Background: Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. Methods: After limiting our DNA sequencing analysis to MM samples (n = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. Results: Four genes were potentially prognostic [RAC1, FGFR1, CARD11, CIITA; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., SPEN, PDGFRB, GNAS, MAP2K1, EGFR, TSC2) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for RAC1 and MAP2K1. Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort (n = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up (n = 224) showed that somatic mutations in SPEN and RAC1 reached borderline prognostic significance [log-rank favorable (p = 0.09) and adverse (p = 0.07), respectively]. Somatic mutations in SPEN, and to a lesser extent RAC1, were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity (p = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., BRAF, RAS, CDKN2A, PTEN, TP53), such as RAC1 and SPEN, may have prognostic significance in MM.
Resource type:
Article
Affiliation Label Tesim:
Department of Dermatology, UNC Lineberger Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Biostatistics, and Department of Cell Biology and Physiology
DOI:
https://doi.org/10.17615/n84y-5q28
Identifier:
https://dx.doi.org/10.3389/fonc.2018.00584
ISSN:
2234-943X
Journal Issue:
JAN
Journal Title:
Frontiers in Oncology
Journal Volume:
9
Keyword:
Prognostic significance, RAC1, Cutaneous melanoma, SPEN, The Cancer Genome Atlas Project, RNA sequencing, UV signature, and Next generation sequencing
License Label:
Attribution 3.0 United States
ORCID:
Other Affiliation:
, Vanderbilt-Ingram Cancer Center, University of Sydney, Queensland Institute of Medical Research, and University of California, Los Angeles
Genetic Dissection of the Regulatory Mechanisms of Ace2 in the Infected Mouse Lung
Creator:
Cui, Y., Bergmann, S., Xu, F., Baric, R.S., Lu, L., Williams, R.W., Schughart, K., Gao, J., Ashbrook, D.G., Sims, A.C., Jonsson, C.B., and Li, K.
Date of publication:
2021
Abstract Tesim:
Acute lung injury (ALI) is an important cause of morbidity and mortality after viral infections, including influenza A virus H1N1, SARS-CoV, MERS-CoV, and SARS-CoV-2. The angiotensin I converting enzyme 2 (ACE2) is a key host membrane-bound protein that modulates ALI induced by viral infection, pulmonary acid aspiration, and sepsis. However, the contributions of ACE2 sequence variants to individual differences in disease risk and severity after viral infection are not understood. In this study, we quantified H1N1 influenza-infected lung transcriptomes across a family of 41 BXD recombinant inbred strains of mice and both parents—C57BL/6J and DBA/2J. In response to infection Ace2 mRNA levels decreased significantly for both parental strains and the expression levels was associated with disease severity (body weight loss) and viral load (expression levels of viral NA segment) across the BXD family members. Pulmonary RNA-seq for 43 lines was analyzed using weighted gene co-expression network analysis (WGCNA) and Bayesian network approaches. Ace2 not only participated in virus-induced ALI by interacting with TNF, MAPK, and NOTCH signaling pathways, but was also linked with high confidence to gene products that have important functions in the pulmonary epithelium, including Rnf128, Muc5b, and Tmprss2. Comparable sets of transcripts were also highlighted in parallel studies of human SARS-CoV-infected primary human airway epithelial cells. Using conventional mapping methods, we determined that weight loss at two and three days after viral infection maps to chromosome X—the location of Ace2. This finding motivated the hierarchical Bayesian network analysis, which defined molecular endophenotypes of lung infection linked to Ace2 expression and to a key disease outcome. Core members of this Bayesian network include Ace2, Atf4, Csf2, Cxcl2, Lif, Maml3, Muc5b, Reg3g, Ripk3, and Traf3. Collectively, these findings define a causally-rooted Ace2 modulatory network relevant to host response to viral infection and identify potential therapeutic targets for virus-induced respiratory diseases, including those caused by influenza and coronaviruses.
Obesity-Driven Deficiencies of Specialized Pro-resolving Mediators May Drive Adverse Outcomes During SARS-CoV-2 Infection
Creator:
Shaikh, S.R., Gowdy, K.M., Pal, A., Oestreich, K.J., and Beck, M.
