitive detection of EVs have shown promise with high specificity and sensitivity to differentiate early-cancer cases vs healthy individuals, potentially outperforming current gold-standard imaging-based cancer diagnosis. Ultimately, clinical translation will be dictated by how these new EV biomarker-based platforms perform in larger sample cohorts. Applying ultrasensitive, scalable, and reproducible EV detection platforms with better design considerations based upon the biomarker discovery pipeline should guide the field towards clinically useful liquid biopsy biomarkers.
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Affiliation(s)
- Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jared Sipes
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Ashley L Tetlow
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Souvik Saha
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
| | - Ajay Bansal
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
- Division of Genomic Diagnostics, University of Kansas Health System, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, United States
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Samaržija I. The Potential of Extracellular Matrix- and Integrin Adhesion Complex-Related Molecules for Prostate Cancer Biomarker Discovery. Biomedicines 2023; 12:79. [PMID: 38255186 PMCID: PMC10813710 DOI: 10.3390/biomedicines12010079] [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: 11/18/2023] [Revised: 12/16/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Prostate cancer is among the top five cancer types according to incidence and mortality. One of the main obstacles in prostate cancer management is the inability to foresee its course, which ranges from slow growth throughout years that requires minimum or no intervention to highly aggressive disease that spreads quickly and resists treatment. Therefore, it is not surprising that numerous studies have attempted to find biomarkers of prostate cancer occurrence, risk stratification, therapy response, and patient outcome. However, only a few prostate cancer biomarkers are used in clinics, which shows how difficult it is to find a novel biomarker. Cell adhesion to the extracellular matrix (ECM) through integrins is among the essential processes that govern its fate. Upon activation and ligation, integrins form multi-protein intracellular structures called integrin adhesion complexes (IACs). In this review article, the focus is put on the biomarker potential of the ECM- and IAC-related molecules stemming from both body fluids and prostate cancer tissue. The processes that they are involved in, such as tumor stiffening, bone turnover, and communication via exosomes, and their biomarker potential are also reviewed.
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Affiliation(s)
- Ivana Samaržija
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Adeuyan O, Gordon ER, Kenchappa D, Bracero Y, Singh A, Espinoza G, Geskin LJ, Saenger YM. An update on methods for detection of prognostic and predictive biomarkers in melanoma. Front Cell Dev Biol 2023; 11:1290696. [PMID: 37900283 PMCID: PMC10611507 DOI: 10.3389/fcell.2023.1290696] [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: 09/07/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
The approval of immunotherapy for stage II-IV melanoma has underscored the need for improved immune-based predictive and prognostic biomarkers. For resectable stage II-III patients, adjuvant immunotherapy has proven clinical benefit, yet many patients experience significant adverse events and may not require therapy. In the metastatic setting, single agent immunotherapy cures many patients but, in some cases, more intensive combination therapies against specific molecular targets are required. Therefore, the establishment of additional biomarkers to determine a patient's disease outcome (i.e., prognostic) or response to treatment (i.e., predictive) is of utmost importance. Multiple methods ranging from gene expression profiling of bulk tissue, to spatial transcriptomics of single cells and artificial intelligence-based image analysis have been utilized to better characterize the immune microenvironment in melanoma to provide novel predictive and prognostic biomarkers. In this review, we will highlight the different techniques currently under investigation for the detection of prognostic and predictive immune biomarkers in melanoma.
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Affiliation(s)
- Oluwaseyi Adeuyan
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Emily R. Gordon
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Divya Kenchappa
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Yadriel Bracero
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ajay Singh
- Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Larisa J. Geskin
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, United States
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Savva KV, Kawka M, Vadhwana B, Penumaka R, Patton I, Khan K, Perrott C, Das S, Giot M, Mavroveli S, Hanna GB, Ni MZ, Peters CJ. The Biomarker Toolkit - an evidence-based guideline to predict cancer biomarker success and guide development. BMC Med 2023; 21:383. [PMID: 37794461 PMCID: PMC10552368 DOI: 10.1186/s12916-023-03075-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND An increased number of resources are allocated on cancer biomarker discovery, but very few of these biomarkers are clinically adopted. To bridge the gap between Biomarker discovery and clinical use, we aim to generate the Biomarker Toolkit, a tool designed to identify clinically promising biomarkers and promote successful biomarker translation. METHODS All features associated with a clinically useful biomarker were identified using mixed-methodology, including systematic literature search, semi-structured interviews, and an online two-stage Delphi-Survey. Validation of the checklist was achieved by independent systematic literature searches using keywords/subheadings related to clinically and non-clinically utilised breast and colorectal cancer biomarkers. Composite aggregated scores were generated for each selected publication based on the presence/absence of an attribute listed in the Biomarker Toolkit checklist. RESULTS Systematic literature search identified 129 attributes associated with a clinically useful biomarker. These were grouped in four main categories including: rationale, clinical utility, analytical validity, and clinical validity. This checklist was subsequently developed using semi-structured interviews with biomarker experts (n=34); and 88.23% agreement was achieved regarding the identified attributes, via the Delphi survey (consensus level:75%, n=51). Quantitative validation was completed using clinically and non-clinically implemented breast and colorectal cancer biomarkers. Cox-regression analysis suggested that total score is a significant driver of biomarker success in both cancer types (BC: p>0.0001, 95.0% CI: 0.869-0.935, CRC: p>0.0001, 95.0% CI: 0.918-0.954). CONCLUSIONS This novel study generated a validated checklist with literature-reported attributes linked with successful biomarker implementation. Ultimately, the application of this toolkit can be used to detect biomarkers with the highest clinical potential and shape how biomarker studies are designed/performed.
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Affiliation(s)
- Katerina-Vanessa Savva
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK.
| | - Michal Kawka
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Bhamini Vadhwana
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Rahul Penumaka
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Imogen Patton
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Komal Khan
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Claire Perrott
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Saranya Das
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Maxime Giot
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Stella Mavroveli
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - George B Hanna
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Melody Zhifang Ni
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Christopher J Peters
- Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Jordan HA, Thomas SN. Novel proteomic technologies to address gaps in pre-clinical ovarian cancer biomarker discovery efforts. Expert Rev Proteomics 2023; 20:439-450. [PMID: 38116719 DOI: 10.1080/14789450.2023.2295861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION An estimated 20,000 women in the United States will receive a diagnosis of ovarian cancer in 2023. Late-stage diagnosis is associated with poor prognosis. There is a need for novel diagnostic biomarkers for ovarian cancer to improve early-stage detection and novel prognostic biomarkers to improve patient treatment. AREAS COVERED This review provides an overview of the clinicopathological features of ovarian cancer and the currently available biomarkers and treatment options. Two affinity-based platforms using proximity extension assays (Olink) and DNA aptamers (SomaLogic) are described in the context of highly reproducible and sensitive multiplexed assays for biomarker discovery. Recent developments in ion mobility spectrometry are presented as novel techniques to apply to the biomarker discovery pipeline. Examples are provided of how these aforementioned methods are being applied to biomarker discovery efforts in various diseases, including ovarian cancer. EXPERT OPINION Translating novel ovarian cancer biomarkers from candidates in the discovery phase to bona fide biomarkers with regulatory approval will have significant benefits for patients. Multiplexed affinity-based assay platforms and novel mass spectrometry methods are capable of quantifying low abundance proteins to aid biomarker discovery efforts by enabling the robust analytical interrogation of the ovarian cancer proteome.
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Affiliation(s)
- Helen A Jordan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Stefani N Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
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Ruas JS, Silva FLT, Euzébio MF, Biazon TO, Daiggi CMM, Nava D, Franco MT, Cardinalli IA, Cassone AE, Pereira LH, Seidinger AL, Maschietto M, Jotta PY. Somatic Copy Number Alteration in Circulating Tumor DNA for Monitoring of Pediatric Patients with Cancer. Biomedicines 2023; 11:biomedicines11041082. [PMID: 37189699 DOI: 10.3390/biomedicines11041082] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023] Open
Abstract
Pediatric tumors share few recurrent mutations and are instead characterized by copy number alterations (CNAs). The cell-free DNA (cfDNA) is a prominent source for the detection of cancer-specific biomarkers in plasma. We profiled CNAs in the tumor tissues for further evaluation of alterations in 1q, MYCN and 17p in the circulating tumor DNA (ctDNA) in the peripheral blood at diagnosis and follow-up using digital PCR. We report that among the different kinds of tumors (neuroblastoma, Wilms tumor, Ewing sarcoma, rhabdomyosarcoma, leiomyosarcoma, osteosarcoma and benign teratoma), neuroblastoma presented the greatest amount of cfDNA, in correlation with tumor volume. Considering all tumors, cfDNA levels correlated with tumor stage, metastasis at diagnosis and metastasis developed during therapy. In the tumor tissue, at least one CNA (at CRABP2, TP53, surrogate markers for 1q and 17p, respectively, and MYCN) was observed in 89% of patients. At diagnosis, CNAs levels were concordant between tumor and ctDNA in 56% of the cases, and for the remaining 44%, 91.4% of the CNAs were present only in cfDNA and 8.6% only in the tumor. Within the cfDNA, we observed that 46% and 23% of the patients had MYCN and 1q gain, respectively. The use of specific CNAs as targets for liquid biopsy in pediatric patients with cancer can improve diagnosis and should be considered for monitoring of the disease response.
