Clinical Research and Public Health
Abstract
BACKGROUND. Lower-grade gliomas (LGGs) vary widely in terms of the patient’s overall survival (OS). There is a lack of valid method that could exactly predict the survival. The effects of intratumoral immune infiltration on clinical outcome have been widely reported. Thus, we aim to develop an immune infiltration signature to predict the survival of LGG patients. METHODS. We analyzed 1216 LGGs from 5 public datasets, including 2 RNA-Seq datasets and 3 microarray datasets. Least absolute shrinkage and selection operator (LASSO) Cox regression was used to select an immune infiltration signature and build a risk score. The performance of the risk score was assessed in the training set (329 patients), internal validation set (140 patients), and 4 external validation sets (405, 118, 88, and 136 patients). RESULTS. An immune infiltration signature consisting of 20 immune metagenes was used to generate a risk score. The performance of the risk score was thoroughly verified in the training and validation sets. Additionally, we found that the risk score was positively correlated with the expression levels of TGFβ and PD-L1, which were important targets of combination immunotherapy. Furthermore, a nomogram incorporating the risk score, patient’s age, and tumor grade was developed to predict the OS, and it performed well in all the training and validation sets (C-index: 0.873, 0.881, 0.781, 0.765, 0.721, and 0.753, respectively). CONCLUSIONS. The risk score based on the immune infiltration signature has reliable prognostic and predictive value for patients with LGGs and might be a potential biomarker for the co-targeting immunotherapy. FUNDING. The National Natural Science Foundation of China (Grant No. 81472370 and 81672506), the Natural Science Foundation of Beijing (Grant No. J180005), the National High Technology Research and Development Program of China (863 Program, Grant No. 2014AA020610) and the National Basic Research Program of China (973 Program, Grant No. 2014CB542006).
Authors
Lai-Rong Song, Jian-Cong Weng, Cheng-Bei Li, Xu-Lei Huo, Huan Li, Shu-Yu Hao, Zhen Wu, Liang Wang, Da Li, Jun-Ting Zhang
Abstract
Background: Metabolic disorders such as type 2 diabetes have been associated with a decrease in insulin pulse frequency and amplitude. We hypothesized that the T-allele at rs7903146 in TCF7L2, previously associated with β–cell dysfunction, would be associated with changes in these insulin pulse characteristics. Methods: 29 nondiabetic subjects (age = 46 ± 2, BMI = 28 ± 1 Kg/M2) participated in this study. Of these, 16 were homozygous for the C allele at rs7903146 and 13 were homozygous for the T allele. Deconvolution of peripheral C-peptide concentrations allowed the reconstruction of portal insulin secretion over time. This data was used for subsequent analyses. Pulse orderliness was assessed by Approximate Entropy (ApEn) and the dispersion of insulin pulses was measured by a Frequency Dispersion Index (FDI) applied to a Fourier Transform of individual insulin secretion rates. Results: During fasting conditions, the CC genotype group exhibited decreased pulse disorderliness compared to the TT genotype group (1.10 ± 0.03 vs. 1.19 ± 0.04, p = 0.03). FDI decreased in response to hyperglycemia in the CC genotype group, perhaps reflecting less entrainment of insulin secretion during fasting.Conclusion: Diabetes-associated variation in TCF7L2 is associated with decreased orderliness and pulse dispersion unchanged by hyperglycemia. Quantification of ApEn and FDI could represent novel markers of β-cell health.
