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Cisneros E, Martínez-Padilla A, Cardenas C, Márquez J, Ortega de Mues A, Roza C. Identification of Potential Visceral Pain Biomarkers in Colon Exudates from Mice with Experimental Colitis: An Exploratory In Vitro Study. THE JOURNAL OF PAIN 2023; 24:874-887. [PMID: 36638875 DOI: 10.1016/j.jpain.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023]
Abstract
Chronic visceral pain (CVP) is extremely difficult to diagnose, and available analgesic treatment options are quite limited. Identifying the proteins secreted from the colonic nociceptors, or their neighbor cells within the tube walls, in the context of disorders that course with visceral pain, might be useful to decipher the mechanism involved in the establishment of CVP. Addressing this question in human with gastrointestinal disorders entails multiple difficulties, as there is not a clear classification of disease severity, and colonic secretion is not easy to manage. We propose using of a murine model of colitis to identify new algesic molecules and pathways that could be explored as pain biomarkers or analgesia targets. Descending colons from naïve and colitis mice with visceral hyperalgesia were excised and maintained ex vivo. The proteins secreted in the perfusion fluid before and during acute noxious distension were evaluated using high-resolution mass spectrometry (MS). Haptoglobin (Hp), PZD and LIM domain protein 3 (Pdlim3), NADP-dependent malic enzyme (Me1), and Apolipoprotein A-I (Apoa1) were increased during visceral insult, whilst Triosephosphate isomerase (Tpi1), Glucose-6-phosphate isomerase (Gpi1), Alpha-enolase (Eno1), and Isoform 2 of Tropomyosin alpha-1 chain (Tpm1) were decreased. Most identified proteins have been described in the context of different chronic pain conditions and, according to gene ontology analysis, they are also involved in diverse biological processes of relevance. Thus, animal models that mimic human conditions in combination with unbiased omics approaches will ultimately help to identify new pathophysiological mechanisms underlying pain that might be useful in diagnosing and treating pain. PERSPECTIVE: Our study utilizes an unbiased proteomic approach to determine, first, the clinical relevance of a murine model of colitis and, second, to identify novel molecules/pathways involved in nociception that would be potential biomarkers or targets for chronic visceral pain.
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Affiliation(s)
- Elsa Cisneros
- Facultad de Ciencias de la Salud, Universidad Internacional de la Rioja (UNIR), Logroño, La Rioja, Spain
| | - Anabel Martínez-Padilla
- Canceromics Lab, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto de Investigación Biomédica de Málaga (IBIMA-Plataforma BIONAND), Universidad de Málaga, Málaga, Spain
| | - Casimiro Cardenas
- Canceromics Lab, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto de Investigación Biomédica de Málaga (IBIMA-Plataforma BIONAND), Universidad de Málaga, Málaga, Spain; Proteomics Unit, Central Facility of Research Infrastructures (SCAI), Universidad de Málaga, Málaga, Spain
| | - Javier Márquez
- Canceromics Lab, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto de Investigación Biomédica de Málaga (IBIMA-Plataforma BIONAND), Universidad de Málaga, Málaga, Spain
| | | | - Carolina Roza
- Departamento de Biología de Sistemas, Facultad de Medicina, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain.
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Proteomic analysis of rat colonic mucosa following acupuncture treatment for irritable bowel syndrome with diarrhea. PLoS One 2022; 17:e0273853. [PMID: 36094925 PMCID: PMC9467358 DOI: 10.1371/journal.pone.0273853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/16/2022] [Indexed: 11/19/2022] Open
Abstract
To investigate the molecular pathological mechanisms of irritable bowel syndrome with diarrhea (IBS-D) and elucidate the effects of acupuncture on IBS-D colonic mucosa protein abundance in rats, a label-free high-throughput liquid chromatography-tandem mass spectrometry (LC-MS)-based proteomics analysis was used to survey the global changes of colonic mucosa proteins between different groups. Sixteen Sprague-Dawley (SD) male rats were randomly divided into four groups: the control group (C); the IBS-D model group (M); the syndrome differentiation acupuncture group (SD) and the traditional acupuncture group (T). IBS-D model rats were obtained using the CAS (chronic acute combining stress model) method. Comparative bioinformatics analysis of the proteomic data was analyzed using MaxQuant software, Perseus software, online tools DAVID, VENNY and STRING. Functional enrichment and network analyses revealed a close relationship between IBS-D and several biological processes including energy metabolism, muscular excitation/contraction, and both traditional acupuncture and syndrome differentiation acupuncture can reverse the impairments of normal energy metabolism. Moreover, the syndrome differentiation acupuncture can regulate the protein cluster relating inflammation, wound repair and cell protection against oxidative stress which is associated with acupuncture analgesic effect. Differentially expressed proteins Atp5a1 and Bpnt1 were selected as representative proteins and subjected to western blotting. In conclusion, our study provides further insight into the pathological and molecular mechanisms of IBS-D and acupuncture treatments, and serves as an experimental basis for clinical applications.
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Tang HY, Jiang AJ, Wang XY, Wang H, Guan YY, Li F, Shen GM. Uncovering the pathophysiology of irritable bowel syndrome by exploring the gut-brain axis: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1187. [PMID: 34430628 PMCID: PMC8350700 DOI: 10.21037/atm-21-2779] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022]
Abstract
Objective To improve the pathophysiological understanding of irritable bowel syndrome (IBS) by exploring the gut-brain axis. Background Disorders of gut-brain interaction (DGBIs) are gastrointestinal (GI) disorders in which alterations in bowel functions occur. IBS, which is one of the most studied DGBIs, is linked with abdominal distress or pain without obvious structural or biochemical anomalies. Methods The etiology of IBS has not been clearly described but is known to be multifactorial, involving GI motility changes, post-infectious reactivity, visceral hypersensitivity, gut-brain interactions, microbiota dysbiosis, small intestinal bacterial overgrowth, food sensitivity, carbohydrate malabsorption, and intestinal inflammation. Conclusions One of the main features of IBS is the occurrence of structural and functional disruptions in the gut-brain axis, which alter reflective and perceptual nervous system reactions. Herein, we provide a brief summary of this topic. Furthermore, we discuss animal models, which are important in the study of IBS, especially as it is linked with stressors. These animal models cannot fully represent the human disease but serve as important tools for understanding this complicated disorder. In the future, technologies, such as organ-on-a-chip models and metabolomics, will provide novel information regarding the pathophysiology of IBS, which will play an important role in treatment development. Finally, we take a brief glance at how acupuncture treatments may hold potential for patients with IBS.