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Affiliation(s)
| | - Felipe Luz Torres Silva
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Mayara Ferreira Euzébio
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Tássia Oliveira Biazon
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | | | - Daniel Nava
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | | | | | | | | | - Ana Luiza Seidinger
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
| | - Mariana Maschietto
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
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Exact Probability Distribution for the ROC Area under Curve. Cancers (Basel) 2023; 15:cancers15061788. [PMID: 36980674 PMCID: PMC10046879 DOI: 10.3390/cancers15061788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The Receiver Operating Characteristic (ROC) is a de facto standard for determining the accuracy of in vitro diagnostic (IVD) medical devices, and thus the exactness in its probability distribution is crucial toward accurate statistical inference. We show the exact probability distribution of the ROC AUC-value, hence exact critical values and p-values are readily obtained. Because the exact calculations are computationally intense, we demonstrate a method of geometric interpolation, which is exact in a special case but generally an approximation, vastly increasing computational speeds. The method is illustrated through open access data, demonstrating superiority of 26 composite biomarkers relative to a predicate device. Especially under correction for testing of multiple hypotheses, traditional asymptotic approximations are encumbered by considerable imprecision, adversely affecting IVD device development. The ability to obtain exact p-values will allow more efficient IVD device development.
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Ren AH, Filippou PS, Soosaipillai A, Dimitrakopoulos L, Korbakis D, Leung F, Kulasingam V, Bernardini MQ, Diamandis EP. Mucin 13 (MUC13) as a candidate biomarker for ovarian cancer detection: potential to complement CA125 in detecting non-serous subtypes. Clin Chem Lab Med 2023; 61:464-472. [PMID: 36380677 DOI: 10.1515/cclm-2022-0491] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Ovarian cancer is the most lethal gynecological malignancy in developed countries. One of the key associations with the high mortality rate is diagnosis at late stages. This clinical limitation is primarily due to a lack of distinct symptoms and detection at the early stages. The ovarian cancer biomarker, CA125, is mainly effective for identifying serous ovarian carcinomas, leaving a gap in non-serous ovarian cancer detection. Mucin 13 (MUC13) is a transmembrane, glycosylated protein with aberrant expression in malignancies, including ovarian cancer. We explored the potential of MUC13 to complement CA125 as an ovarian cancer biomarker, by evaluating its ability to discriminate serous and non-serous subtypes of ovarian cancer at FIGO stages I-IV from benign conditions. METHODS We used our newly developed, high sensitivity ELISA to measure MUC13 protein in a large, well-defined cohort of 389 serum samples from patients with ovarian cancer and benign conditions. RESULTS MUC13 and CA125 serum levels were elevated in malignant compared to benign cases (p<0.0001). Receiver-operating characteristic (ROC) curve analysis showed similar area under the curve (AUC) of 0.74 (MUC13) and 0.76 (CA125). MUC13 concentrations were significantly higher in mucinous adenocarcinomas compared to benign controls (p=0.0005), with AUC of 0.80. MUC13 and CA125 showed significant elevation in early-stage cases (stage I-II) in relation to benign controls (p=0.0012 and p=0.014, respectively). CONCLUSIONS We report the novel role of MUC13 as a serum ovarian cancer biomarker, where it could complement CA125 for detecting some subtypes of non-serous ovarian carcinoma and early-stage disease.
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Affiliation(s)
- Annie H Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Panagiota S Filippou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Lampros Dimitrakopoulos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Dimitrios Korbakis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Felix Leung
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, University Health Network, Toronto, ON, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
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12
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Quraish RU, Hirahata T, Quraish AU, ul Quraish S. An Overview: Genetic Tumor Markers for Early Detection and Current Gene Therapy Strategies. Cancer Inform 2023; 22:11769351221150772. [PMID: 36762284 PMCID: PMC9903029 DOI: 10.1177/11769351221150772] [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: 07/05/2022] [Accepted: 12/24/2022] [Indexed: 02/04/2023] Open
Abstract
Genomic instability is considered a fundamental factor involved in any neoplastic disease. Consequently, the genetically unstable cells contribute to intratumoral genetic heterogeneity and phenotypic diversity of cancer. These genetic alterations can be detected by several diagnostic techniques of molecular biology and the detection of alteration in genomic integrity may serve as reliable genetic molecular markers for the early detection of cancer or cancer-related abnormal changes in the body cells. These genetic molecular markers can detect cancer earlier than any other method of cancer diagnosis, once a tumor is diagnosed, then replacement or therapeutic manipulation of these cancer-related abnormal genetic changes can be possible, which leads toward effective and target-specific cancer treatment and in many cases, personalized treatment of cancer could be performed without the adverse effects of chemotherapy and radiotherapy. In this review, we describe how these genetic molecular markers can be detected and the possible ways for the application of this gene diagnosis for gene therapy that can attack cancerous cells, directly or indirectly, which lead to overall improved management and quality of life for a cancer patient.
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Affiliation(s)
| | - Tetsuyuki Hirahata
- Tetsuyuki Hirahata, Hirahata Gene Therapy Laboratory, HIC Clinic #1105, Itocia Office Tower 11F, 2-7-1, Yurakucho, Chiyoda-ku, Tokyo 100-0006, Japan.
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13
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Predicting Prognosis and Platinum Resistance in Ovarian Cancer: Role of Immunohistochemistry Biomarkers. Int J Mol Sci 2023; 24:ijms24031973. [PMID: 36768291 PMCID: PMC9916805 DOI: 10.3390/ijms24031973] [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: 11/11/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/20/2023] Open
Abstract
Ovarian cancer is a lethal reproductive tumour affecting women worldwide. The advancement in presentation and occurrence of chemoresistance are the key factors for poor survival among ovarian cancer women. Surgical debulking was the mainstay of systemic treatment for ovarian cancer, which was followed by a successful start to platinum-based chemotherapy. However, most women develop platinum resistance and relapse within six months of receiving first-line treatment. Thus, there is a great need to identify biomarkers to predict platinum resistance before enrolment into chemotherapy, which would facilitate individualized targeted therapy for these subgroups of patients to ensure better survival and an improved quality of life and overall outcome. Harnessing the immune response through immunotherapy approaches has changed the treatment way for patients with cancer. The immune outline has emerged as a beneficial tool for recognizing predictive and prognostic biomarkers clinically. Studying the tumour microenvironment (TME) of ovarian cancer tissue may provide awareness of actionable targets for enhancing chemotherapy outcomes and quality of life. This review analyses the relevance of immunohistochemistry biomarkers as prognostic biomarkers in predicting chemotherapy resistance and improving the quality of life in ovarian cancer.
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14
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Savva KV, Das B, Antonowicz S, Hanna GB, Peters CJ. Progress with Metabolomic Blood Tests for Gastrointestinal Cancer Diagnosis-An Assessment of Biomarker Translation. Cancer Epidemiol Biomarkers Prev 2022; 31:2095-2105. [PMID: 36215181 DOI: 10.1158/1055-9965.epi-22-0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/27/2022] [Accepted: 09/30/2022] [Indexed: 12/30/2022] Open
Abstract
There is an urgent need for cost-effective, non-invasive tools to detect early stages of gastrointestinal cancer (colorectal, gastric, and esophageal cancers). Despite many publications suggesting circulating metabolites acting as accurate cancer biomarkers, few have reached the clinic. In upper gastrointestinal cancer this is critically important, as there is no test to complement gold-standard endoscopic evaluation in patients with mild symptoms that do not meet referral criteria. Therefore, this study aimed to describe and solve this translational gap. Studies reporting diagnostic accuracy of metabolomic blood-based gastrointestinal cancer biomarkers from 2007 to 2020 were systematically reviewed and progress of each biomarker along the discovery-validation-adoption pathway was mapped. Successful biomarker translation was defined as a composite endpoint, including patent protection/FDA approval/recommendation in national guidelines. The review found 77 biomarker panels of gastrointestinal cancer, including 25 with an AUROC >0.9. All but one was stalled at the discovery phase, 9.09% were patented and none were clinically approved, confirming the extent of biomarker translational gap. In addition, there were numerous "re-discoveries," including histidine, discovered in 7 colorectal studies. Finally, this study quantitatively supports the presence of a translational gap between discovery and clinical adoption, despite clear evidence of highly performing biomarkers with significant potential clinical value.
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Affiliation(s)
- Katerina-Vanessa Savva
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - Bibek Das
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - Stefan Antonowicz
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
| | - Christopher J Peters
- Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, London, United Kingdom
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15
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Artificial Intelligence in cancer pathology—hope or hype? THE LANCET DIGITAL HEALTH 2022; 4:e766-e767. [DOI: 10.1016/s2589-7500(22)00193-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
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16
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Desaire H, Go EP, Hua D. Advances, obstacles, and opportunities for machine learning in proteomics. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101069. [PMID: 36381226 PMCID: PMC9648337 DOI: 10.1016/j.xcrp.2022.101069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The fields of proteomics and machine learning are both large disciplines, each producing well over 5,000 publications per year. However, studies combining both fields are still relatively rare, with only about 2% of recent proteomics papers including machine learning. This review, which focuses on the intersection of the fields, is intended to inspire proteomics researchers to develop skills and knowledge in the application of machine learning. A brief tutorial introduction to machine learning is provided, and research advances that rely on both fields, particularly as they relate to proteomics tools development and biomarker discovery, are highlighted. Key knowledge gaps and opportunities for scientific advancement are also enumerated.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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17
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Charles Jacob HK, Signorelli R, Charles Richard JL, Kashuv T, Lavania S, Middleton A, Gomez BA, Ferrantella A, Amirian H, Tao J, Ergonul AB, Boone MM, Hadisurya M, Tao WA, Iliuk A, Kashyap MK, Garcia-Buitrago M, Dawra R, Saluja AK. Identification of novel early pancreatic cancer biomarkers KIF5B and SFRP2 from “first contact” interactions in the tumor microenvironment. J Exp Clin Cancer Res 2022; 41:258. [PMID: 36002889 PMCID: PMC9400270 DOI: 10.1186/s13046-022-02425-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/23/2022] [Indexed: 12/27/2022] Open
Abstract
Abstract
Background
Pancreatic cancer is one of the most difficult cancers to detect early and most patients die from complications arising due to distant organ metastases. The lack of bona fide early biomarkers is one of the primary reasons for late diagnosis of pancreatic cancer. It is a multifactorial disease and warrants a novel approach to identify early biomarkers.