Date of publication:
2020
Abstract Tesim:
Obesity is a major independent risk factor for increased morbidity and mortality upon infection with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), which is responsible for the current coronavirus disease pandemic (COVID-19). Therefore, there is a critical need to identify underlying metabolic factors associated with obesity that could be contributing toward increased susceptibility to SARS-CoV-2 in this vulnerable population. Here, we focus on the critical role of potent endogenous lipid metabolites known as specialized pro-resolving mediators (SPMs) that are synthesized from polyunsaturated fatty acids. SPMs are generated during the transition of inflammation to resolution and have a vital role in directing damaged tissues to homeostasis; furthermore, SPMs display anti-viral activity in the context of influenza infection without being immunosuppressive. We cover evidence from rodent and human studies to show that obesity, and its co-morbidities, induce a signature of SPM deficiency across immunometabolic tissues. We further discuss how the effects of obesity upon SARS-CoV-2 infection are likely exacerbated with environmental exposures that promote chronic pulmonary inflammation and augment SPM deficits. Finally, we highlight potential approaches to overcome the loss of SPMs using dietary and pharmacological interventions. Collectively, this mini-review underscores the need for mechanistic studies on how SPM deficiencies driven by obesity and environmental exposures may exacerbate the response to SARS-CoV-2.
Resource type:
Article
Affiliation Label Tesim:
Department of Nutrition
DOI:
https://doi.org/10.17615/jpe8-9h04
Identifier:
https://dx.doi.org/10.3389/fimmu.2020.01997
ISSN:
1664-3224
Journal Title:
Frontiers in Immunology
Journal Volume:
11
Keyword:
resolvins, protectins, maresins, antibodies, COVID-19, and lipoxins
Language Label:
English
License Label:
Attribution 3.0 United States
ORCID:
Other Affiliation:
and The Ohio State University Wexner Medical Center
Person:
Shaikh, S.R., Gowdy, K.M., Pal, A., Oestreich, K.J., and Beck, M.
The role of language in emotion: predictions from psychological constructionism
Creator:
Lindquist, Kristen A., Shablack, Holly, and MacCormack, Jennifer K.
Date of publication:
2015
Abstract Tesim:
Common sense suggests that emotions are physical types that have little to do with the words we use to label them. Yet recent psychological constructionist accounts reveal that language is a fundamental element in emotion that is constitutive of both emotion experiences and perceptions. According to the psychological constructionist Conceptual Act Theory (CAT), an instance of emotion occurs when information from one’s body or other people’s bodies is made meaningful in light of the present situation using concept knowledge about emotion. The CAT suggests that language plays a role in emotion because language supports the conceptual knowledge used to make meaning of sensations from the body and world in a given context. In the present paper, we review evidence from developmental and cognitive science to reveal that language scaffolds concept knowledge in humans, helping humans to acquire abstract concepts such as emotion categories across the lifespan. Critically, language later helps individuals use concepts to make meaning of on-going sensory perceptions. Building on this evidence, we outline predictions from a psychological constructionist model of emotion in which language serves as the “glue” for emotion concept knowledge, binding concepts to embodied experiences and in turn shaping the ongoing processing of sensory information from the body and world to create emotional experiences and perceptions.
Nurse managers' perceptions and experiences regarding staff nurse empowerment: a qualitative study
Creator:
Franck, Erik, Van heusden, Danny, Timmermans, Olaf, Peremans, Lieve, Havens, Donna S., Van Bogaert, Peter, and de Wit, Marlinde
Date of publication:
2015
Abstract Tesim:
Aim: To study nurse managers' perceptions and experiences of staff nurse structural empowerment and its impact on the nurse manager leadership role and style.
Maladaptive autonomic regulation in PTSD accelerates physiological aging
Creator:
Porges, Stephen W., Lamb, Damon G., Porges, Eric C., and Williamson, John B.