Authors
Marcello C. Laurenti, Chiara Dalla Man, Ron T. Varghese, James C. Andrews, Robert A. Rizza, Aleksey Matveyenko, Giuseppe De Nicolao, Claudio Cobelli, Adrian Vella
Abstract
BACKGROUND. Seizure-induced inhibition of respiration plays a critical role in sudden unexpected death in epilepsy (SUDEP). However, the mechanisms underlying seizure-induced central apnea in pediatric epilepsy are unknown. METHODS. We studied eight pediatric patients with intractable epilepsy undergoing intracranial electroencephalography (iEEG). We recorded respiration during seizures and during electrical stimulation mapping of 174 forebrain sites. A machine learning algorithm was used to delineate brain regions that inhibit respiration. RESULTS. In two patients, apnea coincided with seizure spread to the amygdala. Supporting a role for the amygdala in breathing inhibition in children, electrically stimulating the amygdala produced apnea in all eight subjects (3- to 17-years-old). These effects did not depend on epilepsy type and were relatively specific to the amygdala as no other site affected breathing. Remarkably, patients were unaware that they had stopped breathing, and none reported dyspnea or arousal, findings critical for SUDEP. Finally, a machine learning algorithm based on 45 stimulation sites and 210 stimulation trials identified a focal subregion in the human amygdala that consistently produced apnea. This site, which we refer to as the Amygdala Inhibition of Respiration (AIR) site includes the medial subregion of the basal nuclei, cortical and medial nuclei, amygdala transition areas, and intercalated neurons. CONCLUSIONS. A focal site in the amygdala inhibits respiration and induces apnea (AIR site) when electrically stimulated and during seizures in children with epilepsy. This site may prove valuable for determining those at greatest risk for SUDEP and as a therapeutic target. TRIAL REGISTRATION. This study was not affiliated with any formal clinical trial. FUNDING. NIH, CNS, Roy J. Carver Charitable Trust.
Authors
Ariane E. Rhone, Christopher K. Kovach, Gail I.S. Harmata, Alyssa W. Sullivan, Daniel Tranel, Michael A. Ciliberto, Matthew A. Howard, George B. Richerson, Mitchell Steinschneider, John A. Wemmie, Brian J. Dlouhy
Abstract
Background Salt-sensitive hypertension is often accompanied by insulin resistance in obese individuals, but the underlying mechanisms are obscure. Microvascular function is known to affect both salt-sensitivity of blood pressure and metabolic insulin sensitivity. We hypothesized that excessive salt intake increases blood pressure and decreases insulin-mediated glucose disposal, at least in part by impairing insulin-mediated muscle microvascular recruitment (IMMR). Methods In 20 lean and 20 abdominally obese individuals, we assessed mean arterial pressure (MAP; 24h ABPM), insulin-mediated whole body glucose disposal (M/I-value; hyperinsulinemic, euglycemic clamp technique), IMMR (contrast enhanced ultrasound), osmolyte and water balance, and excretion of mineralocorticoids, glucocorticoids, and amino and organic acids after a low and high salt diet during seven days in a randomized double-blind cross-over design. Results On a low, as compared to a high salt intake, MAP was lower, M/I-value was lower and IMMR was greater in both lean and abdominally obese individuals. In addition, Ln IMMR was inversely associated with MAP in lean participants on a low salt diet only. On a high salt diet, free water clearance decreased, and excretion of glucocorticoids and of amino acids involved in the urea cycle increased. Conclusion Our findings imply that hemodynamic and metabolic changes resulting from alterations in salt intake are not necessarily associated. Moreover, they are consistent with the concept that a high salt intake increases muscle glucose uptake as a response to high-salt-induced, glucocorticoid-drive muscle catabolism to stimulate urea production and thereby renal water conservation. Clinical Trial Registration Number: NCT02068781
Authors
Monica T.J. Schütten, Yvo H.A.M. Kusters, Alfons J.H.M. Houben, Hanneke E. C. Niessen, Jos op 't Roodt, Jean L.J. M. Scheijen, Marjo P. van de Waarenburg, Casper G. Schalkwijk, Peter W. de Leeuw, Coen D.A. Stehouwer
Abstract
BACKGROUND RNA sequencing (RNA-Seq) is a molecular tool to analyze global transcriptional changes, deduce pathogenic mechanisms, and discover biomarkers. We performed RNA-Seq to investigate gene expression and biological pathways in urinary cells and kidney allograft biopsies during an acute rejection episode and to determine whether urinary cell gene expression patterns are enriched for biopsy transcriptional profiles.METHODS We performed RNA-Seq of 57 urine samples collected from 53 kidney allograft recipients (patients) with biopsies classified as acute T cell–mediated rejection (TCMR; n = 22), antibody-mediated rejection (AMR; n = 8), or normal/nonspecific changes (No Rejection; n = 27). We also performed RNA-Seq of 49 kidney allograft biopsies from 49 recipients with biopsies classified as TCMR (n = 12), AMR (n = 17), or No Rejection (n = 20). We analyzed RNA-Seq data for differential gene expression, biological pathways, and gene set enrichment across diagnoses and across biospecimens.RESULTS We identified unique and shared gene signatures associated with biological pathways during an episode of TCMR or AMR compared with No Rejection. Gene Set Enrichment Analysis demonstrated enrichment for TCMR biopsy signature and AMR biopsy signature in TCMR urine and AMR urine, irrespective of whether the biopsy and urine were from the same or different patients. Cell type enrichment analysis revealed a diverse cellular landscape with an enrichment of immune cell types in urinary cells compared with biopsies.CONCLUSIONS RNA-Seq of urinary cells and biopsies, in addition to identifying enriched gene signatures and pathways associated with TCMR or AMR, revealed genomic changes between TCMR and AMR, as well as between allograft biopsies and urinary cells.