Methods
In order to characterize the proteome, Extracellular vesicles (EVs) isolated from different in vitro conditions mimicking tumor-microenvironment interactions between pancreatic cancer epithelial and stromal cells were analyzed using high throughput mass spectrometry. The biological activity of the secreted EVome was analyzed by investigating changes in distant organ metastases and associated early changes in the microbiome. Candidate biomarkers (KIF5B, SFRP2, LOXL2, and MMP3) were selected and validated on a mouse-human hybrid Tissue Microarray (TMA) that was specifically generated for this study. Additionally, a human TMA was used to analyze the expression of KIF5B and SFRP2 in progressive stages of pancreatic cancer.
Results
The EVome of co-cultured epithelial and stromal cells is different from individual cells with distinct protein compositions. EVs secreted from stromal and cancer cells cultures could not induce significant changes in Pre-Metastatic Niche (PMN) modulation, which was assessed by changes in the distant organ metastases. However, they did induce significant changes in the early microbiome, as indicated by differences in α and β-diversities. KIF5B and SFRP2 show promise for early detection and investigation in progressive pancreatic cancer. These markers are expressed in all stages of pancreatic cancer such as low grade PanINs, advanced cancer, and in liver and soft tissue metastases.
Conclusions
Proteomic characterization of EVs derived from mimicking conditions of epithelial and stromal cells in the tumor-microenvironment resulted in the identification of several proteins, some for the first time in EVs. These secreted EVs cannot induce changes in distant organ metastases in in vivo models of EV education, but modulate changes in the early murine microbiome. Among all the proteins that were analyzed (MMP3, KIF5B, SFRP2, and LOXL2), KIF5B and SFRP2 show promise as bona fide early pancreatic cancer biomarkers expressed in progressive stages of pancreatic cancer.
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18
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Rodrigues-Ferreira S, Nahmias C. Predictive biomarkers for personalized medicine in breast cancer. Cancer Lett 2022; 545:215828. [PMID: 35853538 DOI: 10.1016/j.canlet.2022.215828] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 12/14/2022]
Abstract
Breast cancer is one of the most frequent malignancies among women worldwide. Based on clinical and molecular features of breast tumors, patients are treated with chemotherapy, hormonal therapy and/or radiotherapy and more recently with immunotherapy or targeted therapy. These different therapeutic options have markedly improved patient outcomes. However, further improvement is needed to fight against resistance to treatment. In the rapidly growing area of research for personalized medicine, predictive biomarkers - which predict patient response to therapy - are essential tools to select the patients who are most likely to benefit from the treatment, with the aim to give the right therapy to the right patient and avoid unnecessary overtreatment. The search for predictive biomarkers is an active field of research that includes genomic, proteomic and/or machine learning approaches. In this review, we describe current strategies and innovative tools to identify, evaluate and validate new biomarkers. We also summarize current predictive biomarkers in breast cancer and discuss companion biomarkers of targeted therapy in the context of precision medicine.
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Affiliation(s)
- Sylvie Rodrigues-Ferreira
- Gustave Roussy Institute, INSERM U981, Prédicteurs moléculaires et nouvelles cibles en oncologie, Villejuif, France; LabEx LERMIT, Université Paris-Saclay, 92296 Châtenay-Malabry, France; Inovarion, 75005, Paris, France
| | - Clara Nahmias
- Gustave Roussy Institute, INSERM U981, Prédicteurs moléculaires et nouvelles cibles en oncologie, Villejuif, France; LabEx LERMIT, Université Paris-Saclay, 92296 Châtenay-Malabry, France.
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19
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Vali Y, Eijk R, Hicks T, Jones WS, Suklan J, Holleboom AG, Ratziu V, Langendam MW, Anstee QM, Bossuyt PMM. Clinicians' Perspectives on Barriers and Facilitators for the Adoption of Non-Invasive Liver Tests for NAFLD: A Mixed-Method Study. J Clin Med 2022; 11:jcm11102707. [PMID: 35628838 PMCID: PMC9146541 DOI: 10.3390/jcm11102707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
(1) Background: Given the high prevalence of non-alcoholic fatty liver disease (NAFLD) and the limitations of liver biopsies, multiple non-invasive tests (NITs) have been developed to identify non-alcoholic fatty liver disease (NAFLD) patients at-risk of progression. The availability of these new NITs varies from country to country, and little is known about their implementation and adoption in routine clinical practice. This study aims to explore barriers and facilitators that influence the adoption of NAFLD NITs, from healthcare professionals’ perspectives. (2) Methods: A cross-sectional study was performed using an exploratory mixed-methods approach. Twenty-seven clinicians from eight different countries with different specialties filled in our questionnaire. Of those, 16 participated in semi-structured interviews. Qualitative and quantitative data were collected and summarized using the recently published Non-adoption, Abandonment, Scale-up, Spread, and Sustainability (NASSS) framework for new medical technologies in healthcare organizations. (3) Results: Several factors were reported as influencing the uptake of NITs for NAFLD in clinical practice. Among those: insufficient awareness of tests; lack of practical guidelines and evidence for the performance of tests in appropriate patient populations and care settings; and absence of sufficient reimbursement systems were reported as the most important barriers. Other factors, most notably ‘local champions’, proper functional payment systems, and sufficient resources in academic hospitals, were indicated as important facilitating factors. (4) Conclusions: Clinicians see the adoption of NITs for NAFLD as a complex process that is modulated by several factors, such as robust evidence, practical guidelines, a proper payment system, and local champions. Future research could explore perspectives from other stakeholders on the adoption of NITs.
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Affiliation(s)
- Yasaman Vali
- Department of Epidemiology and Data Science, Amsterdam Public Health, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.W.L.); (P.M.M.B.)
- Correspondence: ; Tel.: +31-(0)20-566-8520
| | - Roel Eijk
- Athena Institute, Faculty of Science, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Timothy Hicks
- NIHR Newcastle In Vitro Diagnostics Co-Operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (T.H.); (W.S.J.); (J.S.)
- NIHR Newcastle In Vitro Diagnostics Co-Operative, Newcastle upon Tyne Hospitals Foundation Trust, Newcastle upon Tyne NE1 7RU, UK
| | - William S. Jones
- NIHR Newcastle In Vitro Diagnostics Co-Operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (T.H.); (W.S.J.); (J.S.)
- NIHR Newcastle In Vitro Diagnostics Co-Operative, Newcastle upon Tyne Hospitals Foundation Trust, Newcastle upon Tyne NE1 7RU, UK
| | - Jana Suklan
- NIHR Newcastle In Vitro Diagnostics Co-Operative, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (T.H.); (W.S.J.); (J.S.)
- NIHR Newcastle In Vitro Diagnostics Co-Operative, Newcastle upon Tyne Hospitals Foundation Trust, Newcastle upon Tyne NE1 7RU, UK
| | - Adriaan G. Holleboom
- Department of Internal and Vascular Medicine, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Vlad Ratziu
- Assistance Publique-Hôpitaux de Paris, Hôpital Beaujon, University Paris-Diderot, 75013 Paris, France;
| | - Miranda W. Langendam
- Department of Epidemiology and Data Science, Amsterdam Public Health, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.W.L.); (P.M.M.B.)
| | - Quentin M. Anstee
- The Newcastle Liver Research Group, Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 7RU, UK
| | - Patrick M. M. Bossuyt
- Department of Epidemiology and Data Science, Amsterdam Public Health, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.W.L.); (P.M.M.B.)
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20
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Kim M, Chen C, Wang P, Mulvey JJ, Yang Y, Wun C, Antman-Passig M, Luo HB, Cho S, Long-Roche K, Ramanathan LV, Jagota A, Zheng M, Wang Y, Heller DA. Detection of ovarian cancer via the spectral fingerprinting of quantum-defect-modified carbon nanotubes in serum by machine learning. Nat Biomed Eng 2022; 6:267-275. [PMID: 35301449 PMCID: PMC9108893 DOI: 10.1038/s41551-022-00860-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
Serum biomarkers are often insufficiently sensitive or specific to facilitate cancer screening or diagnostic testing. In ovarian cancer, the few established serum biomarkers are highly specific, yet insufficiently sensitive to detect early-stage disease and to impact the mortality rates of patients with this cancer. Here we show that a 'disease fingerprint' acquired via machine learning from the spectra of near-infrared fluorescence emissions of an array of carbon nanotubes functionalized with quantum defects detects high-grade serous ovarian carcinoma in serum samples from symptomatic individuals with 87% sensitivity at 98% specificity (compared with 84% sensitivity at 98% specificity for the current best clinical screening test, which uses measurements of cancer antigen 125 and transvaginal ultrasonography). We used 269 serum samples to train and validate several machine-learning classifiers for the discrimination of patients with ovarian cancer from those with other diseases and from healthy individuals. The predictive values of the best classifier could not be attained via known protein biomarkers, suggesting that the array of nanotube sensors responds to unidentified serum biomarkers.
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Affiliation(s)
- Mijin Kim
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chen Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peng Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Joseph J Mulvey
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yoona Yang
- Departments of Bioengineering, and Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | | | | | - Hong-Bin Luo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Sun Cho
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Anand Jagota
- Departments of Bioengineering, and Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Daniel A Heller
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
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21
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Karagur ER, Akgun S, Akca H. Computational and Bioinformatics Methods for MicroRNA Gene Prediction. Methods Mol Biol 2022; 2257:349-373. [PMID: 34432287 DOI: 10.1007/978-1-0716-1170-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs) are 20-24-nucleotide-long noncoding RNAs that bind to the untranslated region (3' UTR) of their target mRNAs. The importance of miRNAs in medicine has grown rapidly in the 20 years since the discovery of them. As the regulatory function of miRNAs on biological processes was discovered, they were advocated to play a role in the underlying mechanisms of human pathogenesis. Functional studies have confirmed that miRNAs are promising in preclinical development through deregulation of genes targeted by miRNAs in many cancer cases. In this chapter, we summarize the miRNAs identified for some specific types of cancer and their functions. Besides, miRNAs function as cancer biomarker and their benefits to diagnosis and treatment of cancer are also discussed.