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Affiliation(s)
- He-Yong Tang
- Graduate School of Anhui University of Chinese Medicine, Hefei, China
| | - Ai-Juan Jiang
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Xi-Yang Wang
- Graduate School of Anhui University of Chinese Medicine, Hefei, China
| | - Hao Wang
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Yuan-Yuan Guan
- Department of Acupuncture and Moxibustion, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Fei Li
- Department of Rehabilitation, Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Guo-Ming Shen
- School of Integrated Traditional Chinese and Western Medicine, Anhui University of Traditional Chinese Medicine, Hefei, China
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Chai YN, Qin J, Li YL, Tong YL, Liu GH, Wang XR, Liu CY, Peng MH, Qin CZ, Xing YR. TMT proteomics analysis of intestinal tissue from patients of irritable bowel syndrome with diarrhea: Implications for multiple nutrient ingestion abnormality. J Proteomics 2020; 231:103995. [PMID: 33011346 DOI: 10.1016/j.jprot.2020.103995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 02/08/2023]
Abstract
Diarrheal irritable bowel syndrome (IBS-D) is a chronic functional bowel disease with no clear diagnostic markers and no satisfactory treatment strategies. In recent years, the importance of intestinal microstructure and function in IBS-D has been emphasized. However, the intestinal tissue proteomics of IBS-D patients has not been analyzed. Here, we systematically analyzed the molecule profiling of the intestinal tissues in IBS-D patients through tandem mass tag (TMT)-based proteomics for the first time, aiming to reveal the pathogenesis and provide evidence for diagnosis and treatment of IBS-D. Five IBS-D patients and five healthy subjects were selected, biopsy tissue samples from the junction of sigmoid and rectum were analyzed by TMT proteomics. Differentially expressed proteins were obtained and bioinformatics analysis was performed. Furthermore, parallel reaction monitoring (PRM) and q-PCR detection were applied to validate the differentially expressed proteins. Eighty differentially expressed proteins were screened, 48 of which were up-regulated and 32 were down-regulated (fold change >1.2, P < 0.05). Bioinformatics analysis showed that these proteins were significantly enriched in the nutrient ingestion pathways which are related to immune molecules. SELENBP1, VSIG2, HMGB1, DHCR7, BCAP31 and other molecules were significantly changed. Our study revealed the underlying mechanisms of IBS-D intestinal dysfunction. SIGNIFICANCE: Irritable bowel syndrome with diarrhea (IBS-D) is a worldwide chronic intestinal disease with no definite diagnostic markers. It is still a challenge to accurately locate the pathogenesis of patients for appropriate treatment strategy. Established proteomics studies of IBS-D are only based on urine, blood, or tissue samples from animals. Our study was the first TMT proteomics analysis on intestinal biopsy tissues of patients with IBS-D, which revealed the changes of molecular spectrum of actual intestinal conditions in patients with IBS-D. Some important molecules and signaling pathways have been found abnormal in our study, which were related with nutrient uptake. They not only provided preliminary clues for low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) intolerance, an unsolved conundrum of IBS-D, but also revealed obscure problems of protein, lipid, and other nutrients ingestion in IBS-D patients. Some of these differentially expressed molecules have been preliminarily verified, and will may be potential candidate molecules for diagnostic markers of IBS-D.
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Affiliation(s)
- Yu-Na Chai
- Department of pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jin Qin
- Digestive endoscopy center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yan-le Li
- Digestive department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ya-Lin Tong
- Digestive department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Guang-Hui Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin-Ru Wang
- Department of pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Cheng-Ye Liu
- Department of orthopedics, The Third Affiliated Hospital of Henan University of Science and Technology (Luoyang Dong fang Hospital), Luoyang 471003, China
| | - Ming-Hang Peng
- College of Medicine, Hubei University for Nationalities, Enshi 445000, China
| | - Chong-Zhen Qin
- Department of pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Yu-Rong Xing
- Center of Health Examination, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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Comparative proteomic analysis of the brain and colon in three rat models of irritable bowel syndrome. Proteome Sci 2020; 18:1. [PMID: 32123521 PMCID: PMC7041085 DOI: 10.1186/s12953-020-0157-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
Background Irritable bowel syndrome (IBS) has been gradually recognized as a disorder of the brain-gut interaction, but the molecular changes in the brain and colon that occur in disease development remain poorly understood. We employed proteomic analysis to identify differentially expressed proteins in both the brain and colon of three IBS models. Methods To explore the relevant protein abundance changes in the brain and colon, isobaric tags for relative and absolute quantitation (iTRAQ), liquid chromatography and tandem mass spectrometry (LC-MS) and Western blotting methods were used in three IBS models, including maternal separation (MS, group B), chronic wrap restraint stress (CWRS, group C) and a combination of MS and CWRS (group D). Results We identified 153, 280, and 239 proteins that were common and differentially expressed in the two tissue types of groups B, C and D, respectively; 43 differentially expressed proteins showed the same expression changes among the three groups, including 25 proteins upregulated in the colon and downregulated in the brain, 7 proteins downregulated in the colon and upregulated in the brain, and 3 proteins upregulated and 8 downregulated in both tissues. Gene ontology analysis showed that the differentially expressed proteins were mainly associated with cellular assembly and organization and cellular function and maintenance. Protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions Taken together, the data presented represent a comprehensive and quantitative proteomic analysis of the brain and colon in IBS models, providing new evidence of an abnormal brain-gut interaction in IBS. These data may be useful for further investigation of potential targets in the diagnosis and treatment of IBS.