Date of publication:
2015
Abstract Tesim:
A core manifestation of post-traumatic stress disorder (PTSD) is a disconnection between physiological state and psychological or behavioral processes necessary to adequately respond to environmental demands. Patients with PTSD experience abnormal oscillations in autonomic states supporting either fight and flight behaviors or withdrawal, immobilization, and dissociation without an intervening “calm” state that would provide opportunities for positive social interactions. This defensive autonomic disposition is adaptive in dangerous and life threatening situations, but in the context of every-day life may lead to significant psychosocial distress and deteriorating social relationships. The perpetuation of these maladaptive autonomic responses may contribute to the development of comorbid mental health issues such as depression, loneliness, and hostility that further modify the nature of cardiovascular behavior in the context of internal and external stressors. Over time, changes in autonomic, endocrine, and immune function contribute to deteriorating health, which is potently expressed in brain dysfunction and cardiovascular disease. In this theoretical review paper, we present an overview of the literature on the chronic health effects of PTSD. We discuss the brain networks underlying PTSD in the context of autonomic efferent and afferent contributions and how disruption of these networks leads to poor health outcomes. Finally, we discuss treatment approaches based on our theoretical model of PTSD.
Levels of attention and task difficulty in the modulation of interval duration mismatch negativity
Creator:
Davalos, Deana B. and Campbell, Alana M.
Date of publication:
2015
Abstract Tesim:
Time perception has been described as a fundamental skill needed to engage in a number of higher level cognitive processes essential to successfully navigate everyday life (e.g., planning, sequencing, etc.) Temporal processing is often thought of as a basic neural process that impacts a variety of other cognitive processes. Others, however, have argued that timing in the brain can be affected by a number of variables such as attention and motivation. In an effort to better understand timing in the brain at a basic level with minimal attentional demands, researchers have often employed use of the mismatch negativity (MMN). MMN, specifically duration MMN (dMMN) and interval MMN (iMMN) have been popular methods for studying temporal processing in populations for which attention or motivation may be an issue (e.g., clinical populations, early developmental studies). There are, however, select studies which suggest that attention may in fact modify both temporal processing in general and the MMN event-related potential. It is unclear the degree to which attention affects MMN or whether the effects differ depending on the complexity or difficulty of the MMN paradigm. The iMMN indexes temporal processing and is elicited by introducing a deviant interval duration amid a series of standards. A greater degree of difference in the deviant from the standard elicits a heightened iMMN. Unlike past studies, in which attention was intentionally directed toward a closed-captioned move, the current study had participants partake in tasks involving varying degrees of attention (passive, low, and high) with varying degrees of deviants (small, medium, and large) to better understand the role of attention on the iMMN and to assess whether level of attention paired with changes in task difficulty differentially influence the iMMN electrophysiological responses. Data from 19 subjects were recorded in an iMMN paradigm. The amplitude of the iMMN waveform showed an increase with attention, particularly for intervals that were the most distinct from a standard interval (p < 0.02). Results suggest that the role of attention on the iMMN is complex. Both the degree of attention paid as well as the level of difficulty of the MMN task likely influence the neuronal response within a timing network. These results suggest that electrophysiological perception of time is modified by attention and that the design of the iMMN study is critical to minimize the possible confounding effects of attention. In addition, the implications of these results for future studies assessing interval duration-based MMN in clinical populations is also addressed.
Investigating the shape bias in typically developing children and children with autism spectrum disorders
Creator:
Fein, Deborah, Naigles, Letitia, and Potrzeba, Emily R.