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Affiliation(s)
- Ege Riza Karagur
- Department of Medical Genetic, School of Medicine, Pamukkale University, Denizli, Turkey
- Department of Medical Biology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Sakir Akgun
- Department of Medical Biology, School of Medicine, Kafkas University, Kars, Turkey
| | - Hakan Akca
- Department of Medical Biology, School of Medicine, Pamukkale University, Denizli, Turkey.
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22
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Katz L, Tata A, Woolman M, Zarrine-Afsar A. Lipid Profiling in Cancer Diagnosis with Hand-Held Ambient Mass Spectrometry Probes: Addressing the Late-Stage Performance Concerns. Metabolites 2021; 11:metabo11100660. [PMID: 34677375 PMCID: PMC8537725 DOI: 10.3390/metabo11100660] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023] Open
Abstract
Untargeted lipid fingerprinting with hand-held ambient mass spectrometry (MS) probes without chromatographic separation has shown promise in the rapid characterization of cancers. As human cancers present significant molecular heterogeneities, careful molecular modeling and data validation strategies are required to minimize late-stage performance variations of these models across a large population. This review utilizes parallels from the pitfalls of conventional protein biomarkers in reaching bedside utility and provides recommendations for robust modeling as well as validation strategies that could enable the next logical steps in large scale assessment of the utility of ambient MS profiling for cancer diagnosis. Six recommendations are provided that range from careful initial determination of clinical added value to moving beyond just statistical associations to validate lipid involvements in disease processes mechanistically. Further guidelines for careful selection of suitable samples to capture expected and unexpected intragroup variance are provided and discussed in the context of demographic heterogeneities in the lipidome, further influenced by lifestyle factors, diet, and potential intersect with cancer lipid pathways probed in ambient mass spectrometry profiling studies.
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Affiliation(s)
- Lauren Katz
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy;
| | - Michael Woolman
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Arash Zarrine-Afsar
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
- Correspondence: ; Tel.: +1-416-581-8473
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23
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Borum RM, Moore C, Chan SK, Steinmetz NF, Jokerst JV. A Photoacoustic Contrast Agent for miR-21 via NIR Fluorescent Hybridization Chain Reaction. Bioconjug Chem 2021; 33:1080-1092. [PMID: 34406744 DOI: 10.1021/acs.bioconjchem.1c00375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acids are well-established biomarkers of cancer with immense value in diagnostics and basic research. However, strategies to monitor these species in tissue can be challenging due to the need for amplification of imaging signal from low analyte concentrations with high specificity. Photoacoustic (PA) imaging is gaining traction for molecular imaging of proteins, small biomolecules, and nucleic acids by coupling pulsed near-infrared (NIR) excitation with broadband acoustic detection. This work introduces a PA nucleic acid contrast agent that harnesses NIR fluorophore and quencher-tagged hybridization chain reaction (HCR) for signal amplification. This HCR probe was designed to enable contact quenching between NIR dye-quencher pairs by coercing their direct alignment when miR-21, a microRNA cancer biomarker, is detected. The probe demonstrated a ratiometric PA limit of detection of 148 pM miR-21, sequence specificity against one- and two-base mutations, and selectivity over other microRNAs. It was further tested in live human ovarian cancer (SKOV3) and noncancerous (HEK 293T) cells to exemplify in situ PA activation based on differences in endogenous miR-21 regulation (p = 0.0002). The probe was lastly tested in tissue mimicking phantoms to exemplify sustained contrast in centimeter-range depths and 85.3% photostability after 15 min of laser irradiation. The probe's miR-21-specific activation and its ability to maintain contrast in biologically relevant absorbing and scattering media support its consideration for live-cell PA microscopy and potential cancer diagnostics. Results from this probe also underscore the combined detection power between ratiometric PA signaling and strand amplification for more sensitive DNA-based PA sensors.
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Affiliation(s)
- Raina M Borum
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093. United States
| | - Colman Moore
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093. United States
| | - Soo Khim Chan
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093. United States
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093. United States.,Department of Radiology, University of California, San Diego, La Jolla, California 92093. United States.,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093. United States.,Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093. United States.,Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, California 92093. United States.,Moores Cancer Center, University of California, San Diego, La Jolla, California 92037. United States
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093. United States.,Materials Science and Engineering Program, University of California, San Diego, La Jolla, California 92093. United States.,Department of Radiology, University of California, San Diego, La Jolla, California 92093. United States
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24
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Poojary M, Jishnu PV, Kabekkodu SP. Prognostic Value of Melanoma-Associated Antigen-A (MAGE-A) Gene Expression in Various Human Cancers: A Systematic Review and Meta-analysis of 7428 Patients and 44 Studies. Mol Diagn Ther 2021; 24:537-555. [PMID: 32548799 PMCID: PMC7497308 DOI: 10.1007/s40291-020-00476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Members of the melanoma-associated antigen-A (MAGE-A) subfamily are overexpressed in many cancers and can drive cancer progression, metastasis, and therapeutic recurrence. Objective This study is the first comprehensive meta-analysis evaluating the prognostic utility of MAGE-A members in different cancers. Methods A systematic literature search was conducted in PubMed, Google Scholar, Science Direct, and Web of Science. The pooled hazard ratios with 95% confidence intervals were estimated to evaluate the prognostic significance of MAGE-A expression in various cancers. Results In total, 44 eligible studies consisting of 7428 patients from 11 countries were analysed. Univariate and multivariate analysis for overall survival, progression-free survival, and disease-free survival showed a significant association between high MAGE-A expression and various cancers (P < 0.00001). Additionally, subgroup analysis demonstrated that high MAGE-A expression was significantly associated with poor prognosis for lung, gastrointestinal, breast, and ovarian cancer in both univariate and multivariate analysis for overall survival. Conclusion Overexpression of MAGE-A subfamily members is linked to poor prognosis in multiple cancers. Therefore, it could serve as a potential prognostic marker of poor prognosis in cancers. Electronic supplementary material The online version of this article (10.1007/s40291-020-00476-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manish Poojary
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
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Mao CP, Wang SC, Su YP, Tseng SH, He L, Wu AA, Roden RBS, Xiao J, Hung CF. Protein detection in blood with single-molecule imaging. SCIENCE ADVANCES 2021; 7:7/33/eabg6522. [PMID: 34380620 PMCID: PMC8357237 DOI: 10.1126/sciadv.abg6522] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The ability to characterize individual biomarker protein molecules in patient blood samples could enable diagnosis of diseases at an earlier stage, when treatment is typically more effective. Single-molecule imaging offers a promising approach to accomplish this goal. However, thus far, single-molecule imaging methods have not been translated into the clinical setting. The detection limit of these methods has been confined to the picomolar (10-12 M) range, several orders of magnitude higher than the circulating concentrations of biomarker proteins present in many diseases. Here, we describe single-molecule augmented capture (SMAC), a single-molecule imaging technique to quantify and characterize individual protein molecules of interest down to the subfemtomolar (<10-15 M) range. We demonstrate SMAC in a variety of applications with human blood samples, including the analysis of disease-associated secreted proteins, membrane proteins, and rare intracellular proteins. SMAC opens the door to the application of single-molecule imaging in noninvasive disease profiling.
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Affiliation(s)
- Chih-Ping Mao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Shih-Chin Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yu-Pin Su
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Ssu-Hsueh Tseng
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Liangmei He
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Annie A Wu
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Richard B S Roden
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore MD, USA
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26
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Ruiz-Ordoñez I, Piedrahita JM, Arévalo JA, Agualimpia A, Tobón GJ. Lymphomagenesis predictors and related pathogenesis. J Transl Autoimmun 2021; 4:100098. [PMID: 33889831 PMCID: PMC8050773 DOI: 10.1016/j.jtauto.2021.100098] [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: 03/10/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/23/2022] Open
Abstract
Sjögren's syndrome (SS) is a systemic autoimmune disease characterised by a wide range of clinical manifestations and complications, including B-cell lymphoma. This study aims to describe the predictors associated with lymphomagenesis in patients with Sjögren's syndrome, emphasising the pathophysiological bases that support this association. We performed a review of the literature published through a comprehensive search strategy in PubMed/MEDLINE, Scopus, and Web of science. Forty publications describing a total of 45,208 patients with SS were retrieved. The predictors were grouped according to their pathophysiological role in the lymphoproliferation process. Also, some new biomarkers such as MicroRNAs, P2X7 receptor-NLRP3 inflammasome, Thymic stromal lymphopoietin, and Three-prime repair exonuclease 1 (TREX1) were identified. The knowledge of the pathophysiology allows the discrimination of markers that participate in the initial stages. Considering that the lymphoproliferation process includes the progression of lymphoma towards more aggressive subtypes, it is essential to recognise biomarkers associated with a worse prognosis.
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Affiliation(s)
- Ingrid Ruiz-Ordoñez
- Fundación Valle del Lili, Centro de Investigaciones Clínicas, Cra 98 No. 18-49, Cali, 760032, Colombia
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
| | - Juan-Manuel Piedrahita
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia
| | - Javier-Andrés Arévalo
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia
| | - Andrés Agualimpia
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Fundación Valle del Lili, Unidad de Reumatología, Cra 98 No. 18-49, Cali. 760032, Colombia
| | - Gabriel J Tobón
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Fundación Valle del Lili, Unidad de Reumatología, Cra 98 No. 18-49, Cali. 760032, Colombia
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Al-Shaheri FN, Alhamdani MSS, Bauer AS, Giese N, Büchler MW, Hackert T, Hoheisel JD. Blood biomarkers for differential diagnosis and early detection of pancreatic cancer. Cancer Treat Rev 2021; 96:102193. [PMID: 33865174 DOI: 10.1016/j.ctrv.2021.102193] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is currently the most lethal tumor entity and case numbers are rising. It will soon be the second most frequent cause of cancer-related death in the Western world. Mortality is close to incidence and patient survival after diagnosis stands at about five months. Blood-based diagnostics could be one crucial factor for improving this dismal situation and is at a stage that could make this possible. Here, we are reviewing the current state of affairs with its problems and promises, looking at various molecule types. Reported results are evaluated in the overall context. Also, we are proposing steps toward clinical utility that should advance the development toward clinical application by improving biomarker quality but also by defining distinct clinical objectives and the respective diagnostic accuracies required to achieve them. Many of the discussed points and conclusions are highly relevant to other solid tumors, too.