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Yu Q, Liu X, Huang H, Zheng X, Pan X, Fang J, Meng L, Zhou C, Zhang X, Li Z, Zou D. Mass spectrometry-based metabolomics for irritable bowel syndrome biomarkers. Therap Adv Gastroenterol 2019; 12:1756284819886425. [PMID: 35154385 PMCID: PMC8832300 DOI: 10.1177/1756284819886425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/18/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a common gastrointestinal disorder without obvious structural abnormalities or consistent associated biomarkers, making its diagnosis difficult. In the present study, we used a urine-based metabolomics approach to identify IBS biomarkers. METHODS We used an ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) on urine samples from patients suffering from IBS and healthy controls. Data were coupled for multivariate statistical analysis methods. RESULTS We selected 30 differential metabolites associated with IBS and found steroid hormone biosynthesis and histidine metabolism alterations in patients with IBS that may be involved in the pathogenesis of the disease. In addition, we identified a panel of five metabolite markers composed of cortisone, citric acid, tiglylcarnitine, N6,-N6,-N6-trimethyl-L-lysine and L-histidine that could be used to discriminate between patients and healthy controls and may be appropriate as IBS diagnosis biomarkers. CONCLUSION Our findings indicate that metabolomics combined with pattern recognition can be useful to identify disease diagnostic IBS markers. CLINICAL TRIAL REGISTRATION ChiCTR1800020072.
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Affiliation(s)
- Qihong Yu
- Digestive Department, Changhai Hospital, Shanghai, China
| | - Xinru Liu
- Institute of Human Phenotypes, Fudan University, Shanghai, China
| | - Haojie Huang
- Digestive Department, Changhai Hospital, Shanghai, China
| | | | - Xue Pan
- Digestive Department, Changhai Hospital, Shanghai, China
| | - Junwei Fang
- Core Facility of Basic Medical Sciences, College of Basic Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Liyuan Meng
- Core Facility of Basic Medical Sciences, College of Basic Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Chunhua Zhou
- Digestive Department, Changhai Hospital, Shanghai, China
| | - Xiaocui Zhang
- Core Facility of Basic Medical Sciences, College of Basic Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zhaoshen Li
- Digestive Department, Changhai Hospital, Shanghai 200433
| | - Duowu Zou
- Digestive Department, Changhai Hospital, Shanghai 200433
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Rodiño-Janeiro BK, Pardo-Camacho C, Santos J, Martínez C. Mucosal RNA and protein expression as the next frontier in IBS: abnormal function despite morphologically intact small intestinal mucosa. Am J Physiol Gastrointest Liver Physiol 2019; 316:G701-G719. [PMID: 30767681 DOI: 10.1152/ajpgi.00186.2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Irritable bowel syndrome (IBS) is one of the commonest gastrointestinal disorders. Although long-time considered a pure functional disorder, intense research in past years has rendered a very complex and varied array of observations indicating the presence of structural and molecular abnormalities underlying characteristic motor and sensitive changes and clinical manifestations. Analysis of gene and protein expression in the intestinal mucosa has shed light on the molecular mechanisms implicated in IBS physiopathology. This analysis uncovers constitutive and inductive genetic and epigenetic marks in the small and large intestine that highlight the role of epithelial barrier, immune activation, and mucosal processing of foods and toxins and several new molecular pathways in the origin of IBS. The incorporation of innovative high-throughput techniques into IBS research is beginning to provide new insights into highly structured and interconnected molecular mechanisms modulating gene and protein expression at tissue level. Integration and correlation of these molecular mechanisms with clinical and environmental data applying systems biology/medicine and data mining tools emerge as crucial steps that will allow us to get meaningful and more definitive comprehension of IBS-detailed development and show the real mechanisms and causality of the disease and the way to identify more specific diagnostic biomarkers and effective treatments.
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Affiliation(s)
- Bruno Kotska Rodiño-Janeiro
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain
| | - Cristina Pardo-Camacho
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain
| | - Javier Santos
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas , Madrid , Spain
| | - Cristina Martínez
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca , Barcelona , Spain.,Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina) , Barcelona , Spain
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Yamamoto M, Pinto-Sanchez MI, Bercik P, Britz-McKibbin P. Metabolomics reveals elevated urinary excretion of collagen degradation and epithelial cell turnover products in irritable bowel syndrome patients. Metabolomics 2019; 15:82. [PMID: 31111238 DOI: 10.1007/s11306-019-1543-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/09/2019] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Irritable bowel syndrome (IBS), the most commonly diagnosed functional gastrointestinal (GI) disorder in developed countries, is characterized by chronic abdominal pain, and altered bowel habits. OBJECTIVES Accurate and timely diagnosis is challenging as it relies on symptoms and an evolving set of exclusion criteria to distinguish it from other related GI disorders reflecting a complex etiology that remains poorly understood. Herein, nontargeted metabolite profiling of repeat urine specimens collected from a cohort of IBS patients (n = 42) was compared to healthy controls (n = 20) to gain insights into the underlying pathophysiology. METHODS An integrated data workflow for characterization of the urine metabolome with stringent quality control was developed to authenticate reliably measured (CV < 30%) and frequently detected (> 75%) metabolites using multisegment injection-capillary electrophoresis-mass spectrometry. Complementary statistical methods were then used to rank differentially excreted urinary metabolites after normalization to osmolality that were subsequently identified by high resolution tandem mass spectrometry and their electrophoretic migration behavior. RESULTS Our work revealed ten consistently elevated urinary metabolites in repeat samples collected from IBS patients at two different time points (q < 0.05 after age and Benjamini-Hochberg/FDR adjustment), which were associated with greater collagen degradation and intestinal mucosal turn-over processes likely due to low-grade inflammation. IBS-specific metabolites identified in urine included a series of hydroxylysine metabolites (O-glycosylgalactosyl-hydroxylysine, O-galactosyl-hydroxylysine, lysine), mannopyranosy-L-tryptophan, imidazole propionate, glutamine, serine, ornithine, dimethylglycine and dimethylguanosine. A major limitation in this retrospective case-control study was significant co-morbidity of IBS patients with other illnesses, including depression and prescribed medications as compared to healthy controls. CONCLUSION This work provides new mechanistic insights into the pathophysiology of IBS while also offering a convenient way to monitor patient disease progression and treatment responses to therapy based on a panel of urinary metabolites that avoids invasive blood sampling, colonoscopy and/or tissue biopsies.