Authors
Akanksha Verma, Thangamani Muthukumar, Hua Yang, Michelle Lubetzky, Michael F. Cassidy, John R. Lee, Darshana M. Dadhania, Catherine Snopkowski, Divya Shankaranarayanan, Steven P. Salvatore, Vijay K. Sharma, Jenny Z. Xiang, Iwijn De Vlaminck, Surya V. Seshan, Franco B. Mueller, Karsten Suhre, Olivier Elemento, Manikkam Suthanthiran
Abstract
BACKGROUND. The relative stabilities of the intact and defective HIV genomes over time during effective antiretroviral therapy (ART) have not been fully characterized. METHODS. We used the intact proviral DNA assay (IPDA) to estimate the rate of change of intact and defective proviruses in HIV-infected adults on ART over several years. We used linear spline models with a knot at seven years; these included a random intercept and slope up to the knot. We also estimated the influence of covariates on starting levels and rates of change. RESULTS. We studied 81 individuals for a median of 7.3 (IQR 5.9–9.6) years. In a model allowing for a change in the rate of decline, we found evidence for a more rapid rate of decline in intact genomes from initial suppression through seven years (15.7% per year decline; CI –22.8%, –8.0%) followed by a slower rate of decline after seven years (3.6% per year; CI –8.1%, +1.1%). The estimated half-life of the reservoir was 4.0 years (CI 2.7–8.3) until year seven and 18.7 years (CI 8.2–infinite) thereafter. There was substantial variability between individuals in the rate of decline until year seven. Intact provirus declined at a faster rate than defective provirus (P < 0.001). Individuals with higher CD4+ T cell nadir values had a faster rate of decline in intact provirus. CONCLUSIONS. These findings provide evidence that the biology of the replication-competent (intact) reservoir differs from that of the replication-incompetent (non-intact) pool of proviruses. The IPDA will likely be informative when investigating the impact of interventions targeting the reservoir. FUNDING. This work was supported the Delaney AIDS Research Enterprise (DARE; AI096109, A127966). The SCOPE cohort receives additional support from the UCSF/Gladstone Institute of Virology & Immunology CFAR (P30 AI027763), the CFAR Network of Integrated Systems (R24 AI067039) and the amfAR Institute for HIV Cure Research (amfAR 109301). Additional support was provided by the I4C and Beat-HIV Collaboratories, the Howard Hughes Medical Institute, Gilead, and the Bill and Melinda Gates Foundation.