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Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany.
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Markus W Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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Zhang J, Jin J, Ai Y, Zhu K, Xiao C, Xie C, Jin X. Computer Tomography Radiomics-Based Nomogram in the Survival Prediction for Brain Metastases From Non-Small Cell Lung Cancer Underwent Whole Brain Radiotherapy. Front Oncol 2021; 10:610691. [PMID: 33643912 PMCID: PMC7905101 DOI: 10.3389/fonc.2020.610691] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/14/2020] [Indexed: 12/25/2022] Open
Abstract
Prognostic parameters and models were believed to be helpful in improving the treatment outcome for patients with brain metastasis (BM). The purpose of this study was to investigate the feasibility of computer tomography (CT) radiomics based nomogram to predict the survival of patients with BM from non-small cell lung cancer (NSCLC) treated with whole brain radiotherapy (WBRT). A total of 195 patients with BM from NSCLC who underwent WBRT from January 2012 to December 2016 were retrospectively reviewed. Radiomics features were extracted and selected from pretherapeutic CT images with least absolute shrinkage and selection operator (LASSO) regression. A nomogram was developed and evaluated by integrating radiomics features and clinical factors to predict the survival of individual patient. Five radiomics features were screened out from 105 radiomics features according to the LASSO Cox regression. According to the optimal cutoff value of radiomics score (Rad-score), patients were stratified into low-risk (Rad-score <= −0.14) and high-risk (Rad-score > −0.14) groups. Multivariable analysis indicated that sex, karnofsky performance score (KPS) and Rad-score were independent predictors for overall survival (OS). The concordance index (C-index) of the nomogram in the training cohort and validation cohort was 0.726 and 0.660, respectively. An area under curve (AUC) of 0.786 and 0.788 was achieved for the short-term and long-term survival prediction, respectively. In conclusion, the nomogram based on radiomics features from CT images and clinical factors was feasible to predict the OS of BM patients from NSCLC who underwent WBRT.
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Affiliation(s)
- Ji Zhang
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Juebin Jin
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yao Ai
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kecheng Zhu
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chengjian Xiao
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Congying Xie
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Radiation and Medical Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiance Jin
- Department of Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Ask EH, Tschan-Plessl A, Gjerdingen TJ, Sætersmoen ML, Hoel HJ, Wiiger MT, Olweus J, Wahlin BE, Lingjærde OC, Horowitz A, Cashen AF, Watkins M, Fehniger TA, Holte H, Kolstad A, Malmberg KJ. A Systemic Protein Deviation Score Linked to PD-1+ CD8+ T Cell Expansion That Predicts Overall Survival in Diffuse Large B Cell Lymphoma. MED 2021; 2:180-195.e5. [DOI: 10.1016/j.medj.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/01/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022]
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30
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Amin M, Tang S, Shalamanova L, Taylor RL, Wylie S, Abdullah BM, Whitehead KA. Polyamine biomarkers as indicators of human disease. Biomarkers 2021; 26:77-94. [PMID: 33439737 DOI: 10.1080/1354750x.2021.1875506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The significant increase of periodontitis, chronic kidney disease (CKD), Alzheimer's disease and cancer can be attributed to an ageing population. Each disease produces a range of biomarkers that can be indicative of disease onset and progression. Biomarkers are defined as cellular (intra/extracellular components and whole cells), biochemical (metabolites, ions and toxins) or molecular (nucleic acids, proteins and lipids) alterations which are measurable in biological media such as human tissues, cells or fluids. An interesting group of biomarkers that merit further investigation are the polyamines. Polyamines are a group of molecules consisting of cadaverine, putrescine, spermine and spermidine and have been implicated in the development of a range of systemic diseases, in part due to their production in periodontitis. Cadaverine and putrescine within the periodontal environment have demonstrated cell signalling interfering abilities, by way of leukocyte migration disruption. The polyamines spermine and spermidine in tumour cells have been shown to inhibit cellular apoptosis, effectively prolonging tumorigenesis and continuation of cancer within the host. Polyamine degradation products such as acrolein have been shown to exacerbate renal damage in CKD patients. Thus, the use of such molecules has merit to be utilized in the early indication of such diseases in patients.
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Affiliation(s)
- Mohsin Amin
- Microbiology at Interfaces, Manchester Metropolitan University, Manchester, UK.,Department of Engineering and Technology, Built Environment, Liverpool John Moores University, Liverpool, UK
| | - Shiying Tang
- Microbiology at Interfaces, Manchester Metropolitan University, Manchester, UK.,Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Liliana Shalamanova
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Rebecca L Taylor
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Stephen Wylie
- Department of Engineering and Technology, Civil Engineering, Liverpool John Moores University, Liverpool, UK
| | - Badr M Abdullah
- Department of Engineering and Technology, Built Environment, Liverpool John Moores University, Liverpool, UK
| | - Kathryn A Whitehead
- Microbiology at Interfaces, Manchester Metropolitan University, Manchester, UK.,Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
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31
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Ganzinelli M, Linardou H, Alvisi MF, Caiola E, Lo Russo G, Cecere FL, Bettini AC, Psyrri A, Milella M, Rulli E, Fabbri A, De Maglie M, Romanelli P, Murray S, Broggini M, Marabese M, Garassino MC. Single-arm, open label prospective trial to assess prediction of the role of ERCC1/XPF complex in the response of advanced NSCLC patients to platinum-based chemotherapy. ESMO Open 2021; 6:100034. [PMID: 33422766 PMCID: PMC7809372 DOI: 10.1016/j.esmoop.2020.100034] [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: 10/19/2020] [Revised: 11/24/2020] [Accepted: 12/06/2020] [Indexed: 11/05/2022] Open
Abstract
Background Platinum-based therapy, combined or not with immune checkpoint inhibitors, represents a front-line choice for patients with non-small-cell lung cancer (NSCLC). Despite the improved outcomes in the last years for this malignancy, only a sub-group of patients have long-term benefit. Excision repair cross-complementation group 1 (ERCC1) has been considered a potential biomarker to predict the outcome of platinum-based chemotherapy in NSCLC. However, the ERCC1 gene is transcribed in four splice variants where the isoform 202 was described as the only one active and able to complex Xeroderma pigmentosum group F-complementing protein (XPF). Here, we prospectively investigated if the active form of ERCC1, as assessed by the ERCC1/XPF complex (ERCC1/XPF), could predict the sensitivity to platinum compounds. Patients and methods Prospectively enrolled, patients with advanced NSCLC treated with a first-line regimen containing platinum were centrally evaluated for ERCC1/XPF by a proximity ligation assay. Overall survival (OS), progression-free survival (PFS) and objective response rate (ORR) were analyzed. Results The absence of the ERCC1/XPF in the tumor suggested a trend of worst outcomes in terms of both OS [hazard ratio (HR) 1.41, 95% confidence interval (CI) 0.67-2.94, P = 0.373] and PFS (HR 1.61, 95% CI 0.88-3.03, P = 0.123). ORR was marginally influenced in ERCC1/XPF-negative and -positive groups [odds ratio (stable disease + progressive disease versus complete response + partial response) 0.87, 95% CI 0.25-3.07, P = 0.832]. Conclusion The lack of ERCC1/XPF complex in NSCLC tumor cells might delineate a group of patients with poor outcomes when treated with platinum compounds. ERCC1/XPF absence might well identify patients for whom a different therapeutic approach could be necessary. This is the first study investigating the ERCC1/XPF complex as a platinum-based therapy response biomarker in NSCLC. The lack of ERCC1/XPF complex might delineate a group of patients with poor outcomes when treated with platinum compounds. ERCC1/XPF absence might identify tumors for whom a different therapeutic approach than platinum compounds could be necessary.
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Affiliation(s)
- M Ganzinelli
- Unit of Thoracic Oncology, Medical Oncology Department 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - H Linardou
- 4th Oncology Department, Metropolitan Hospital, Athens, Greece
| | - M F Alvisi
- Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - E Caiola
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - G Lo Russo
- Unit of Thoracic Oncology, Medical Oncology Department 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F L Cecere
- Division of Medical Oncology 1, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - A C Bettini
- UO Oncologia Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - A Psyrri
- Section of Oncology, Department of Internal Medicine, Attikon Hospital, National Kapodistrian University of Athens, Athens, Greece
| | - M Milella
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - E Rulli
- Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - A Fabbri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M De Maglie
- Mouse and Animal Pathology Lab, Fondazione Filarete, Milan, Italy; Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - P Romanelli
- Mouse and Animal Pathology Lab, Fondazione Filarete, Milan, Italy; Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - S Murray
- Biomarker Solutions Ltd, London, UK
| | - M Broggini
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy.
| | - M Marabese
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - M C Garassino
- Unit of Thoracic Oncology, Medical Oncology Department 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Poulsen TBG, Karamehmedovic A, Aboo C, Jørgensen MM, Yu X, Fang X, Blackburn JM, Nielsen CH, Kragstrup TW, Stensballe A. Protein array-based companion diagnostics in precision medicine. Expert Rev Mol Diagn 2020; 20:1183-1198. [PMID: 33315478 DOI: 10.1080/14737159.2020.1857734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The development of companion diagnostics (CDx) will increase efficacy and cost-benefit markedly, compared to the currently prevailing trial-and-error approach for treatment. Recent improvements in high-throughput protein technology have resulted in large amounts of predictive biomarkers that are potentially useful components of future CDx assays. Current high multiplex protein arrays are suitable for discovery-based approaches, while low-density and more simple arrays are suitable for use in point-of-care facilities. AREA COVERED This review discusses the technical platforms available for protein array focused CDx, explains the technical details of the platforms and provide examples of clinical use, ranging from multiplex arrays to low-density clinically applicable arrays. We thereafter highlight recent predictive biomarkers within different disease areas, such as oncology and autoimmune diseases. Lastly, we discuss some of the challenges connected to the implementation of CDx assays as point-of-care tests. EXPERT OPINION Recent advances in the field of protein arrays have enabled high-density arrays permitting large biomarker discovery studies, which are beneficial for future CDx assays. The density of protein arrays range from a single protein to proteome-wide arrays, allowing the discovery of protein signatures that may correlate with drug response. Protein arrays will undoubtedly play a key role in future CDx assays.
