Category: Methodology

Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome

Abstract:

BACKGROUND: Systems biologic approaches such as Weighted Gene Co-expression Network Analysis (WGCNA) can effectively integrate gene expression and trait data to identify pathways and candidate biomarkers. Here we show that the additional inclusion of genetic marker data allows one to characterize network relationships as causal or reactive in a chronic fatigue syndrome (CFS) data set.

RESULTS: We combine WGCNA with genetic marker data to identify a disease-related pathway and its causal drivers, an analysis which we refer to as “Integrated WGCNA” or IWGCNA. Specifically, we present the following IWGCNA approach: 1) construct a co-expression network, 2) identify trait-related modules within the network, 3) use a trait-related genetic marker to prioritize genes within the module, 4) apply an integrated gene screening strategy to identify candidate genes and 5) carry out causality testing to verify and/or prioritize results. By applying this strategy to a CFS data set consisting of microarray, SNP and clinical trait data, we identify a module of 299 highly correlated genes that is associated with CFS severity. Our integrated gene screening strategy results in 20 candidate genes. We show that our approach yields biologically interesting genes that function in the same pathway and are causal drivers for their parent module. We use a separate data set to replicate findings and use Ingenuity Pathways Analysis software to functionally annotate the candidate gene pathways.

CONCLUSION: We show how WGCNA can be combined with genetic marker data to identify disease-related pathways and the causal drivers within them. The systems genetics approach described here can easily be used to generate testable genetic hypotheses in other complex disease studies.

 

Source: Presson AP, Sobel EM, Papp JC, Suarez CJ, Whistler T, Rajeevan MS, Vernon SD, Horvath S. Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.BMC Syst Biol. 2008 Nov 6;2:95. doi: 10.1186/1752-0509-2-95. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625353/ (Full article)

 

Bayesian biomarker identification based on marker-expression proteomics data

Abstract:

We are studying variable selection in multiple regression models in which molecular markers and/or gene-expression measurements as well as intensity measurements from protein spectra serve as predictors for the outcome variable (i.e., trait or disease state).

Finding genetic biomarkers and searching genetic-epidemiological factors can be formulated as a statistical problem of variable selection, in which, from a large set of candidates, a small number of trait-associated predictors are identified. We illustrate our approach by analyzing the data available for chronic fatigue syndrome (CFS).

CFS is a complex disease from several aspects, e.g., it is difficult to diagnose and difficult to quantify. To identify biomarkers we used microarray data and SELDI-TOF-based proteomics data. We also analyzed genetic marker information for a large number of SNPs for an overlapping set of individuals. The objectives of the analyses were to identify markers specific to fatigue that are also possibly exclusive to CFS. The use of such models can be motivated, for example, by the search for new biomarkers for the diagnosis and prognosis of cancer and measures of response to therapy. Generally, for this we use Bayesian hierarchical modeling and Markov Chain Monte Carlo computation.

 

Source: Bhattacharjee M, Botting CH, Sillanpää MJ. Bayesian biomarker identification based on marker-expression proteomics data. Genomics. 2008 Dec;92(6):384-92. doi: 10.1016/j.ygeno.2008.06.006. Epub 2008 Aug 15. http://www.sciencedirect.com/science/article/pii/S0888754308001420 (Full article)

 

Teaching medical students about medically unexplained illnesses: a preliminary study

Abstract:

BACKGROUND: This study examined how an interactive seminar focusing on two medically unexplained illnesses, chronic fatigue syndrome (CFS) and fibromyalgia, influenced medical student attitudes toward CFS, a more strongly stigmatized illness.

METHODS: Forty-five fourth year medical students attended a 90 minute interactive seminar on the management of medically unexplained illnesses that was exemplified with CFS and fibromyalgia. A modified version of the CFS attitudes test was administered immediately before and after the seminar.

RESULTS: Pre-seminar assessment revealed neutral to slightly favorable toward CFS. At the end of the seminar, significantly more favorable attitudes were found toward CFS in general (t (42) = 2.77; P < 0.01) and for specific items that focused on (1) supporting more CFS research funding (t (42) = 4.32; P < 0.001; (2) employers providing flexible hours for people with CFS (t (42) = 3.52, P < 0.01); and (3) viewing CFS as not primarily a psychological disorder (t (42) = 2.87, P < 0.01). Thus, a relatively brief exposure to factual information on specific medically unexplained illnesses was associated with more favorable attitudes toward CFS in fourth year medical students.

CONCLUSION: This type of instruction may lead to potentially more receptive professional attitudes toward providing care to these underserved patients.

 

Source: Friedberg F, Sohl SJ, Halperin PJ. Teaching medical students about medically unexplained illnesses: a preliminary study. Med Teach. 2008;30(6):618-21. doi: 10.1080/01421590801946970. https://www.ncbi.nlm.nih.gov/pubmed/18608944

 

Comparison of two exercise testing protocols in patients with chronic fatigue syndrome

Abstract:

This study examined whether a linear exercise stress-testing protocol generated different peak exercise performance variables than a stepwise exercise testing protocol in patients with chronic fatigue syndrome (CFS). We conducted a comparative study with patients randomly allocated to one of two exercise testing protocols.