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Affiliation(s)
- Mai Yamamoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | | | - Premysl Bercik
- Farncombe Family Digestive Health Institute, McMaster University, Hamilton, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada.
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Abstract
Background Sex and subtype differences within patients with irritable bowel syndrome (IBS) complicate the understanding of disorder pathogenesis and hinder the design of efficacious, therapeutic interventions. Objectives The aims of this study were to harness the power of shotgun proteomic analysis, identify circulating proteins that differentiate African American female patients with IBS from healthy controls (HC), and gain biological insight on symptomatology. Methods Serum proteome analysis was performed upon a cohort of overweight, African American female participants with constipation predominant IBS symptoms (n = 5) and HC (n = 5), matched on age, sex, years of education, body mass index, and 11 physiological markers. Tandem mass tags for multiplexed proteomic analysis were performed, incorporating reverse-phase liquid chromatography and liquid chromatography-tandem mass spectrometry. Results Participants with IBS did not differ from HC in demographics, clinical characteristics, or initial proteomic analysis. Nested case control analysis of six samples (IBS: n = 3, HC: n = 3), hierarchically clustered into two main groups, with 12 out of 1,317 proteins significantly different in levels of expression: TGFβ1, PF4V1, PF4, APP, MMP9, PPBP, CTGF, SRGN, THBS1, WRN, LTBP1 (Isoform 3), and IGLV5-48. Top associations of identified proteins in DAVID and STRING resources (upregulated in HC vs. IBS) involve platelet alpha granule lumen, platelet activation/degranulation, extracellular region, and secretion by cell. Discussion Differentially expressed proteins between participants with IBS and HC involving platelet-related associations prompt inquiry as to differences in serotonergic signaling, inflammatory or immunomodulatory mechanisms underlying IBS symptomatology. Although preliminary and requiring validation in larger cohorts, these findings bear relevance to understanding pathogenic processes of IBS and biological effects of the disorder.
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Identification of serum proteome signature of irritable bowel syndrome: Potential utility of the tool for early diagnosis and patient's stratification. J Proteomics 2018; 188:167-172. [PMID: 28757466 DOI: 10.1016/j.jprot.2017.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 02/08/2023]
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Founds S. Systems biology for nursing in the era of big data and precision health. Nurs Outlook 2018; 66:283-292. [DOI: 10.1016/j.outlook.2017.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 11/25/2017] [Accepted: 11/26/2017] [Indexed: 12/19/2022]
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Heitkemper MM, Cain KC, Shulman RJ, Burr RL, Ko C, Hollister EB, Callen N, Zia J, Han CJ, Jarrett ME. Stool and urine trefoil factor 3 levels: associations with symptoms, intestinal permeability, and microbial diversity in irritable bowel syndrome. Benef Microbes 2018; 9:345-355. [PMID: 29633639 DOI: 10.3920/bm2017.0059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Previously we showed that urine trefoil factor 3 (TFF3) levels were higher in females with irritable bowel syndrome (IBS) compared to non-IBS females. To assess if TFF3 is associated with symptoms and/or reflect alterations in gastrointestinal permeability and gut microbiota in an IBS population, we correlated stool and urine TFF3 levels with IBS symptoms, intestinal permeability, stool microbial diversity and relative abundance of predominant bacterial families and genera. We also tested the relationship of stool TFF3 to urine TFF3, and compared results based on hormone contraception use. Samples were obtained from 93 females meeting Rome III IBS criteria and completing 4-week symptom diaries. TFF3 levels were measured by ELISA. Permeability was assessed with the urine lactulose/mannitol (L/M) ratio. Stool microbiota was assessed using 16S rRNA. Stool TFF3, but not urine TFF3, was associated positively with diarrhoea and loose stool consistency. Higher stool TFF3 was also associated with lower L/M ratio and microbial diversity. Of the 20 most abundant bacterial families Mogibacteriaceae and Christensenellaceae were inversely related to stool TFF3, with only Christensenellaceae remaining significant after multiple comparison adjustment. There were no significant relationships between stool or urine TFF3 levels and other symptoms, nor between stool and urine levels. In premenopausal females, urine TFF3 levels were higher in those reporting hormone contraception. Collectively these results suggest that higher stool TFF3 levels are associated with IBS symptoms (loose/diarrhoeal stools), lower gut permeability, and altered stool bacteria composition (decreased diversity and decreased Christensenellaceae), which further suggests that TFF3 may be an important marker of host-bacteria interaction.
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Affiliation(s)
- M M Heitkemper
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
| | - K C Cain
- 2 Department of Biostatistics and Office of Nursing Research, University of Washington, 1959 NE Pacific Street, Seattle, WA, USA
| | - R J Shulman
- 3 Children's Nutrition Research Center, Baylor College of Medicine, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | - R L Burr
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
| | - C Ko
- 4 University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - E B Hollister
- 5 Department of Pathology and Immunology, Baylor College of Medicine, Texas Children's Microbiome Center, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | - N Callen
- 6 Department of Family and Child Nursing, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - J Zia
- 4 University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - C J Han
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
| | - M E Jarrett
- 1 Department of Biobehavioral Nursing and Health Informatics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-7266, USA
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Rodiño-Janeiro BK, Martínez C, Fortea M, Lobo B, Pigrau M, Nieto A, González-Castro AM, Salvo-Romero E, Guagnozzi D, Pardo-Camacho C, Iribarren C, Azpiroz F, Alonso-Cotoner C, Santos J, Vicario M. Decreased TESK1-mediated cofilin 1 phosphorylation in the jejunum of IBS-D patients may explain increased female predisposition to epithelial dysfunction. Sci Rep 2018; 8:2255. [PMID: 29396473 PMCID: PMC5797119 DOI: 10.1038/s41598-018-20540-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/17/2018] [Indexed: 02/08/2023] Open
Abstract
Disturbed intestinal epithelial barrier and mucosal micro-inflammation characterize irritable bowel syndrome (IBS). Despite intensive research demonstrating ovarian hormones modulation of IBS severity, there is still limited knowledge on the mechanisms underlying female predominance in this disorder. Our aim was to identify molecular pathways involved in epithelial barrier dysfunction and female predominance in diarrhea-predominant IBS (IBS-D) patients. Total RNA and protein were obtained from jejunal mucosal biopsies from healthy controls and IBS-D patients meeting the Rome III criteria. IBS severity was recorded based on validated questionnaires. Gene and protein expression profiles were obtained and data integrated to explore biological and molecular functions. Results were validated by western blot. Tight junction signaling, mitochondrial dysfunction, regulation of actin-based motility by Rho, and cytoskeleton signaling were differentially expressed in IBS-D. Decreased TESK1-dependent cofilin 1 phosphorylation (pCFL1) was confirmed in IBS-D, which negatively correlated with bowel movements only in female participants. In conclusion, deregulation of cytoskeleton dynamics through TESK1/CFL1 pathway underlies epithelial intestinal dysfunction in the small bowel mucosa of IBS-D, particularly in female patients. Further understanding of the mechanisms involving sex-mediated regulation of mucosal epithelial integrity may have significant preventive, diagnostic, and therapeutic implications for IBS.