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Affiliation(s)
- Thomas B G Poulsen
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China
| | - Azra Karamehmedovic
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China
| | - Christopher Aboo
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China
| | - Malene Møller Jørgensen
- Department of Clinical Immunology, Aalborg University Hospital , Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University , Aalborg, Denmark
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics , Beijing, China
| | - Xiangdong Fang
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences , China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , China
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa.,Sengenics Corporation Pte Ltd , Singapore
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet , Copenhagen, Denmark
| | - Tue W Kragstrup
- Department of Biomedicine, Aarhus University , Aarhus, Denmark.,Department of Rheumatology, Aarhus University Hospital , Aarhus, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University , Aalborg, Denmark
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Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
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Zhao XT, Zhu Y, Zhou JF, Gao YJ, Liu FZ. Development of a novel 7 immune-related genes prognostic model for oral cancer: A study based on TCGA database. Oral Oncol 2020; 112:105088. [PMID: 33220636 DOI: 10.1016/j.oraloncology.2020.105088] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/16/2020] [Accepted: 10/31/2020] [Indexed: 12/24/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is an aggressive tumor whose prognosis has little improvement in the last three decades. Various immune-related genes have been suggested as significant roles in the development and progression of malignant cancers. In this study, we acquired and integrated differentially expressed genes of OSCC patients, including immune-related genes and transcription factors (TFs), from The Cancer Genome Atlas (TCGA) database. TF-mediated network was established to exploring the regulatory mechanisms of prognostic immune-related genes. A 7 immune-related genes prognostic model for OSCC was obtained, including CGB8, CTLA4, TNFRSF19, CCL26, NRG1, TPM2 and PLAU, which was further proved to be an independent prognostic indicator after adjusting for other clinical factors. The immune-related genes prognostic index was significantly negatively correlated to the infiltration abundances of B cells (P < 0.05) and CD8+ T cells (P < 0.05). The novel proposed immune-based prognostic model not only provided a promising biomarker and a way to monitor the long-term treatment of OSCC, but also gave a new insight into a potential immunotherapy strategy.
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Affiliation(s)
- Xiao-Tong Zhao
- Department of Otorhinolaryngology and Head and Neck Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Yan Zhu
- Department of Pathology, the People's Hospital of Jiangsu Province (The First Affiliated Hospital of Nanjing Medial University), Nanjing, Jiangsu 210029, China
| | | | | | - Fang-Zhou Liu
- Department of Head & Neck Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210029, China.
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35
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Fortino V, Scala G, Greco D. Feature set optimization in biomarker discovery from genome-scale data. Bioinformatics 2020; 36:3393-3400. [PMID: 32119073 DOI: 10.1093/bioinformatics/btaa144] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION Omics technologies have the potential to facilitate the discovery of new biomarkers. However, only few omics-derived biomarkers have been successfully translated into clinical applications to date. Feature selection is a crucial step in this process that identifies small sets of features with high predictive power. Models consisting of a limited number of features are not only more robust in analytical terms, but also ensure cost effectiveness and clinical translatability of new biomarker panels. Here we introduce GARBO, a novel multi-island adaptive genetic algorithm to simultaneously optimize accuracy and set size in omics-driven biomarker discovery problems. RESULTS Compared to existing methods, GARBO enables the identification of biomarker sets that best optimize the trade-off between classification accuracy and number of biomarkers. We tested GARBO and six alternative selection methods with two high relevant topics in precision medicine: cancer patient stratification and drug sensitivity prediction. We found multivariate biomarker models from different omics data types such as mRNA, miRNA, copy number variation, mutation and DNA methylation. The top performing models were evaluated by using two different strategies: the Pareto-based selection, and the weighted sum between accuracy and set size (w = 0.5). Pareto-based preferences show the ability of the proposed algorithm to search minimal subsets of relevant features that can be used to model accurate random forest-based classification systems. Moreover, GARBO systematically identified, on larger omics data types, such as gene expression and DNA methylation, biomarker panels exhibiting higher classification accuracy or employing a number of features much lower than those discovered with other methods. These results were confirmed on independent datasets. AVAILABILITY AND IMPLEMENTATION github.com/Greco-Lab/GARBO. CONTACT dario.greco@tuni.fi. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- V Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - G Scala
- Faculty of Medicine and Health Technology, Tampere University, Tampere 33100, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - D Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere 33100, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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36
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Alizadeh Savareh B, Asadzadeh Aghdaie H, Behmanesh A, Bashiri A, Sadeghi A, Zali M, Shams R. A machine learning approach identified a diagnostic model for pancreatic cancer through using circulating microRNA signatures. Pancreatology 2020; 20:1195-1204. [PMID: 32800647 DOI: 10.1016/j.pan.2020.07.399] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/29/2020] [Accepted: 07/25/2020] [Indexed: 02/08/2023]
Abstract
Late diagnosis of pancreatic cancer (PC) due to the limited effectiveness of modern testing approaches, causes many patients to miss the chance of surgery and consequently leads to a high mortality rate. Pivotal improvements in circulating microRNA expression levels in PC patients make it possible to diagnose and treat patients at earlier stages. A list of circulating miRNAs was identified in this study using bioinformatics methods in association with pancreatic cancer through analyzing four GEO microarray datasets. The value of top miRNAs was then assessed via using a machine learning method. Taking the advantage of a combinatorial approach consisting of Particle Swarm Optimization (PSO) + Artificial Neural Network (ANN) and Neighborhood Component Analysis (NCA) iterations on a collection of top differentially expressed circulating miRNAs in PC patients, facilitated ranking them by significance. MiRNA's functional analysis in the final index was performed by predicting target genes and constructing PPI networks. Remarkably, the final model consist of miR-663a, miR-1469, miR-92a-2-5p, miR-125b-1-3p and miR-532-5p showed great diagnostic results on investigated cases and the validation set (Accuracy: 0.93, Sensitivity: 0.93, and Specificity: 0.92). Kaplan-Meier survival assessments of the top-ranked miRNAs revealed that three miRNAs, hsa-miR-1469, hsa-miR-663a and hsa-miR-532-5p, had meaningful associations with the prognosis of patients with pancreatic cancer. This miRNA index may serve as a non-invasive and potential PC diagnostic model, although experimental testing is needed.
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Affiliation(s)
- Behrouz Alizadeh Savareh
- PhD in Medical Informatics, National Agency for Strategic Research in Medical Education, Tehran, Iran; Department of health information management, school of management and medical information sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Asadzadeh Aghdaie
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Behmanesh
- Student Research Committee, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Azadeh Bashiri
- Department of health information management, school of management and medical information sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roshanak Shams
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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37
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Fiala C, Diamandis EP. The Outcomes of Scientific Debates Should Be Published: The Arivale Story. J Appl Lab Med 2020; 5:1070-1075. [PMID: 32830260 DOI: 10.1093/jalm/jfaa110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022]
Abstract
There is an ongoing scientific debate regarding the merits and shortcomings of P4 Medicine (predictive, preventive, personalized, and participatory) and O4 Medicine (overtesting, overdiagnosis, overtreatment, and overcharging). P4 Medicine promises to revolutionize scientific wellness through longitudinal big data collection, denoted as "dense phenotyping," which could uncover early, actionable signs of disease, thus allowing earlier interventions and possible disease reversal. On the other hand, O4 Medicine draws attention to the potential side effects of P4 Medicine: overtesting, overdiagnosis, overtreatment, and overcharging fees. Preliminary data from the P4 Medicine concept have been recently published. A novel biotechnology company, Arivale, provided customers with services based on P4 Medicine principles; however it could not sustain its operations and closed its doors in April 2019. In this report, we provide our own insights as to why Arivale failed. While we do not discount that in the future, improved testing strategies may provide a path to better health, we suggest that until the evidence is provided, selling of such products to the public, especially through the "direct to consumer" approach, should be discouraged. We hope that our analysis will provide useful information for the burgeoning fields of personalized medicine, preventive medicine, and direct to consumer health testing.