Twenty-eight women with CFS completed two self-reported measures (the CFS Symptom List and the CFS Activities and Participation Questionnaire) and then performed until exhaustion either the linear or the stepwise exercise testing protocol with continuous monitoring of physiological variables (heart rate and oxygen uptake).

At baseline, we found no significant differences in demographic features and health status between groups (p > 0.05). Based on ratio peak workload/peak oxygen uptake, mechanical efficiency was lower among the subjects performing the stepwise protocol (p = 0.002). When we analyzed the mean linear regression slope values between oxygen uptake and workload from each subject’s minute-by-minute exercise data points, we found that mechanical efficiency was lower among the subjects performing the stepwise protocol (p = 0.039). Apart from mechanical efficiency, we found no differences in exercise performance data between groups (p > 0.05).

Our results suggest that the difference between linear and stepwise exercise protocols cannot account for all discrepancies of previous studies on exercise performance data in women with CFS, but they do suggest that the nature of the exercise testing protocol influences mechanical efficiency in these patients. Further study is warranted.

 

Source: Nijs J, Zwinnen K, Meeusen R, de Geus B, De Meirleir K. Comparison of two exercise testing protocols in patients with chronic fatigue syndrome. J Rehabil Res Dev. 2007;44(4):553-9. http://www.rehab.research.va.gov/jour/07/44/4/Nijs.html (Full article)

 

Immunoassay with cytomegalovirus early antigens from gene products p52 and CM2 (UL44 and UL57) detects active infection in patients with chronic fatigue syndrome

Abstract:

AIMS: To investigate whether the use of recombinant early antigens for detection of antibodies to human cytomegalovirus (HCMV) gene products CM(2) (UL44, UL57) and p52 (UL44) is specific in the diagnosis and differentiation of active HCMV infection in a subset of patients with chronic fatigue syndrome (CFS), a diagnosis which is often missed by the current ELISA assay that uses crude viral lysate antigen.

METHODS: At a single clinic from 1999 to 2001, a total of 4774 serological tests were performed in 1135 patients with patients using two immunoassays, Copalis and ELISA. The Copalis immunoassay utilised HCMV early gene products of UL44 and UL57 recombinant antigens for detection of HCMV IgM antibody, and viral capsid antigen for detection of HCMV IgG antibody. The ELISA immunoassay utilised viral crude lysate as antigen for detection of both HCMV IgG and IgM.

RESULTS: 517 patients (45.6%) were positive for HCMV IgG by both assays. Of these, 12 (2.2%) were positive for HCMV(V) IgM serum antibody by HCMV ELISA assay, and 61 (11.8%) were positive for IgM HCMV serum antibody by Copalis assay. The Copalis assay that uses HCMV early recombinant gene products CM(2) (UL44, UL57) and p52 (UL44) in comparison with ELISA was 98% specific.

CONCLUSIONS: Immunoassays that use early antigen recombinant HCMV CM(2) and p52 are five times more sensitive than HCMV ELISA assay using viral lysate, and are specific in the detection and differentiation of active HCMV infection in a subset of patients with CFS.

 

Source: Beqaj SH, Lerner AM, Fitzgerald JT. Immunoassay with cytomegalovirus early antigens from gene products p52 and CM2 (UL44 and UL57) detects active infection in patients with chronic fatigue syndrome. J Clin Pathol. 2008 May;61(5):623-6. Epub 2007 Nov 23. https://www.ncbi.nlm.nih.gov/pubmed/18037660

 

The chronic fatigue syndrome: a comparative pathway analysis

Abstract:

In this paper, we introduce a method to detect pathological pathways of a disease. We aim to identify biological processes rather than single genes affected by the chronic fatigue syndrome (CFS). So far, CFS has neither diagnostic clinical signals nor abnormalities that could be diagnosed by laboratory examinations. It is also unclear if the CFS represents one disease or can be subdivided in different categories. We use information from clinical trials, the gene ontology (GO) database as well as gene expression data to identify undirected dependency graphs (UDGs) representing biological processes according to the GO database. The structural comparison of UDGs of sick versus non-sick patients allows us to make predictions about the modification of pathways due to pathogenesis.

 

Source: Emmert-Streib F. The chronic fatigue syndrome: a comparative pathway analysis. J Comput Biol. 2007 Sep;14(7):961-72. https://www.ncbi.nlm.nih.gov/pubmed/17803373

 

Publication trends in chronic fatigue syndrome: comparisons with fibromyalgia and fatigue: 1995-2004

Abstract:

OBJECTIVE: In order to identify publishing patterns in chronic fatigue syndrome (CFS), we compared the annual number of peer review articles for CFS, fibromyalgia (FM), and non-CFS fatigue over a recent decade (1995-2004).