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Affiliation(s)
- Bruno K Rodiño-Janeiro
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.
| | - Cristina Martínez
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Marina Fortea
- Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Beatriz Lobo
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Marc Pigrau
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Adoración Nieto
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Ana María González-Castro
- Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Eloísa Salvo-Romero
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.,Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Danila Guagnozzi
- Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Cristina Pardo-Camacho
- Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Cristina Iribarren
- Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
| | - Fernando Azpiroz
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain
| | - Carmen Alonso-Cotoner
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain
| | - Javier Santos
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain.
| | - Maria Vicario
- Translational Mucosal Immunology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca; Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain
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Abstract
INTRODUCTION Biobehavioral research requires the ability to objectively measure the presence and/or severity of disease, symptoms and their burden, or to determine the effect of treatment on outcomes. Biomarker research has advanced care for patients across the lifespan. There have been significant advancements in biological marker use for nursing research in recent years. The purposes of this article are to define the characteristics of a valid biomarker; review common biological sources of genetic, hormonal, and proteomic biomarkers with attention to practical strengths, weaknesses, and challenges for specimen selection and quality; and discuss potential use of biomarkers in clinical and research settings. METHODS Authors draw on the literature and research experiences to address the issues relevant to incorporating biomarkers into nursing research. RESULTS AND DISCUSSION An overview of the practical aspects of incorporating biomarkers into nursing research, and the resultant actual and potential clinical applications, are discussed.
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15
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Khan MM, Tran BQ, Jang YJ, Park SH, Fondrie WE, Chowdhury K, Yoon SH, Goodlett DR, Chae SW, Chae HJ, Seo SY, Goo YA. Assessment of the Therapeutic Potential of Persimmon Leaf Extract on Prediabetic Subjects. Mol Cells 2017; 40:466-475. [PMID: 28681595 PMCID: PMC5547216 DOI: 10.14348/molcells.2017.2298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
Dietary supplements have exhibited myriads of positive health effects on human health conditions and with the advent of new technological advances, including in the fields of proteomics, genomics, and metabolomics, biological and pharmacological activities of dietary supplements are being evaluated for their ameliorative effects in human ailments. Recent interests in understanding and discovering the molecular targets of phytochemical-gene-protein-metabolite dynamics resulted in discovery of a few protein signature candidates that could potentially be used to assess the effects of dietary supplements on human health. Persimmon (Diospyros kaki) is a folk medicine, commonly used as dietary supplement in China, Japan, and South Korea, owing to its different beneficial health effects including anti-diabetic implications. However, neither mechanism of action nor molecular biomarkers have been discovered that could either validate or be used to evaluate effects of persimmon on human health. In present study, Mass Spectrometry (MS)-based proteomic studies were accomplished to discover proteomic molecular signatures that could be used to understand therapeutic potentials of persimmon leaf extract (PLE) in diabetes amelioration. Saliva, serum, and urine samples were analyzed and we propose that salivary proteins can be used for evaluating treatment effectiveness and in improving patient compliance. The present discovery proteomics study demonstrates that salivary proteomic profile changes were found as a result of PLE treatment in prediabetic subjects that could specifically be used as potential protein signature candidates.
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Affiliation(s)
- Mohd M. Khan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
- Present address: University of Maryland School of Medicine, Baltimore, MD 21201,
USA
| | - Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
| | - Yoon-Jin Jang
- Department of Pharmacology, Chonbuk National University Medical School, Jeonju 54907,
Korea
| | - Soo-Hyun Park
- Clinical Trial Center for Functional Foods, Chonbuk National University Hospital, Jeonju 54907,
Korea
| | | | | | - Sung Hwan Yoon
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
| | - David R. Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
| | - Soo-Wan Chae
- Department of Pharmacology, Chonbuk National University Medical School, Jeonju 54907,
Korea
- Clinical Trial Center for Functional Foods, Chonbuk National University Hospital, Jeonju 54907,
Korea
| | - Han-Jung Chae
- Department of Pharmacology, Chonbuk National University Medical School, Jeonju 54907,
Korea
| | - Seung-Young Seo
- Department of Internal Medicine, Research Institute of Clinical Medicine, Chonbuk National University Medical School and Hospital, Jeonju 54907,
Korea
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201,
USA
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16
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Tsigaridas A, Papanikolaou IS, Vaiopoulou A, Anagnostopoulos AK, Viazis N, Karamanolis G, Karamanolis DG, Tsangaris GT, Mantzaris GJ, Gazouli M. Proteomics and irritable bowel syndrome. Expert Rev Proteomics 2017; 14:461-468. [PMID: 28395553 DOI: 10.1080/14789450.2017.1317600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Irritable bowel syndrome (IBS) is a gastrointestinal disease that according to Rome IV criteria is subdivided into four subtypes. The pathophysiology of this disease is not well understood due to numerous factors playing multiple roles in disease development, such as diet, stress and hormones. IBS has a variety of symptoms and overlaps with many other gastrointestinal and non-gastrointestinal diseases. Area covered: This review aims to present an overview of implementation of proteomics in experimental studies in the field of IBS. Expert commentary: Proteomics is commonly used for biomarker discovery in and has also been extensively used in IBS research. The necessity of a sensitive and specific biomarker for IBS is apparent, but despite the intensive research performed in this field, an appropriate biomarker is not yet available.
