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The Current Status of Molecular Biomarkers for Inflammatory Bowel Disease. Biomedicines 2022; 10:biomedicines10071492. [PMID: 35884797 PMCID: PMC9312796 DOI: 10.3390/biomedicines10071492] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Diagnosis and prognosis of inflammatory bowel disease (IBD)-a chronic inflammation that affects the gastrointestinal tract of patients-are challenging, as most clinical symptoms are not specific to IBD, and are often seen in other inflammatory diseases, such as intestinal infections, drug-induced colitis, and monogenic diseases. To date, there is no gold-standard test for monitoring IBD. Endoscopy and imaging are essential diagnostic tools that provide information about the disease's state, location, and severity. However, the invasive nature and high cost of endoscopy make it unsuitable for frequent monitoring of disease activity in IBD patients, and even when it is possible to replace endoscopy with imaging, high cost remains a concern. Laboratory testing of blood or feces has the advantage of being non-invasive, rapid, cost-effective, and standardizable. Although the specificity and accuracy of laboratory testing alone need to be improved, it is increasingly used to monitor disease activity or to diagnose suspected IBD cases in combination with endoscopy and/or imaging. The literature survey indicates a dearth of summarization of biomarkers for IBD testing. This review introduces currently available non-invasive biomarkers of clinical importance in laboratory testing for IBD, and discusses the trends and challenges in the IBD biomarker studies.
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Núñez L, Marrón-Liñares GM, Crespo-Leiro MG, Barge-Caballero E, Álvarez-López E, Suarez-Fuentetaja N, Paniagua-Martin MJ, Pombo J, Muñiz J, Tan CD, Rodríguez ER, Vázquez-Rodríguez JM, Hermida-Prieto M. AGT haplotype in ITGA4 gene is related to antibody-mediated rejection in heart transplant patients. PLoS One 2019; 14:e0219345. [PMID: 31335901 PMCID: PMC6650139 DOI: 10.1371/journal.pone.0219345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/05/2019] [Indexed: 11/29/2022] Open
Abstract
Introduction One of the main problems involved in heart transplantation (HT) is antibody-mediated rejection (AMR). Many aspects of AMR are still unresolved, including its etiology, diagnosis and treatment. In this project, we hypothesize that variants in genes involved in B-cell biology in HT patients can yield diagnostic and prognostic information about AMR. Methods Genetic variants in 61 genes related to B-cell biology were analyzed by next generation sequencing in 46 HT patients, 23 with and 23 without AMR. Results We identified 3 single nucleotide polymorphisms in ITGA4 gene (c.1845G>A, c.2633A>G, and c.2883C>T) that conformed the haplotype AGT-ITGA4. This haplotype is associated with the development of AMR. Moreover, AMR patients with the haplotype AGT-ITGA4 present lower levels of integrin α-4 in serum samples compared to the reference GAC haplotype in control patients. Conclusion We can conclude that polymorphisms in genes related to the biology of B-cells could have an important role in the development of AMR. In fact, the AGT haplotype in ITGA4 gene could potentially increase the risk of AMR.
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Affiliation(s)
- Lucía Núñez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - Grecia M. Marrón-Liñares
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - María G. Crespo-Leiro
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Eduardo Barge-Caballero
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Eloy Álvarez-López
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Suarez-Fuentetaja
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - María Jesús Paniagua-Martin
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Jorge Pombo
- Servicio de Anatomía Patológica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, A Coruña, Spain
| | - Javier Muñiz
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - Carmela D. Tan
- Department of Pathology, The Cleveland Clinic, Cleveland, Ohio, United States of America
| | - E. René Rodríguez
- Department of Pathology, The Cleveland Clinic, Cleveland, Ohio, United States of America
| | - José Manuel Vázquez-Rodríguez
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Manuel Hermida-Prieto
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
- * E-mail:
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Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases. Sci Rep 2019; 9:7190. [PMID: 31076612 PMCID: PMC6510750 DOI: 10.1038/s41598-019-43699-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are heterogeneous chronic autoimmune diseases that may share underlying pathogenic mechanisms. Herein, we compared simultaneously analyzed blood transcriptomes from patients with PBC, PSC, and IBD. Microarray-based measurements were conducted using RNA isolated from whole blood samples from 90, 45, 95 and 93 patients with PBC, PSC, CD, and UC, respectively, and 47 healthy controls. Expression levels of selected transcripts were analyzed by quantitative reverse-transcribed PCR using an independent cohort of 292, 71 and 727 patients with PBC, PSC, and IBD, respectively. Of 4026, 2650 and 4967 probe sets differentially expressed (adjusted p-value < 0.05) in samples from patients with PBC, PSC, and IBD, respectively, compared with healthy controls, 1946 were common to all three comparisons. Functional analyses indicated that most terms enriched for genes differentially expressed in PBC, PSC, and IBD patients compared with healthy controls were related to mitochondrial function, the vesicle endomembrane system, and GTPase-mediated processes. This study indicates that microarray-based profiling of blood gene expression supports research into the molecular mechanisms underlying disease, rather than being useful for selection of diagnostic biomarkers for use in clinical practice.