METHOD: Citations were drawn from Ovid/Medline, PsychInfo, and the Journal of Chronic Fatigue Syndrome for peer review articles focusing on CFS, FM, and fatigue for each year of the decade ending in 2004. Statistics included chi-square, tests for differences in proportions, and regression-based curve estimation.

RESULTS: The frequency of CFS peer review articles did not significantly change from the first half to the second half of the decade (1995-2004). By comparison, the output of both FM and fatigue articles significantly increased (P<.0001). A quadratic model (inverted U shape; P<.02) best fit the data for CFS annual publication frequency. By comparison, exponential models best fit the data for both FM (P<.0001) and fatigue (P<.0001) citations. The highest percentage of citations (15-16%) for both CFS and FM fell within the domains of diagnosis, physiopathology, and psychology. For fatigue, almost one third (31.4%) of the citations were focused on etiology, while psychology (11.5%) and physiopathology (10.4%) articles were the next most cited. Based on first-author affiliation, CFS articles were most likely to originate in the United States (37.7%), England (31.4%), and the Netherlands (4.9%).

CONCLUSION: The output of CFS peer review articles has not increased over the past decade, while the number of FM and fatigue articles has increased substantially.

 

Source: Friedberg F, Sohl S, Schmeizer B. Publication trends in chronic fatigue syndrome: comparisons with fibromyalgia and fatigue: 1995-2004. J Psychosom Res. 2007 Aug;63(2):143-6. https://www.ncbi.nlm.nih.gov/pubmed/17662750

 

Spectroscopic diagnosis of chronic fatigue syndrome by multivariate analysis of visible and near-infrared spectra

Abstract:

We have recently evaluated the possibility of visible and near-infrared (Vis-NIR) spectroscopy for diagnosis of chronic fatigue syndrome(CFS). Vis-NIR spectra in the 600-1,100 nm region for sera from CFS patients and healthy donors were subjected to principal component analysis (PCA) and soft independent modeling of class analogy (SIMCA) to develop multivariate models to discriminate between CFS patients and healthy donors. The PCA and SIMCA model predicted successful prediction of the masked samples. Furthermore, taking advantage of Vis-NIR spectroscopy to enable noninvasive analysis, our preliminary results have shown that SIMCA model from Vis-NIR spectra of thumb has achieved 70-80% correct determinations. In this review, we will introduce the potential of the Vis-NIR spectroscopy for CFS diagnosis.

 

Source: Sakudo A, Kuratsune H, Hakariya Y, Kobayashi T, Ikuta K. Spectroscopic diagnosis of chronic fatigue syndrome by multivariate analysis of visible and near-infrared spectra. Nihon Rinsho. 2007 Jun;65(6):1051-6. [Article in Japanese] https://www.ncbi.nlm.nih.gov/pubmed/17561696

 

Evaluation of fatigue by using acceleration plethysmography

Abstract:

We evaluated the fatigue of patients with chronic fatigue syndrome by using acceleration plethysmography. The changes in the acceleration plethysmography were relatively dominant in the sympathetic nervous system from the viewpoint of the autonomic nervous system, and the fluctuation in the time-series data of the acceleration plethysmography was decreased from the viewpoint of chaos or complexity system. We found the relation between the level of fatigue and the changes in acceleration plethysmography. Therefore, the acceleration plethysmography might be useful for the evaluation of fatigue.

 

Source: Yamaguti K. Evaluation of fatigue by using acceleration plethysmography. Nihon Rinsho. 2007 Jun;65(6):1034-42. [Article in Japanese] https://www.ncbi.nlm.nih.gov/pubmed/17561694

 

Continuous measurement of BRSI in chronic fatigue syndrome

Abstract:

This paper discusses the development of a system to measure continuous cardiac baroreceptor measurement during a 45-minute 70-degree head-up tilt (HUT) of five groups of subjects suffering the following: chronic fatigue syndrome (CFS), CFS with fibromyalgia (CFS-FM), CFS with postural orthostatic tachycardia syndrome (CFS-POTS), controls with POTS (CON-POTS), and controls (CON). The duration of the test was 56-minutes, which included a five-minute supine baseline, a 45-minute HUT and a six-minute recovery period. The system was developed in LabView, and can provide a comparative time analyses of weighted BRSI averages. Baroreflex effectiveness index (BEI) was also investigated over the course of lags 0, 1 and 2 as well as an assessment of overall BEI performance between groups.

 

Source: Donnelly DL, Rockland RH, Reisman SS, Quigley KS. Continuous measurement of BRSI in chronic fatigue syndrome. Conf Proc IEEE Eng Med Biol Soc. 2004;2:906-8. https://www.ncbi.nlm.nih.gov/pubmed/17271825