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Affiliation(s)
| | - Ioannis S Papanikolaou
- b Hepatogastroenterology Unit, Second Department of Internal Medicine and Research Institute, Attikon University General Hospital, Medical School , National and Kapodistrian University of Athens , Athens , Greece
| | - Anna Vaiopoulou
- c Department of Basic Medical Sciences, Laboratory of Biology Medical School , National and Kapodistrian University of Athens , Athens , Greece
| | | | - Nikos Viazis
- a Gastroenterology Unit , Evangelismos Hospital , Athens , Greece
| | - George Karamanolis
- e Gastroenterology Unit, 2nd Department of Surgery, 'Aretaieio' University Hospital, Medical School , National and Kapodistrian University of Athens , Athens , Greece
| | | | - George T Tsangaris
- d Proteomics Research Unit , Biomedical Research Foundation of the Academy of Athens (IIBEAA) , Athens , Greece
| | | | - Maria Gazouli
- c Department of Basic Medical Sciences, Laboratory of Biology Medical School , National and Kapodistrian University of Athens , Athens , Greece
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17
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Li Y, Su X, Wu P, Wang J, Guo Y, Zhu J, Wang Q, Chen J, Yang F, Wei W. Proteomics analysis of IBS-D with spleen and kidney yang deficiency. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2017. [DOI: 10.1016/j.jtcms.2017.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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18
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Chapman JD, Edgar JS, Goodlett DR, Goo YA. Use of captive spray ionization to increase throughput of the data-independent acquisition technique PAcIFIC. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1101-7. [PMID: 27060837 PMCID: PMC4830633 DOI: 10.1002/rcm.7544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 01/30/2016] [Accepted: 02/21/2016] [Indexed: 05/05/2023]
Abstract
RATIONALE The Precursor Acquisition Independent From Ion Count (PAcIFIC) method is a data-independent acquisition technique capable of identifying proteins over eight orders of magnitude in a single analysis in human plasma. Widespread application of this technique in proteomic studies is hindered by its time-intensive nature. There exists a need to explore strategies to increase the throughput of the PAcIFIC method. METHODS The PAcIFIC acquisition technique was optimized for use with an Orbitrap mass spectrometer fitted with a captive spray ionization (CSI) source. Chromatographic methods, PAcIFIC acquisition parameters, for example, channels interrogated per chromatographic gradient, time span of chromatographic gradient, and sample loading amount, were investigated to achieve a maximum number of peptide and protein identifications on a yeast proteome where protein copy number had been previously determined. RESULTS A 24-hour CSI PAcIFIC method was developed with minimal reduction of peptide and protein identifications from the 4.2-day nano-electrospray ionization (nESI) PAcIFIC method. Analysis of a yeast cell lysate with the 4.2-day nESI PAcIFIC method resulted in 13,468 peptide and 2120 protein identifications. A 24-hour CSI PAcIFIC method resulted in 11,277 peptide and 1753 protein identifications. Increased sample loading of the CSI system allowed for an 8% increase in peptide and protein identifications. CONCLUSIONS A dramatic decrease in the overall analysis time of the PAcIFIC method (24 h with CSI versus 100.8 h with nESI) was achieved with minimal reduction of peptide and protein identifications. Furthermore, the CSI PAcIFIC method demonstrated a high degree of sensitivity and capability of identifying proteins across a large dynamic range observed with the nESI PAcIFIC method (CSI PAcIFIC identified proteins as low as 46 molecules per cell).
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Affiliation(s)
- John D Chapman
- Department of Medicinal Chemistry, School of Pharmacy, University of
Washington, Seattle, WA
| | - J. Scott Edgar
- Department of Medicinal Chemistry, School of Pharmacy, University of
Washington, Seattle, WA
| | - David R. Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy,
University of Maryland, Baltimore, MD
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19
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Mermelekas G, Vlahou A, Zoidakis J. SRM/MRM targeted proteomics as a tool for biomarker validation and absolute quantification in human urine. Expert Rev Mol Diagn 2015; 15:1441-54. [DOI: 10.1586/14737159.2015.1093937] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Filip S, Vougas K, Zoidakis J, Latosinska A, Mullen W, Spasovski G, Mischak H, Vlahou A, Jankowski J. Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine. PLoS One 2015. [PMID: 26208298 PMCID: PMC4514849 DOI: 10.1371/journal.pone.0133773] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.
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Affiliation(s)
- Szymon Filip
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantinos Vougas
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Agnieszka Latosinska
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - William Mullen
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - Goce Spasovski
- Ss. Cyril and Methodius University in Skopje, Nephrology Department, Skopje, Former Yugoslav Republic of Macedonia
| | - Harald Mischak
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Joachim Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research, Aachen, Germany
- * E-mail:
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21
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Pike BL, Paden KA, Alcala AN, Jaep KM, Gormley RP, Maue AC, Christmann BS, Elson CO, Riddle MS, Porter CK. Immunological Biomarkers in Postinfectious Irritable Bowel Syndrome. J Travel Med 2015; 22:242-50. [PMID: 26058758 DOI: 10.1111/jtm.12218] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/18/2015] [Accepted: 03/16/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND There is a recognized need for biological markers to facilitate diagnoses of irritable bowel syndrome (IBS) and to distinguish it from other functional and organic disorders. As postinfectious IBS (PI-IBS) is believed to account for as many as one third of all IBS cases, here we sought to identify differences in specific cytokines and serologic responses across patients with idiopathic IBS and PI-IBS and healthy controls. METHODS At total of 120 US military personnel were identified from the Defense Medical Surveillance System-based International Classification of Diseases, 9th Revision, Clinical Modification (ICD9-CM) codes recorded during medical encounters and were grouped based on infectious gastroenteritis (IGE) episode (Shigella, Campylobacter, Salmonella, or an unspecified pathogen) followed by IBS, IBS without antecedent IGE, or IGE without subsequent IBS within 2 years of the IGE exposure. Sera from subjects were assayed for cytokine levels and antibodies against a panel of microbiome antigens. RESULTS In total, 10 of 118 markers considered were shown to differ between IBS patients and healthy controls, including cytokines interleukin-6 (IL-6), IL-8, IL-1β, and macrophage inflammatory protein-1β (MIP-1β), as well as antibody responses to microbial antigens. Antimicrobial antibody response profiles also differed between PI-IBS cases compared with IBS cases without an antecedent episode of acute IGE. Comparisons also suggest that immunoglobulin A (IgA) and IgG profiles may point to pathogen-specific origins among PI-IBS cases. CONCLUSION Taken together, these results provide further evidence as to the molecular distinctness of classes of IBS cases and that serum biomarkers may prove useful in elucidating their pathobiological pathways.