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Ostrowski J, Dabrowska M, Lazowska I, Paziewska A, Balabas A, Kluska A, Kulecka M, Karczmarski J, Ambrozkiewicz F, Piatkowska M, Goryca K, Zeber-Lubecka N, Kierkus J, Socha P, Lodyga M, Klopocka M, Iwanczak B, Bak-Drabik K, Walkowiak J, Radwan P, Grzybowska-Chlebowczyk U, Korczowski B, Starzynska T, Mikula M. Redefining the Practical Utility of Blood Transcriptome Biomarkers in Inflammatory Bowel Diseases. J Crohns Colitis 2019; 13:626-633. [PMID: 30541017 PMCID: PMC6486489 DOI: 10.1093/ecco-jcc/jjy205] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS The study investigates the practical utility of whole-blood gene expression profiling to diagnose inflammatory bowel diseases [IBDs]. METHODS The discovery cohorts included 102 and 51 paediatric IBD patients and controls, and 95 and 46 adult IBD patients and controls, respectively. The replication cohorts included 447 and 76 paediatric IBD patients and controls, and 271 and 108 adult IBD patients and controls, respectively. In the discovery phase, RNA samples extracted from whole peripheral blood were analysed using RNA-Seq, and the predictive values of selected biomarkers were validated using quantitative polymerase chain reaction [qPCR]. RESULTS In all, 15 differentially expressed transcripts [adjusted p ≤0.05] were selected from the discovery sequencing datasets. The receiver operating characteristic curves and area under the curve [ROC-AUC] in replication analyses showed high discriminative power [AUC range, 0.91-0.98] for 11 mRNAs in paediatric patients with active IBD. By contrast, the AUC-ROC values ranged from 0.63 to 0.75 in comparison among inactive paediatric IBDs and active/inactive adult IBDs, indicating a lack of discriminative power. The best multi-mRNA diagnostic classifier showed moderate discriminative power [AUC = 0.81] for paediatric inactive IBD, but was not able to discriminate active or inactive adult IBD patients from controls. The AUC-ROC values did not confirm an ability of the mRNAs abundances to discriminate between active ulcerative colitis and active Crohn's disease in paediatric or adult populations. CONCLUSIONS This study identifies and validates blood transcriptional biomarkers that could be used in clinical settings as diagnostic predictors of IBD clinical activity in paediatric, but not adult, IBD patients.
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Affiliation(s)
- Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland,Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland,Corresponding author: Jerzy Ostrowski, MD, PhD; Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland. Tel.: +48 225462575; e-mail:
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Izabella Lazowska
- Department of Pediatric Gastroenterology and Nutrition, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jaroslaw Kierkus
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children’s Memorial Health Institute, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children’s Memorial Health Institute, Warsaw, Poland
| | - Michal Lodyga
- Department of Internal Medicine and Gastroenterology with IBD Subdivision, Central Clinical Hospital of the Ministry of the Interior, Warsaw, Poland
| | - Maria Klopocka
- Vascular Diseases and Internal Medicine, Nicolaus Copernicus University in Torun, Collegium Medicum, Bydgoszcz, Poland
| | - Barbara Iwanczak
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Bak-Drabik
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Jaroslaw Walkowiak
- Department of Pediatric Gastroenterology & Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Radwan
- Department of Gastroenterology, Medical University of Lublin, Lublin, Poland
| | | | | | - Teresa Starzynska
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
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Shi J, Cheng C, Ma J, Liew CC, Geng X. Gene expression signature for detection of gastric cancer in peripheral blood. Oncol Lett 2018; 15:9802-9810. [PMID: 29928354 PMCID: PMC6004726 DOI: 10.3892/ol.2018.8577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer (stomach cancer) is the fifth most common malignancy and the third leading cause of cancer-associated mortality worldwide. Identifying gastric cancer patients at an early and curable stage of the disease is essential if mortality rates for this disease are to decrease. A non-invasive blood-based test that is an indicator of gastric cancer risk would likely be of benefit in identifying gastric cancer patients at an early stage, and such a test may enhance clinical decision making. This study identified a four-gene expression signature in peripheral blood samples associated with gastric cancer. A total of 216 blood samples were collected, including those from 36 gastric cancer patients, 55 healthy controls and 125 patients with other carcinomas, and gene expression profiles were examined using an Affymetrix Gene Profiling microarray. Blood gene expression profiles were compared between patients with stomach cancer, healthy controls and patients affected with other malignancies. A four-gene panel was identified comprising purine-rich element binding protein B, structural maintenance of chromosomes 1A, DENN/MADD domain containing 1B and programmed cell death 4. The four-gene panel discriminated gastric cancer with an area under the receiver-operating-characteristic curve of 0.99, an accuracy of 95%, sensitivity of 92% and specificity of 96%. The non-invasive nature of the blood test, together with the relatively high accuracy of the four-gene panel may assist physicians in gastric cancer screening decision making.