Date of publication:
2015
Abstract Tesim:
Young typically developing (TD) children have been observed to utilize word learning strategies such as the noun bias and shape bias; these improve their efficiency in acquiring and categorizing novel terms. Children using the shape bias extend object labels to new objects of the same shape; thus, the shape bias prompts the categorization of object words based on the global characteristic of shape over local, discrete details. Individuals with autism spectrum disorders (ASDs) frequently attend to minor details of objects rather than their global structure. Therefore, children with ASD may not use shape bias to acquire new words. Previous research with children with ASD has provided evidence that they parallel TD children in showing a noun bias, but not a shape bias (Tek et al., 2008). However, this sample was small and individual and item differences were not investigated in depth. In an extension of Tek et al. (2008) with twice the sample size and a wider developmental timespan, we tested 32 children with ASD and 35 TD children in a longitudinal study across 20 months using the intermodal preferential looking paradigm. Children saw five triads of novel objects (target, shape-match, color-match) in both NoName and Name trials; those who looked longer at the shape-match during the Name trials than the NoName trials demonstrated a shape bias. The TD group showed a significant shape bias at all visits, beginning at 20 months of age while the language-matched ASD group did not show a significant shape bias at any visit. Within the ASD group, though, some children did show a shape bias; these children had larger vocabularies concurrently and longitudinally. Degree of shape bias elicitation varied by item, but did not seem related to perceptual complexity. We conclude that shape does not appear to be an organizing factor for word learning by children with ASD.
Increased reward value of non-social stimuli in children and adolescents with autism
Creator:
Dichter, Gabriel S., Sabatino-DiCrisco, Antoinette, Damiano, Cara R., Platt, Michael L., Miller, Stephanie, Turner-Brown, Lauren, Kovac, Megan, Watson, Karli K., Hannah, Eleanor, and Sasson, Noah J.
Date of publication:
2015
Abstract Tesim:
An econometric choice task was used to estimate the implicit reward value of social and non-social stimuli related to restricted interests in children and adolescents with (n = 12) and without (n = 22) autism spectrum disorder (ASD). Mixed effects logistic regression analyses revealed that groups differed in valuation of images related to restricted interests: control children were indifferent to cash payouts to view these images, but children with ASD were willing to receive less cash payout to view these images. Groups did not differ in valuation of social images or non-social images not related to restricted interests. Results highlight that motivational accounts of ASD should also consider the reward value of non-social stimuli related to restricted interests in ASD (Dichter and Adolphs, 2012).
behavioral economics, restricted interests, social, autism, reward, and pay-per-view
Language Label:
English
Person:
Dichter, Gabriel S., Sabatino-DiCrisco, Antoinette, Damiano, Cara R., Platt, Michael L., Miller, Stephanie, Turner-Brown, Lauren, Kovac, Megan, Watson, Karli K., Hannah, Eleanor, and Sasson, Noah J.
Examining the Dynamic Structure of Daily Internalizing and Externalizing Behavior at Multiple Levels of Analysis
Creator:
Simms, Leonard J., Gates, Kathleen M., Molenaar, Peter C. M., Beltz, Adriene M., and Wright, Aidan G. C.
Date of publication:
2015
Abstract Tesim:
Psychiatric diagnostic covariation suggests that the underlying structure of psychopathology is not one of circumscribed disorders. Quantitative modeling of individual differences in diagnostic patterns has uncovered several broad domains of mental disorder liability, of which the Internalizing and Externalizing spectra have garnered the greatest support. These dimensions have generally been estimated from lifetime or past-year comorbidity patters, which are distal from the covariation of symptoms and maladaptive behavior that ebb and flow in daily life. In this study, structural models are applied to daily diary data (Median = 94 days) of maladaptive behaviors collected from a sample (N = 101) of individuals diagnosed with personality disorders (PDs). Using multilevel and unified structural equation modeling, between-person, within-person, and person-specific structures were estimated from 16 behaviors that are encompassed by the Internalizing and Externalizing spectra. At the between-person level (i.e., individual differences in average endorsement across days) we found support for a two-factor Internalizing–Externalizing model, which exhibits significant associations with corresponding diagnostic spectra. At the within-person level (i.e., dynamic covariation among daily behavior pooled across individuals) we found support for a more differentiated, four-factor, Negative Affect-Detachment-Hostility-Disinhibition structure. Finally, we demonstrate that the person-specific structures of associations between these four domains are highly idiosyncratic.
internalizing, personality dynamics, unified SEM, personality structure, multilevel SEM, idiographic modeling, Psychology, Social Sciences, psychopathology, and externalizing
Language Label:
English
Person:
Simms, Leonard J., Gates, Kathleen M., Molenaar, Peter C. M., Beltz, Adriene M., and Wright, Aidan G. C.