Authors
Michael J. Peluso, Peter Bacchetti, Kristen D. Ritter, Subul A. Beg, Jun Lai, Jeffrey N. Martin, Peter W. Hunt, Timothy J. Henrich, Janet D. Siliciano, Robert F. Siliciano, Gregory M. Laird, Steven G. Deeks
Chronic liver disease and impaired hepatic glycogen metabolism in argininosuccinate lyase deficiency
Abstract
Background: Liver disease in urea cycle disorders (UCDs) ranges from hepatomegaly and chronic hepatocellular injury to cirrhosis and end-stage liver disease. However, the prevalence and underlying mechanisms are unclear. Methods: We estimated the prevalence of chronic hepatocellular injury in UCDs using data from a multicenter, longitudinal, natural history study. We also used ultrasound with shear wave elastography and FibroTestTM to evaluate liver stiffness and markers of fibrosis in individuals with argininosuccinate lyase deficiency (ASLD), a disorder with high prevalence of elevated serum alanine aminotransferase (ALT). To understand the human observations, we evaluated the hepatic phenotype of the AslNeo/Neo mouse model of ASLD. Results: We demonstrate a high prevalence of elevated ALT in ASLD (37%). Hyperammonemia and use of nitrogen-scavenging agents, two markers of disease severity, were significantly (p<0.001; p=0.001) associated with elevated ALT in ASLD. In addition, ultrasound with shear wave elastography and FibroTestTM revealed increased echogenicity and liver stiffness even in individuals with ASLD and normal aminotransferases. The AslNeo/Neo mice mimic the human disorder with hepatomegaly, elevated aminotransferases, and excessive hepatic glycogen noted prior to death (3-5 weeks of age). This excessive hepatic glycogen is associated with impaired hepatic glycogenolysis and decreased glycogen phosphorylase and is rescued with helper-dependent adenovirus expressing Asl using a liver specific (ApoE) promoter. Conclusions: Our results link urea cycle dysfunction and impaired hepatic glucose metabolism and identify a mouse model of liver disease in the setting of urea cycle dysfunction. Trial Registration: NCT03721367, NCT00237315 Funding: NIH, Burroughs Wellcome Fund, NUCDF, Genzyme/ACMG Foundation, CPRIT
Authors
Lindsay C. Burrage, Simran Madan, Xiaohui Li, Saima Ali, Mahmoud A. Mohammad, Bridget M. Stroup, Ming-Ming Jiang, Racel Cela, Terry Bertin, Jian Dai, Danielle Guffey, Milton Finegold, Sandesh Nagamani, Charles G. Minard, Juan Marini, Prakash Masand, Deborah Schady, Benjamin L. Shneider, Daniel H. Leung, Deeksha Bali, Brendan Lee
Abstract
BACKGROUND. Siponimod (BAF312) is a selective sphingosine 1-phosphate receptor 1 and 5 (S1PR1, S1PR5) modulator recently approved for active secondary progressive multiple sclerosis (SPMS). The immunomodulatory effects of siponimod in SPMS have not been previously described. METHODS. We conducted a multi-centered randomized, double-blind, placebo-controlled AMS04 mechanistic study with 36 SPMS participants enrolled in the EXPAND trial. Gene expression profiles were analyzed using RNA derived from whole blood with Affymetrix Human Gene ST 2.1 microarray technology. We performed flow cytometry based assays to analyze the immune cell composition and microarray gene expression analysis on peripheral blood from siponimod-treated participants with SPMS relative to baseline and placebo during the first year randomization phase. RESULTS. Microarray analysis showed that immune-associated genes involved in T and B cell activation and receptor signaling were largely decreased by siponimod, which is consistent with the reduction of CD4+ T cells, CD8+ T cells, and B cells. Analysis done by flow cytometry showed that within the remaining lymphocyte subsets, there was a reduction in the frequencies of CD4 and CD8 naïve T cells and central memory cells, while T effector memory cells, anti-inflammatory Th2, and T regulatory (Treg) cells were enriched. Transitional Bregs (CD24hiCD38hi) and B1 cell subsets (CD43+CD27+) were enriched, shifting the balance in favor of regulatory B cells over memory B cells. The pro-regulatory shift driven by siponimod treatment included a higher proliferative potential of Tregs compared with non-Tregs, and upregulated expression of PD-1 on Tregs. Additionally, a positive correlation was found between regulatory T cells and regulatory B cells in siponimod treated participants. CONCLUSION. The shift toward an anti-inflammatory and suppressive homeostatic immune system may contribute to the clinical efficacy of siponimod in SPMS. TRIAL REGISTRATION. NCT02330965.