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Affiliation(s)
- Jianing Shi
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Changming Cheng
- Sentinel Center, Shanghai Biomedical Laboratory, Shanghai 200436, P.R. China.,National Engineering Center for Biochip at Shanghai, Shanghai Biochip Co., Ltd., Shanghai 201203, P.R. China
| | - Jun Ma
- Department of Research, Golden Health Diagnostics Inc., Yancheng, Jiangsu 224000, P.R. China
| | - Choong-Chin Liew
- Sentinel Center, Shanghai Biomedical Laboratory, Shanghai 200436, P.R. China.,Department of Research, Golden Health Diagnostics Inc., Yancheng, Jiangsu 224000, P.R. China.,Department of Clinical Pathology and Laboratory Medicine, University of Toronto, Toronto, Ontario, ON M5S 1A8, Canada.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoping Geng
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
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Abstract
Despite advances in our understanding of the pathophysiology underlying inflammatory bowel disease, there remains a significant need for biomarkers that can differentiate between Crohn's disease and ulcerative colitis with high sensitivity and specificity, in a cost-efficient manner. As the focus on personalized approaches to the delivery of medical treatment increases, new biomarkers are being developed to predict an individual's response to therapy and their overall disease course. In this review, we will outline many of the existing and recently developed biomarkers, detailing their role in the assessment of patients with inflammatory bowel disease. We will identify opportunities for improvement in our biomarkers, including better differentiation between the subtypes of inflammatory bowel disease. We will also discuss new targets and strategies in biomarker development, including combining modalities to create biomarker signatures to improve the ability to predict disease courses and response to therapy among individual patients.
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Barnes EL, Liew CC, Chao S, Burakoff R. Use of blood based biomarkers in the evaluation of Crohn’s disease and ulcerative colitis. World J Gastrointest Endosc 2015; 7:1233-1237. [PMID: 26634038 PMCID: PMC4658602 DOI: 10.4253/wjge.v7.i17.1233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/14/2015] [Accepted: 10/13/2015] [Indexed: 02/05/2023] Open
Abstract
Despite significant improvements in our understanding of Crohn’s disease (CD) and ulcerative colitis (UC) in recent years, questions remain regarding the best approaches to assessment and management of these chronic diseases during periods of both relapse and remission. Various serologic biomarkers have been used in the evaluation of patients with both suspected and documented inflammatory bowel disease (IBD), and while each has potential utility in the assessment of patients with IBD, potential limitation remain with each method of assessment. Given these potential shortcomings, there has been increased interest in other means of evaluation of patients with IBD, including an expanding interest in the role of gene expression profiling. Among patients with IBD, gene expression profiles obtained from whole blood have been used to differentiate active from inactive CD, as well as to differentiate between CD, UC, and non-inflammatory diarrheal conditions. There are many opportunities for a non-invasive, blood based test to aid in the assessment of patients with IBD, particularly when considering more invasive means of evaluation including endoscopy with biopsy. Furthermore, as the emphasis on personalized medicine continues to increase, the potential ability of gene expression analysis to predict patient response to individual therapies offers great promise. While whole blood gene expression analysis may not completely replace more traditional means of evaluating patients with suspected or known IBD, it does offer significant potential to expand our knowledge of the underlying genes involved in the development of these diseases.