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Affiliation(s)
- Clare Fiala
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
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38
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Ren AH, Prassas I, Soosaipillai A, Jarvi S, Gallinger S, Kulasingam V, Diamandis EP. Investigating a novel multiplex proteomics technology for detection of changes in serum protein concentrations that may correlate to tumor burden. F1000Res 2020; 9:732. [PMID: 33274048 PMCID: PMC7682495 DOI: 10.12688/f1000research.24654.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
Background: To account for cancer heterogeneity, we previously introduced the concept of "personalized" tumor markers, which are biomarkers that are informative in subsets of patients or even a single patient. Recent developments in various multiplex protein technologies create excitement for the discovery of markers of tumor burden in individual patients, but the reliability of the technologies remains to be tested for this purpose. Here, we sought to explore the potential of a novel proteomics platform, which utilizes a multiplexed antibody microarray, to detect changes in serum protein concentration that may correlate to tumor burden in pancreatic cancer. Methods: We applied the Quantibody® Human Kiloplex Array to simultaneously measure 1,000 proteins in sera obtained pre- and post-surgically from five pancreatic cancer patients. We expected that proteins which decreased post-surgery may correlate to tumor burden. Sera from two healthy individuals, split into two aliquots each, were used as controls. To validate the multiplexed results, we used single-target ELISA assays to measure the proteins with the largest serum concentration changes after surgery in sera collected pre- and post-surgically from the previous five patients and 10 additional patients. Results: The multiplexed array revealed nine proteins with more than two-fold post-surgical decrease in at least two of five patients. However, validation using single ELISAs showed that only two proteins tested displayed more than two-fold post-surgical decrease in one of the five original patients. In the independent cohort, six of the proteins tested showed at least a two-fold decrease post-surgery in at least one patient. Conclusions: Our study found that the Quantibody® Human Kiloplex Array results could not be reliably replicated with individual ELISA assays and most hits would likely represent false positives if applied to biomarker discovery. These findings suggest that data from novel, high-throughput proteomic platforms need stringent validation to avoid false discoveries.
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Affiliation(s)
- Annie He Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Stephanie Jarvi
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Steven Gallinger
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Pancreatic Surgical Oncology Program, University Health Network, Canada, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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39
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Ren AH, Prassas I, Soosaipillai A, Jarvi S, Gallinger S, Kulasingam V, Diamandis EP. Investigating a novel multiplex proteomics technology for detection of changes in serum protein concentrations that may correlate to tumor burden. F1000Res 2020; 9:732. [PMID: 33274048 PMCID: PMC7682495 DOI: 10.12688/f1000research.24654.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 03/31/2024] Open
Abstract
Background: To account for cancer heterogeneity, we previously introduced the concept of "personalized" tumor markers, which are biomarkers that are informative in subsets of patients or even a single patient. Recent developments in various multiplex protein technologies create excitement for the discovery of markers of tumor burden in individual patients, but the reliability of the technologies remains to be tested for this purpose. Here, we sought to explore the potential of a novel proteomics platform, which utilizes a multiplexed antibody microarray, to detect changes in serum protein concentration that may correlate to tumor burden in pancreatic cancer. Methods: We applied the Quantibody® Human Kiloplex Array to simultaneously measure 1,000 proteins in sera obtained pre- and post-surgically from five pancreatic cancer patients. We expected that proteins which decreased post-surgery may correlate to tumor burden. Sera from two healthy individuals, split into two aliquots each, were used as controls. To validate the multiplexed results, we used single-target ELISA assays to measure the proteins with the largest serum concentration changes after surgery in sera collected pre- and post-surgically from the previous five patients and 10 additional patients. Results: The multiplexed array revealed nine proteins with more than two-fold post-surgical decrease in at least two of five patients. However, validation using single ELISAs showed that only two proteins tested displayed more than two-fold post-surgical decrease in one of the five original patients. In the independent cohort, six of the proteins tested showed at least a two-fold decrease post-surgery in at least one patient. Conclusions: Our study found that the Quantibody® Human Kiloplex Array results could not be reliably replicated with individual ELISA assays and most hits would likely represent false positives if applied to biomarker discovery. These findings suggest that data from novel, high-throughput proteomic platforms need stringent validation to avoid false discoveries.
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Affiliation(s)
- Annie He Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Stephanie Jarvi
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Steven Gallinger
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Pancreatic Surgical Oncology Program, University Health Network, Canada, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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40
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Tanadi C, Bambang A, Wendi IP, Sidharta VM, Hananta L, Sumarpo A. The predictive value of PRDM2 in solid tumor: a systematic review and meta-analysis. PeerJ 2020; 8:e8826. [PMID: 32391195 PMCID: PMC7195840 DOI: 10.7717/peerj.8826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background Many studies have reported the presence of Positive Regulatory/Su(var)3-9, Enhancer-of-zeste and Trithorax Domain 2 (PRDM2) downregulation in cancer. However, its potential as a diagnostic biomarker is still unclear. Hence, a systematic review and meta-analysis were conducted to address this issue. Introduction As of 2018, cancer has become the second leading cause of death worldwide. Thus, cancer control is exceptionally vital in reducing mortality. One such example is through early diagnosis of cancer using tumor biomarkers. Having a function as a tumor suppressor gene (TSG), PRDM2 has been linked with carcinogenesis in several solid tumor. This study aims to assess the relationship between PRDM2 downregulation and solid tumor, its relationship with clinicopathological data, and its potential as a diagnostic biomarker. This study also aims to evaluate the quality of the studies, data reliability and confidence in cumulative evidence. Materials & Methods A protocol of this study is registered at the International Prospective Register of Systematic Reviews (PROSPERO) with the following registration number: CRD42019132156. PRISMA was used as a guideline to conduct this review. A comprehensive electronic search was performed from inception to June 2019 in Pubmed, Cochrane Library, ProQuest, EBSCO and ScienceDirect. Studies were screened and included studies were identified based on the criteria made. Finally, data synthesis and quality assessment were conducted. Results There is a significant relationship between PRDM2 downregulation with solid tumor (RR 4.29, 95% CI [2.58–7.13], P < 0.00001). The overall sensitivity and specificity of PRDM2 downregulation in solid tumors is 84% (95% CI [39–98%]) and 86% (95% CI [71–94%]), respectively. There is a low risk of bias for the studies used. TSA results suggested the presence of marked imprecision. The overall quality of evidence for this study is very low. Discussion We present the first meta-analysis that investigated the potential of PRDM2 downregulation as a diagnostic biomarker in solid tumor. In line with previous studies, our results demonstrated that PRDM2 downregulation occurs in solid tumor. A major source of limitation in this study is the small number of studies. Conclusions Our review suggested that PRDM2 is downregulated in solid tumor. The relationship between PRDM2 downregulation and clinicopathological data is still inconclusive. Although the sensitivity and specificity of PRDM2 downregulation are imprecise, its high values, in addition to the evidence that suggested PRDM2 downregulation in solid tumor, hinted that it might still have a potential to be used as a diagnostic biomarker. In order to further strengthen these findings, more research regarding PRDM2 in solid tumors are encouraged.
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Affiliation(s)
- Caroline Tanadi
- Undergraduate Medical Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Alfredo Bambang
- Department of Chemistry and Biochemistry, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Indra Putra Wendi
- Department of Chemistry and Biochemistry, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Veronika M Sidharta
- Department of Histology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Linawati Hananta
- Department of Pharmacology and Pharmacy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Anton Sumarpo
- Department of Chemistry and Biochemistry, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
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41
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Raiter A, Lipovetzki J, Lubin I, Yerushalmi R. GRP78 expression in peripheral blood mononuclear cells is a new predictive marker for the benefit of taxanes in breast cancer neoadjuvant treatment. BMC Cancer 2020; 20:333. [PMID: 32306920 PMCID: PMC7168854 DOI: 10.1186/s12885-020-06835-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Breast cancer treatment is tailored to the specific cancer subtype. Often, systemic treatment is given prior to surgery. Chemotherapy induces significant endoplasmic reticulum (ER) stress-mediated cell death and upregulation of 78-kDa glucose-regulated protein (GRP78). We hypothesized that chemotherapy induces ER stress not only in the tumor tissue but also in immune cells, which may affect the response to anti-cancer treatment. METHODS We determined the surface expression of GRP78 on 15 different peripheral blood mononuclear cell (PBMC) subpopulations in 20 breast cancer patients at three time points of the neoadjuvant treatment, i.e., at baseline, after anthracycline treatment, and after taxanes treatment. For this purpose, we performed flow cytometric analyses and analyzed the data using ANOVA and the Tukey test. Serum cytokine levels were also evaluated, and their levels were correlated with response to treatment using the t-test after log transformation and Mann-Whitney U Wilcoxon W test. RESULTS A significant increase in GRP78 expression in PBMCs was documented during the taxane phase, only in patients who achieved pathological complete response (pCR). GRP78-positive clones correlated with increased serum levels of interferon gamma (IFNγ). CONCLUSIONS The presence of GRP78-positive clones in certain PBMC subpopulations in pCR patients suggests a dynamic interaction between ER stress and immune responsiveness. The correlation of GRP78-positive clones with increased levels of IFNγ supports the idea that GRP78 expression in PBMCs might serve as a new predictive marker to identify the possible benefits of taxanes in the neoadjuvant setting.
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Affiliation(s)
- Annat Raiter
- Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Rabin Medical Center, Beilinson Campus, 49100, Petach Tikva, Israel.
| | - Julia Lipovetzki
- Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Rabin Medical Center, Beilinson Campus, 49100, Petach Tikva, Israel
| | - Ido Lubin
- Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Rabin Medical Center, Beilinson Campus, 49100, Petach Tikva, Israel
| | - Rinat Yerushalmi
- Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Rabin Medical Center, Beilinson Campus, 49100, Petach Tikva, Israel.
- Davidoff Cancer Center, Rabin Medical Center, Beilinson Campus, 49100, Petach Tikva, Israel.