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Affiliation(s)
- Brian L Pike
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Katie Ann Paden
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Ashley N Alcala
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Kayla M Jaep
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Robert P Gormley
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Alexander C Maue
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | | | - Charles O Elson
- Department of Medicine and Microbiology, University of Alabama, Birmingham, AL, USA
| | - Mark S Riddle
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Chad K Porter
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
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22
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Vaidyanathan K. Urinary proteomics and metabolomics in the diagnosis of pediatric disorders. Proteomics Clin Appl 2015; 9:482-9. [PMID: 25631340 DOI: 10.1002/prca.201400093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/24/2014] [Accepted: 01/27/2015] [Indexed: 12/17/2022]
Abstract
Proteomics is the study of structures and functions of proteins, while metabolomics is the study of small-molecule metabolites in the cells, tissues, and organs of the organism. Proteomic technologies have wide applications in medical field. The current revolution in proteomics has led to the discovery of several new protein markers for various disorders. Urinary proteomics and metabolomics have also evolved in the recent years, for the diagnosis of both renal and nonrenal disorders. The urinary proteome varies in normal and abnormal conditions. Different techniques are employed for the analysis of pediatric urinary proteome, the commonest being MS. Before introduction into clinical use, there is the need for careful standardization. Available data suggest that there are differences in urinary proteome between adult and pediatric populations. It is noted that infant urine contains proteins involved in translation and transcription, cellular growth, and metabolic processes, which are not predominant in adult urine. Available data on urinary proteomic and metabolomic profile in common pediatric disorders are also reviewed here.
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Affiliation(s)
- Kannan Vaidyanathan
- Department of Biochemistry, Pushpagiri Institute of Medical Science & Research Center, Tiruvalla, India
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23
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Sajic T, Liu Y, Aebersold R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clin Appl 2015; 9:307-21. [PMID: 25504613 DOI: 10.1002/prca.201400117] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/13/2014] [Accepted: 12/10/2014] [Indexed: 12/17/2022]
Abstract
In medicine, there is an urgent need for protein biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein biomarker discovery and, increasingly, also for protein biomarker validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)-one of the data-independent strategies that have gained wide application of late.
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Affiliation(s)
- Tatjana Sajic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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24
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Chapman JD, Goodlett DR, Masselon CD. Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. MASS SPECTROMETRY REVIEWS 2014; 33:452-70. [PMID: 24281846 DOI: 10.1002/mas.21400] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 05/13/2013] [Accepted: 05/15/2013] [Indexed: 05/20/2023]
Abstract
One of the most important early developments in the field of proteomics was the advent of automated data acquisition routines that allowed high-throughput unattended data acquisition during HPLC introduction of peptide mixtures to a tandem mass spectrometer. Prior to this, data acquisition was orders of magnitude less efficient being based entirely on lists of predetermined ions generated in a prior HPLC-MS experiment. This process, known generically as data-dependent analysis, empowered the development of shotgun proteomics where hundreds to thousands of peptide sequences are matched per experiment. In their most popular implementation, the most abundant ionized species from every precursor ion scan at each moment in chromatographic time are successively selected for isolation, activation and tandem mass analysis. While extremely powerful, this strategy has one primary limitation in that detectable dynamic range is restricted (in a top-down manner) to the peptides that ionize the best. To circumvent the serial nature of the data-dependent process and increase detectable dynamic range, the concepts of multiplexed and data-independent acquisition (DIA) have emerged. Multiplexed-data acquisition is based on more efficient co-selection and co-dissociation of multiple precursor ions in parallel, the data from which is subsequently de-convoluted to provide polypeptide sequences for each individual precursor ion. DIA has similar goals, but there is no real-time ion selection based on prior precursor ion scans. Instead, predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. These approaches aim to fully utilize the capabilities of mass spectrometers to maximize tandem MS acquisition time and to address the need to expand the detectable dynamic range, lower the limit of detection, and improve the overall confidence of peptide identifications and relative protein quantification measurements. This review covers all aspects of multiplexed- and data-independent tandem mass spectrometry in proteomics, from experimental implementations to advances in software for data interpretation.
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Affiliation(s)
- John D Chapman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, 98195-1700
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25
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van Swelm RPL, Kramers C, Masereeuw R, Russel FGM. Application of urine proteomics for biomarker discovery in drug-induced liver injury. Crit Rev Toxicol 2014; 44:823-41. [DOI: 10.3109/10408444.2014.931341] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Lacroix C, Caubet C, Gonzalez-de-Peredo A, Breuil B, Bouyssié D, Stella A, Garrigues L, Le Gall C, Raevel A, Massoubre A, Klein J, Decramer S, Sabourdy F, Bandin F, Burlet-Schiltz O, Monsarrat B, Schanstra JP, Bascands JL. Label-free quantitative urinary proteomics identifies the arginase pathway as a new player in congenital obstructive nephropathy. Mol Cell Proteomics 2014; 13:3421-34. [PMID: 25205225 DOI: 10.1074/mcp.m114.040121] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Obstructive nephropathy is a frequently encountered situation in newborns. In previous studies, the urinary peptidome has been analyzed for the identification of clinically useful biomarkers of obstructive nephropathy. However, the urinary proteome has not been explored yet and should allow additional insight into the pathophysiology of the disease. We have analyzed the urinary proteome of newborns (n = 5/group) with obstructive nephropathy using label free quantitative nanoLC-MS/MS allowing the identification and quantification of 970 urinary proteins. We next focused on proteins exclusively regulated in severe obstructive nephropathy and identified Arginase 1 as a potential candidate molecule involved in the development of obstructive nephropathy, located at the crossroad of pro- and antifibrotic pathways. The reduced urinary abundance of Arginase 1 in obstructive nephropathy was verified in independent clinical samples using both Western blot and MRM analysis. These data were confirmed in situ in kidneys obtained from a mouse obstructive nephropathy model. In addition, we also observed increased expression of Arginase 2 and increased total arginase activity in obstructed mouse kidneys. mRNA expression analysis of the related arginase pathways indicated that the pro-fibrotic arginase-related pathway is activated during obstructive nephropathy. Taken together we have identified a new actor in the development of obstructive nephropathy in newborns using quantitative urinary proteomics and shown its involvement in an in vivo model of disease. The present study demonstrates the relevance of such a quantitative urinary proteomics approach with clinical samples for a better understanding of the pathophysiology and for the discovery of potential therapeutic targets.