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Abstract
BACKGROUND Identifying specific genes that are differentially expressed during inflammatory bowel disease flares may help stratify disease activity. The aim of this study was to identify panels of genes to be able to distinguish disease activity in Crohn's disease (CD) and ulcerative colitis (UC). METHODS Patients were grouped into categories based on disease and severity determined by histological grading. Whole blood was collected by PAXgene Blood RNA collection tubes, (PreAnalytiX) and gene expression analysis using messenger RNA was conducted. Logistic regression was performed on multiple combinations of common probe sets, and data were evaluated in terms of discrimination by computing the area under the receiving operator characteristic curve (ROC-AUC). RESULTS Nine inactive CD, 8 mild CD, 10 moderate-to-severe CD, 9 inactive UC, 8 mild UC, 10 moderate-to-severe UC, and 120 controls were hybridized to Affymetrix U133 Plus 2 microarrays. Panels of 6 individual genes discriminated the stages of disease activity: CD with mild severity {ROC-AUC, 0.89 (95% confidence interval [CI], 0.84%-0.95%)}, CD with moderate-to-severe severity (ROC-AUC 0.98 [95% CI, 0.97-1.0]), UC with mild severity (ROC-AUC 0.92 [95% CI, 0.87-0.96]), and UC with moderate-to-severe severity (ROC-AUC 0.99 [95% CI, 0.97-1.0]). Validation by real-time reverse transcription-PCR confirmed the Affymetrix microarray data. CONCLUSIONS The specific whole blood gene panels reliably distinguished CD and UC and determined the activity of disease, with high sensitivity and specificity in our cohorts of patients. This simple serological test has the potential to become a biomarker to determine the activity of disease.
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Chao S, Ying J, Liew G, Marshall W, Liew CC, Burakoff R. Blood RNA biomarker panel detects both left- and right-sided colorectal neoplasms: a case-control study. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2013; 32:44. [PMID: 23876008 PMCID: PMC3734158 DOI: 10.1186/1756-9966-32-44] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/17/2013] [Indexed: 12/14/2022]
Abstract
Background Colonoscopy is widely regarded to be the gold standard for colorectal cancer (CRC) detection. Recent studies, however, suggest that the effectiveness of colonoscopy is mostly confined to tumors on the left side of the colon (descending, sigmoid, rectum), and that the technology has poor tumor detection for right-sided (cecum, ascending, transverse) lesions. A minimally invasive test that can detect both left-sided and right-sided lesions could increase the effectiveness of screening colonoscopy by revealing the potential presence of neoplasms in the right-sided “blind spot”. Methods We previously reported on a seven-gene, blood-based biomarker panel that effectively stratifies a patient’s risk of having CRC. For the current study, we assessed the effectiveness of the seven-gene panel for the detection of left- and right-sided CRC lesions. Results were evaluated for 314 patients with CRC (left-sided: TNM I, 65; TNM II, 57; TNM III, 60; TNM IV, 17; unknown, 9. right-sided: TNM I, 28; TNM II, 29; TNM III, 38; TNM IV, 12; unknown, 1 and including two samples with both left and right lesions) and 328 control samples. Blood samples were obtained prior to clinical staging and therapy. Most CRC subjects had localized disease (stages I and II, 58%); regional (stage III) and systemic (stage IV) disease represented 32% and 9%, respectively, of the study population. Results The panel detected left-sided (74%, 154/208) and right-sided (85%, 92/108) lesions with an overall sensitivity of 78% (215/316) at a specificity of 66% (215/328). Treatable cancer (stages I to III) was detected with left-sided lesion sensitivity of 76% (138/182) and right-sided sensitivity of 84% (80/95). Conclusion This seven-gene biomarker panel detected right-sided CRC lesions across all cancer stages with a sensitivity that is at least equal to that for left-sided lesions. This study supports the use of this panel as the basis for a patient-friendly, blood-based test that can be easily incorporated into a routine physical examination in advance of colonoscopy to provide a convenient companion diagnostic and a pre-screening alert, ultimately leading to enhanced CRC screening effectiveness.