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42
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Ren AH, Fiala CA, Diamandis EP, Kulasingam V. Pitfalls in Cancer Biomarker Discovery and Validation with Emphasis on Circulating Tumor DNA. Cancer Epidemiol Biomarkers Prev 2020; 29:2568-2574. [PMID: 32277003 DOI: 10.1158/1055-9965.epi-20-0074] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/19/2020] [Accepted: 04/03/2020] [Indexed: 11/16/2022] Open
Abstract
Despite significant investment of funds and resources, few new cancer biomarkers have been introduced to the clinic in the last few decades. Although many candidates produce promising results in the laboratory, deficiencies in sensitivity, specificity, and predictive value make them less than desirable in a patient setting. This review will analyze these challenges in detail as well as discuss false discovery, problems with reproducibility, and tumor heterogeneity. Circulating tumor DNA (ctDNA), an emerging cancer biomarker, is also analyzed, particularly in the contexts of assay specificity, sensitivity, fragmentation, lead time, mutant allele fraction, and clinical relevance. Emerging artificial intelligence technologies will likely be valuable tools in maximizing the clinical utility of ctDNA which is often found in very small quantities in patients with early-stage tumors. Finally, the implications of challenging false discoveries are examined and some insights about improving cancer biomarker discovery are provided.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Annie H Ren
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Clare A Fiala
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. .,Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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43
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Dragani TA, Matarese V, Colombo F. Biomarkers for Early Cancer Diagnosis: Prospects for Success through the Lens of Tumor Genetics. Bioessays 2020; 42:e1900122. [PMID: 32128843 DOI: 10.1002/bies.201900122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 01/15/2020] [Indexed: 12/14/2022]
Abstract
Thousands of candidate cancer biomarkers have been proposed, but so far, few are used in cancer screening. Failure to implement these biomarkers is attributed to technical and design flaws in the discovery and validation phases, but a major obstacle stems from cancer biology itself. Oncogenomics has revealed broad genetic heterogeneity among tumors of the same histology and same tissue (or organ) from different patients, while tumors of different tissue origins also share common genetic mutations. Moreover, there is wide intratumor genetic heterogeneity among cells within any single neoplasm. These findings seriously limit the prospects of finding a single biomarker with high specificity for early cancer detection. Current research focuses on developing biomarker panels, with data assessment by machine-learning algorithms. Whether such approaches will overcome the inherent limitations posed by tumor biology and lead to tests with true clinical value remains to be seen.
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Affiliation(s)
- Tommaso A Dragani
- Department of Research , Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. A. Amadeo, 42, I-20133, Milan, Italy
| | | | - Francesca Colombo
- Department of Research , Fondazione IRCCS Istituto Nazionale dei Tumori, Via G. A. Amadeo, 42, I-20133, Milan, Italy
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44
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Mass Spectrometry-Based Multivariate Proteomic Tests for Prediction of Outcomes on Immune Checkpoint Blockade Therapy: The Modern Analytical Approach. Int J Mol Sci 2020; 21:ijms21030838. [PMID: 32012941 PMCID: PMC7036840 DOI: 10.3390/ijms21030838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 02/06/2023] Open
Abstract
The remarkable success of immune checkpoint inhibitors (ICIs) has given hope of cure for some patients with advanced cancer; however, the fraction of responding patients is 15-35%, depending on tumor type, and the proportion of durable responses is even smaller. Identification of biomarkers with strong predictive potential remains a priority. Until now most of the efforts were focused on biomarkers associated with the assumed mechanism of action of ICIs, such as levels of expression of programmed death-ligand 1 (PD-L1) and mutation load in tumor tissue, as a proxy of immunogenicity; however, their performance is unsatisfactory. Several assays designed to capture the complexity of the disease by measuring the immune response in tumor microenvironment show promise but still need validation in independent studies. The circulating proteome contains an additional layer of information characterizing tumor-host interactions that can be integrated into multivariate tests using modern machine learning techniques. Here we describe several validated serum-based proteomic tests and their utility in the context of ICIs. We discuss test performances, demonstrate their independence from currently used biomarkers, and discuss various aspects of associated biological mechanisms. We propose that serum-based multivariate proteomic tests add a missing piece to the puzzle of predicting benefit from ICIs.
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45
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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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Wang X, Deng H, Wang C, Wei Q, Wang Y, Xiong X, Li C, Li W. A pro-gastrin-releasing peptide imprinted photoelectrochemical sensor based on the in situ growth of gold nanoparticles on a MoS2 nanosheet surface. Analyst 2020; 145:1302-1309. [DOI: 10.1039/c9an02201e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Molecularly imprinted PEC platform for Pro-GRP sensing was prepared using lamellar MoS2 nanosheets assembled with gold nanoparticles as photoactive elements. The molecularly imprinted PEC sensor shows excellent sensing performances towards Pro-GRP.
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Affiliation(s)
- Xing Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education
- Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
| | - Hongping Deng
- Department of Vascular Surgery and Central Laboratory
- Renmin Hospital of Wuhan University
- Wuhan
- 430060
- China
| | - Chen Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education
- Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
| | - Qiuxi Wei
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education
- Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
| | - Yanying Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education
- Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
| | - Xiaoxing Xiong
- Department of Vascular Surgery and Central Laboratory
- Renmin Hospital of Wuhan University
- Wuhan
- 430060
- China
| | - Chunya Li
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education
- Hubei Key Laboratory of Catalysis and Materials Science
- South-Central University for Nationalities
- Wuhan 430074
| | - Wenwen Li
- School of Pharmaceutical Sciences
- Wenzhou Medical University
- Wenzhou 325035
- China
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Karami E, Soliman H, Ruschin M, Sahgal A, Myrehaug S, Tseng CL, Czarnota GJ, Jabehdar-Maralani P, Chugh B, Lau A, Stanisz GJ, Sadeghi-Naini A. Quantitative MRI Biomarkers of Stereotactic Radiotherapy Outcome in Brain Metastasis. Sci Rep 2019; 9:19830. [PMID: 31882597 PMCID: PMC6934477 DOI: 10.1038/s41598-019-56185-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/08/2019] [Indexed: 02/08/2023] Open
Abstract
About 20-40% of cancer patients develop brain metastases, causing significant morbidity and mortality. Stereotactic radiation treatment is an established option that delivers high dose radiation to the target while sparing the surrounding normal tissue. However, up to 20% of metastatic brain tumours progress despite stereotactic treatment, and it can take months before it is evident on follow-up imaging. An early predictor of radiation therapy outcome in terms of tumour local failure (LF) is crucial, and can facilitate treatment adjustments or allow for early salvage treatment. In this study, an MR-based radiomics framework was proposed to derive and investigate quantitative MRI (qMRI) biomarkers for the outcome of LF in brain metastasis patients treated with hypo-fractionated stereotactic radiation therapy (SRT). The qMRI biomarkers were constructed through a multi-step feature extraction/reduction/selection framework using the conventional MR imaging data acquired from 100 patients (133 lesions), and were applied in conjunction with machine learning techniques for outcome prediction and risk assessment. The results indicated that the majority of the features in the optimal qMRI biomarkers characterize the heterogeneity in the surrounding regions of tumour including edema and tumour/lesion margins. The optimal qMRI biomarker consisted of five features that predict the outcome of LF with an area under the curve (AUC) of 0.79, and a cross-validated sensitivity and specificity of 81% and 79%, respectively. The Kaplan-Meier analyses showed a statistically significant difference in local control (p-value < 0.0001) and overall survival (p = 0.01). Findings from this study are a step towards using qMRI for early prediction of local failure in brain metastasis patients treated with SRT. This may facilitate early adjustments in treatment, such as surgical resection or salvage radiation, that can potentially improve treatment outcomes. Investigations on larger cohorts of patients are, however, required for further validation of the technique.
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Affiliation(s)
- Elham Karami
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Hany Soliman
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Mark Ruschin
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Arjun Sahgal
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Sten Myrehaug
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Chia-Lin Tseng
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Gregory J Czarnota
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Brige Chugh
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Angus Lau
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Greg J Stanisz
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Neurosurgery and Pediatric Neurosurgery, Medical University, Lublin, Poland
| | - Ali Sadeghi-Naini
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
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Ghannad M, Olsen M, Boutron I, Bossuyt PM. A systematic review finds that spin or interpretation bias is abundant in evaluations of ovarian cancer biomarkers. J Clin Epidemiol 2019; 116:9-17. [DOI: 10.1016/j.jclinepi.2019.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 06/20/2019] [Accepted: 07/15/2019] [Indexed: 11/26/2022]
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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Griffiths SG, Ezrin A, Jackson E, Dewey L, Doucette AA. A robust strategy for proteomic identification of biomarkers of invasive phenotype complexed with extracellular heat shock proteins. Cell Stress Chaperones 2019; 24:1197-1209. [PMID: 31650515 PMCID: PMC6882979 DOI: 10.1007/s12192-019-01041-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/03/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
As an extension of their orchestration of intracellular pathways, secretion of extracellular heat shock proteins (HSPs) is an emerging paradigm of homeostasis imperative to multicellular organization. Extracellular HSP is axiomatic to the survival of cells during tumorigenesis; proportional representation of specific HSP family members is indicative of invasive potential and prognosis. Further significance has been added by the knowledge that all cancer-derived exosomes have surface-exposed HSPs that reflect the membrane topology of cells that secrete them. Extracellular HSPs are also characteristic of chronic inflammation and sepsis. Accordingly, interrogation of extracellular HSPs secreted from cell culture models may represent a facile means of identifying translational biomarker signatures for targeting in situ. In the current study, we evaluated a simple peptide-based multivalent HSP affinity approach using the Vn96 peptide for low speed pelleting of HSP complexes from bioreactor cultures of cell lines with varying invasive phenotype in xenotransplant models: U87 (glioblastoma multiforme; invasive); HELA (choriocarcinoma; minimally invasive); HEK293T (virally transformed immortalized; embryonic). Proteomic profiling by bottom-up mass spectrometry revealed a comprehensive range of candidate biomarkers including primary HSP ligands. HSP complexes were associated with additional chaperones of prognostic significance such as protein disulfide isomerases, as well as pleiotropic metabolic enzymes, established as proportionally reflective of invasive phenotype. Biomarkers of inflammatory and mechanotransductive phenotype were restricted to the most invasive cell model U87, including chitinase CHI3L1, lamin C, amyloid derivatives, and histone isoforms.
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Affiliation(s)
| | - Alan Ezrin
- NX Development Corporation, Louisville, KY, USA
| | - Emily Jackson
- David H. Murdock Research Institute, Kannapolis, NC, USA
| | - Lisa Dewey
- David H. Murdock Research Institute, Kannapolis, NC, USA
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