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Affiliation(s)
- Chrystelle Lacroix
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Cécile Caubet
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Anne Gonzalez-de-Peredo
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Benjamin Breuil
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - David Bouyssié
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Alexandre Stella
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Luc Garrigues
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Caroline Le Gall
- ‖Methodomics, Toulouse, France; **Institut de Mathématiques de Toulouse, UMR 5219, INSA de Toulouse, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse, France
| | - Anthony Raevel
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Angelique Massoubre
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Julie Klein
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Stéphane Decramer
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; ‡‡Nephrology and Internal Medicine Department, University Children's Hospital, Toulouse, France
| | - Frédérique Sabourdy
- §§Laboratoire de Biochimie Métabolique, IFB, CHU Purpan, and INSERM UMR 1037, CRCT CHU Rangueil, Toulouse, France
| | - Flavio Bandin
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; ‡‡Nephrology and Internal Medicine Department, University Children's Hospital, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Bernard Monsarrat
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Joost-Peter Schanstra
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France;
| | - Jean-Loup Bascands
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France;
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Abstract
PURPOSE This article provides an update and overview of a nursing research program focused on understanding the pathophysiology and management of irritable bowel syndrome (IBS). METHODS This review includes English language papers from the United States, Europe, and Asia (e.g., South Korea) from 1999 to 2013. We addressed IBS as a health problem, emerging etiologies, diagnostic and treatment approaches and the importance of a biopsychosocial model. RESULTS IBS is a chronic, functional gastrointestinal disorder characterized by recurrent episodes of abdominal pain and alterations in bowel habit (diarrhea, constipation, mixed). It is a condition for which adults, particularly women ages 20-45, seek health care services in both the United States and South Korea. Clinically, nurses play key roles in symptom prevention and management including designing and implementing approaches to enhance the patients' self-management strategies. Multiple mechanisms are believed to participate in the development and maintenance of IBS symptoms including autonomic nervous system dysregulation, intestinal inflammation, intestinal dysbiosis, dietary intolerances, alterations in emotion regulation, heightened visceral pain sensitivity, hypothalamic-pituitary-adrenal dysregulation, and dysmotility. Because IBS tends to occur in families, genetic factors may also contribute to the pathophysiology. Patients with IBS often report a number of co-morbid disorders and/or symptoms including poor sleep. CONCLUSION The key to planning effective management strategies is to understand the heterogeneity of this disorder. Interventions for IBS include non-pharmacological strategies such as cognitive behavior therapy, relaxation strategies, and exclusion diets.
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Affiliation(s)
- Margaret Heitkemper
- Department of Biobehavioral Nursing & Health Systems, University of Washington, Seattle, USA.
| | - Monica Jarrett
- Department of Biobehavioral Nursing & Health Systems, University of Washington, Seattle, USA
| | - Sang-Eun Jun
- College of Nursing, Keimyung University, Daegu, Korea
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Klein J, Lacroix C, Caubet C, Siwy J, Zurbig P, Dakna M, Muller F, Breuil B, Stalmach A, Mullen W, Mischak H, Bandin F, Monsarrat B, Bascands JL, Decramer S, Schanstra JP. Fetal Urinary Peptides to Predict Postnatal Outcome of Renal Disease in Fetuses with Posterior Urethral Valves (PUV). Sci Transl Med 2013; 5:198ra106. [DOI: 10.1126/scitranslmed.3005807] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Bested AC, Logan AC, Selhub EM. Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: part III - convergence toward clinical trials. Gut Pathog 2013; 5:4. [PMID: 23497650 PMCID: PMC3605358 DOI: 10.1186/1757-4749-5-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/10/2013] [Indexed: 12/14/2022] Open
Abstract
Rapid scientific and technological advances have allowed for a more detailed understanding of the relevance of intestinal microbiota, and the entire body-wide microbiome, to human health and well-being. Rodent studies have provided suggestive evidence that probiotics (e.g. lactobacillus and bifidobacteria) can influence behavior. More importantly, emerging clinical studies indicate that the administration of beneficial microbes, via supplementation and/or fecal microbial transplant (FMT), can influence end-points related to mood state (glycemic control, oxidative status, uremic toxins), brain function (functional magnetic resonance imaging fMRI), and mental outlook (depression, anxiety). However, despite the advances in the area of gastro-biological psychiatry, it becomes clear that there remains an urgent need to explore the value of beneficial microbes in controlled clinical investigations. With the history explored in this series, it is fair to ask if we are now on the cusp of major clinical breakthroughs, or are we merely in the quicksand of Autointoxication II?
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Affiliation(s)
- Alison C Bested
- Complex Chronic Diseases Program, BC Women’s Hospital and Health Centre, B223A-4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
| | - Alan C Logan
- CAMNR, 775 Blithedale Avenue Suite 364, Mill Valley, CA 94941, USA
| | - Eva M Selhub
- Harvard Medical School and Massachusetts General Hospital, 40 Crescent St., Suite 201, Waltham, MA, 02453, USA
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