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Affiliation(s)
- Samuel Chao
- GeneNews Ltd, 2 East Beaver Creek Road, Building 2, Richmond Hill, Ontario, Canada
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Zaatar AM, Lim CR, Bong CW, Lee MML, Ooi JJ, Suria D, Raman R, Chao S, Yang H, Neoh SB, Liew CC. Whole blood transcriptome correlates with treatment response in nasopharyngeal carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2012; 31:76. [PMID: 22986368 PMCID: PMC3504566 DOI: 10.1186/1756-9966-31-76] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/28/2012] [Indexed: 02/07/2023]
Abstract
Background Treatment protocols for nasopharyngeal carcinoma (NPC) developed in the past decade have significantly improved patient survival. In most NPC patients, however, the disease is diagnosed at late stages, and for some patients treatment response is less than optimal. This investigation has two aims: to identify a blood-based gene-expression signature that differentiates NPC from other medical conditions and from controls and to identify a biomarker signature that correlates with NPC treatment response. Methods RNA was isolated from peripheral whole blood samples (2 x 10 ml) collected from NPC patients/controls (EDTA vacutainer). Gene expression patterns from 99 samples (66 NPC; 33 controls) were assessed using the Affymetrix array. We also collected expression data from 447 patients with other cancers (201 patients) and non-cancer conditions (246 patients). Multivariate logistic regression analysis was used to obtain biomarker signatures differentiating NPC samples from controls and other diseases. Differences were also analysed within a subset (n = 28) of a pre-intervention case cohort of patients whom we followed post-treatment. Results A blood-based gene expression signature composed of three genes — LDLRAP1, PHF20, and LUC7L3 — is able to differentiate NPC from various other diseases and from unaffected controls with significant accuracy (area under the receiver operating characteristic curve of over 0·90). By subdividing our NPC cohort according to the degree of patient response to treatment we have been able to identify a blood gene signature that may be able to guide the selection of treatment. Conclusion We have identified a blood-based gene signature that accurately distinguished NPC patients from controls and from patients with other diseases. The genes in the signature, LDLRAP1, PHF20, and LUC7L3, are known to be involved in carcinoma of the head and neck, tumour-associated antigens, and/or cellular signalling. We have also identified blood-based biomarkers that are (potentially) able to predict those patients who are more likely to respond to treatment for NPC. These findings have significant clinical implications for optimizing NPC therapy.
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Affiliation(s)
- Adel M Zaatar
- Mount Miriam Cancer Hospital, 23, Jalan Bulan, Fettes Park, Tanjong Bungah 11200Penang, Malaysia
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Abstract
Crohn's disease is a chronic relapsing condition that has no certain cure. Both genetic susceptibility and nutrition have key roles, but their level of involvement varies between patients. Interacting gene pathways influence the probability of disease development, but these are affected by stress and various environmental factors, including diet. In addition, the role of the gut microbiome must not be underestimated, as it is substantially altered in patients with Crohn's disease. Although an elemental diet might lead to disease remission, reintroducing real foods and sustainable diets in patients with Crohn's disease is currently difficult, and would benefit from the sensitivity and rapid feedback provided by the field of nutrigenomics. Nutrigenomics utilizes high-throughput genomics technologies to reveal changes in gene and protein expression that are modulated by the patient's nutrition. The most widely used technique thus far is transcriptomics, which permits measurement of changes in the expression of thousands of genes simultaneously in one sample. Given the volume of numbers generated in such studies, data-basing and bioinformatics are essential to ensure the correct application of nutrigenomics at the population level. These methods have been successfully applied to animal models of Crohn's disease, and the time is right to move them to human studies.
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Affiliation(s)
- Lynnette R Ferguson
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
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Burakoff R, Chao S, Perencevich M, Ying J, Friedman S, Makrauer F, Odze R, Khurana H, Liew CC. Blood-based biomarkers can differentiate ulcerative colitis from Crohn's disease and noninflammatory diarrhea. Inflamm Bowel Dis 2011; 17:1719-25. [PMID: 21744426 DOI: 10.1002/ibd.21574] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/07/2010] [Indexed: 01/15/2023]
Abstract
BACKGROUND Blood gene expression profiling has been used in several studies to identify patients with a number of conditions and diseases. A blood test with the ability to differentiate Crohn's disease (CD) from ulcerative colitis (UC) and noninflammatory diarrhea would be useful in the clinical management of these diseases. METHODS Affymetrix U133Plus 2.0 GeneChip oligonucleotide arrays were used to generate whole blood gene expression profiles for 21 patients with UC, 24 patients with CD, and 10 control patients with diarrhea, but without colonic pathology. RESULTS A supervised learning method (logistic regression) was used to identify specific panels of probe sets which were able to discriminate between UC and CD and from controls. The UC panel consisted of the four genes, CD300A, KPNA4, IL1R2, and ELAVL1; the CD panel comprised the four genes CAP1, BID, NIT2, and NPL. These panels clearly differentiated between CD and UC. CONCLUSIONS Gene expression profiles from blood can differentiate patients with CD from those with UC and from noninflammatory diarrheal disorders.
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Affiliation(s)
- Robert Burakoff
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
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