Bioinformatic analyses identifies novel protein-coding pharmacogenomic markers associated with paclitaxel sensitivity in NCI60 cancer cell lines

<p>Abstract</p> <p>Background</p> <p>Paclitaxel is a microtubule-stabilizing drug that has been commonly used in treating cancer. Due to genetic heterogeneity within patient populations, therapeutic response rates often vary. Here we used the NCI60 panel to identify SNPs associated with paclitaxel sensitivity. Using the panel's GI50 response data available from Developmental Therapeutics Program, cell lines were categorized as either sensitive or resistant. PLINK software was used to perform a genome-wide association analysis of the cellular response to paclitaxel with the panel's SNP-genotype data on the Affymetrix 125 k SNP array. FastSNP software helped predict each SNP's potential impact on their gene product. mRNA expression differences between sensitive and resistant cell lines was examined using data from BioGPS. Using Haploview software, we investigated for haplotypes that were more strongly associated with the cellular response to paclitaxel. Ingenuity Pathway Analysis software helped us understand how our identified genes may alter the cellular response to paclitaxel.</p> <p>Results</p> <p>43 SNPs were found significantly associated (FDR < 0.005) with paclitaxel response, with 10 belonging to protein-coding genes (<it>CFTR</it>, <it>ROBO1</it>, <it>PTPRD</it>, <it>BTBD12</it>, <it>DCT</it>, <it>SNTG1</it>, <it>SGCD</it>, <it>LPHN2</it>, <it>GRIK1</it>, <it>ZNF607</it>). SNPs in <it>GRIK1</it>, <it>DCT</it>, <it>SGCD </it>and <it>CFTR </it>were predicted to be intronic enhancers, altering gene expression, while SNPs in <it>ZNF607 </it>and <it>BTBD12 </it>cause conservative missense mutations. mRNA expression analysis supported these findings as <it>GRIK1</it>, <it>DCT</it>, <it>SNTG1</it>, <it>SGCD </it>and <it>CFTR </it>showed significantly (p < 0.05) increased expression among sensitive cell lines. Haplotypes found in <it>GRIK1, SGCD, ROBO1, LPHN2</it>, and <it>PTPRD </it>were more strongly associated with response than their individual SNPs.</p> <p>Conclusions</p> <p>Our study has taken advantage of available genotypic data and its integration with drug response data obtained from the NCI60 panel. We identified 10 SNPs located within protein-coding genes that were not previously shown to be associated with paclitaxel response. As only five genes showed differential mRNA expression, the remainder would not have been detected solely based on expression data. The identified haplotypes highlight the role of utilizing SNP combinations within genomic loci of interest to improve the risk determination associated with drug response. These genetic variants represent promising biomarkers for predicting paclitaxel response and may play a significant role in the cellular response to paclitaxel.</p

Latent class analysis of comorbidity patterns among women with generalized and localized vulvodynia: preliminary findings

Ruby HN Nguyen,1 Christin Veasley,2 Derek Smolenski1,3 1Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 2National Vulvodynia Association, Silver Spring, MD, 3National Center for Telehealth and Technology, Defense Centers of Excellence, Department of Defense, Tacoma, WA, USA Background: The pattern and extent of clustering of comorbid pain conditions with vulvodynia is largely unknown. However, elucidating such patterns may improve our understanding of the underlying mechanisms involved in these common causes of chronic pain. We sought to describe the pattern of comorbid pain clustering in a population-based sample of women with diagnosed vulvodynia. Methods: A total of 1457 women with diagnosed vulvodynia self-reported their type of vulvar pain as localized, generalized, or both. Respondents were also surveyed about the presence of comorbid pain conditions, including temporomandibular joint and muscle disorders, interstitial cystitis, fibromyalgia, chronic fatigue syndrome, irritable bowel syndrome, endometriosis, and chronic headache. Age-adjusted latent class analysis modeled extant patterns of comorbidity by vulvar pain type, and a multigroup model was used to test for the equality of comorbidity patterns using a comparison of prevalence. A two-class model (no/single comorbidity versus multiple comorbidities) had the best fit in individual and multigroup models. Results: For the no/single comorbidity class, the posterior probability prevalence of item endorsement ranged from 0.9% to 24.4%, indicating a low probability of presence. Conversely, the multiple comorbidity class showed that at least two comorbid conditions were likely to be endorsed by at least 50% of women in that class, and irritable bowel syndrome and fibromyalgia were the most common comorbidities regardless of type of vulvar pain. Prevalence of the multiple comorbidity class differed by type of vulvar pain: both (37.6% prevalence, referent), generalized (21.6% prevalence, adjusted odds ratio 0.41, 95% confidence interval 0.27&ndash;0.61), or localized (12.5% prevalence, adjusted odds ratio 0.31, 95% confidence interval 0.21&ndash;0.47). Conclusion: This novel work provides insight into potential shared mechanisms of vulvodynia by describing that a prominent comorbidity pattern involves having both irritable bowel syndrome and fibromyalgia. In addition, the prevalence of a multiple comorbidity class pattern increases with increasing severity of vulvar pain. Keywords: vulvodynia, generalized, localized, comorbidit

Mucosal versus muscle pain sensitivity in provoked vestibulodynia

Kathryn Witzeman,1 Ruby HN Nguyen,2 Alisa Eanes,3 Sawsan As-Sanie,4 Denniz Zolnoun51Department of Obstetrics and Gynecology, Denver Health Medical Center, Denver, CO, 2Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, 3Pelvic Pain Research Unit, Division of Advanced Laparoscopy and Pelvic Pain, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, 4Department of Obstetrics and Gynecology, Division of Minimally Invasive Gynecologic Surgery, University of Michigan, Ann Arbor, MI, 5Department of Obstetrics and Gynecology and Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, NC, USABackground: An estimated 8.3%&ndash;16% of women experience vulvovaginal discomfort during their lifetime. Frequently these patients report provoked pain on contact or with attempted intercourse, commonly referred to as provoked vestibulodynia (PVD). Despite the burden of this condition, little is known about its potential etiologies including pelvic floor muscular dysfunction and mucosal components. This knowledge would be beneficial in developing targeted therapies including physical therapy.Objective: To explore the relative contribution of mucosal versus muscle pain sensitivity on pain report from intercourse among women with PVD.Design: In this proof of concept study, 54 women with PVD underwent a structured examination assessing mucosal and pelvic muscle sensitivity.Methods: We examined three mucosal sites in the upper and lower vestibule. Patients were asked to rate their pain on cotton swab palpation of the mucosa using a 10-point visual analog scale. Muscle pain was assessed using transvaginal application of pressure on right and left puborectalis, and the perineal muscle complex. The Gracely pain scale (0&ndash;100) was used to assess the severity of pain with intercourse, with women rating the lowest, average, and highest pain levels; a 100 rating the highest level of pain.Results: The lower vestibule&rsquo;s mucosa 5.81 (standard deviation =2.83) was significantly more sensitive than the upper vestibule 2.52 (standard deviation =2.6) (P&lt;0.01) on exam. However, mucosal sensitivity was not associated with intercourse pain, while muscle sensitivity was moderately associated with both average and highest intensity of intercourse pain (r=-0.46, P=0.01 and r=-0.42, P=0.02), respectively.Conclusion: This preliminary study suggests that mucosal measures alone may not sufficiently capture the spectrum of clinical pain report in women with PVD, which is consistent with the empirical success of physical therapy in this population.Keywords: vulvodynia, provoked vestibulodynia, pain sensitivity, pelvic floor muscle pain, vulvar pain, pressure pain threshold, dyspareuni

Facing others in pain : why context matters

Judging pain in another is challenging, largely because pain is a subjective phenomenon to which observers have no direct access. Despite this ambiguity, inferences often are made that can drive important clinical decisions, such as estimating another’s pain intensity, with significant implications for patient treatment and outcomes. This chapter focuses upon the influence of the context upon observer cognitive, emotional, and behavioral responses toward others in pain. In doing so, we consider context in its broadest form: characteristics of the patient/person in pain, the observer, and the situation, as well as elements of the reported pain experience, itself. Despite the increased understanding of and appreciation for the role of context in observer judgments, knowledge of how context, judgment, and treatment outcomes interact remains sketchy and in need of translational research. Such research is needed if we are to build our current base of knowledge and translate that knowledge into improved approaches to the assessment and treatment of patients in pain