Authors
Qi Wu, Elizabeth A. Mills, Qin Wang, Catherine A. Dowling, Caitlyn Fisher, Britany Kirch, Steven K. Lundy, David A. Fox, Yang Mao-Draayer
Abstract
BACKGROUND. The circadian system entrains behavioral and physiological rhythms to environmental cycles and modern lifestyles disrupt this entrainment. We investigated a timed exercise intervention to phase shift the internal circadian rhythm. METHODS. In fifty-two young, sedentary adults, dim light melatonin onset (DLMO) was measured before and after five days of morning (10h after DLMO; n = 26) or evening (20h after DLMO; n = 26) exercise. Phase shifts were calculated as the difference in DLMO before and after exercise. RESULTS. Morning exercise induced phase advance shifts (0.62 ± 0.18h) that were significantly greater than phase shifts from evening exercise (-0.02 ± 0.18h; P = 0.01). Chronotype also influenced the effect of timed exercise. For later chronotypes, both morning and evening exercise induced phase advances (0.54 ± 0.29h and 0.46 ±0.25h, respectively). In contrast, earlier chronotypes had phase advances from morning exercise (0.49 ± 0.25h), but phase delays from evening exercise (-0.41 ± 0.29h). CONCLUSION. Late chronotypes, who experience the most severe circadian misalignment, may benefit from phase advances induced by exercise in the morning or evening, but evening exercise may exacerbate circadian misalignment in early chronotypes. Thus, personalized exercise timing prescription based on chronotype could alleviate circadian misalignment in young adults. TRIAL REGISTRATION. www.clinicaltrials.gov, NCT # NCT04097886.FUNDING. National Institutes of Health grants UL1TR001998 and TL1TR001997, the Barnstable Brown Diabetes and Obesity Center, the Pediatric Exercise Physiology Laboratory Endowment, the Arvle and Ellen Turner Thacker Research Fund, and the University of Kentucky.
Authors
J. Matthew Thomas, Philip A. Kern, Heather M. Bush, Kristen J. McQuerry, W. Scott Black, Jody L. Clasey, Julie S. Pendergast
Abstract
BACKGROUND. Mitochondrial dysfunction, a proposed mechanism of COPD pathogenesis, is associated with the leakage of mitochondrial DNA (mtDNA), which may be detected extracellularly in various bodily fluids. Despite evidence for the increased prevalence of chronic kidney disease in COPD subjects and for mitochondrial dysfunction in the kidneys of murine COPD models, whether urine mtDNA (u-mtDNA) associates with measures of disease severity in COPD is unknown. METHODS. Cell-free u-mtDNA, defined as copy number of mitochondrially-encoded NADH dehydrogenase-1 (MTND1) gene, was measured by real-time quantitative PCR and normalized to urine creatinine in cell-free urine samples from participants in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) cohort. Urine albumin/creatinine ratios (UACR) were measured in the same samples. Associations between u-mtDNA and UACR and clinical disease parameters, including FEV1 % predicted, clinical measures of exercise tolerance, respiratory symptom burden, and chest CT measures of lung structure were examined. RESULTS. U-mtDNA and UACR levels were measured in never smokers (n = 64), smokers without airflow obstruction (n = 109), participants with mild/moderate COPD (n = 142), and participants with severe COPD (n = 168). U-mtDNA was associated with increased respiratory symptom burden, especially among smokers without COPD. Significant sex differences in u-mtDNA levels were observed with females having higher u-mtDNA levels across all study subgroups. U-mtDNA associated with worse spirometry and CT emphysema in males only, and worse respiratory symptoms in females only. Similar associations were not found with UACR. CONCLUSION. U-mtDNA levels may help to identify distinct clinical phenotypes and underlying pathobiological differences in males versus females with COPD.
Authors
William Z. Zhang, Michelle C. Rice, Katherine L. Hoffman, Clara Oromendia, Igor Barjaktarevic, J. Michael Wells, Annette T. Hastie, Wassim W. Labaki, Christopher B. Cooper, Alejandro P. Comellas, Gerard J. Criner, Jerry A. Krishnan, Robert Paine III, Nadia N. Hansel, Russell P. Bowler, R. Graham Barr, Stephen P. Peters, Prescott G. Woodruff, Jeffrey L. Curtis, Meilan K. Han, Karla V. Ballman, Fernando J. Martinez, Augustine M.K. Choi, Kiichi Nakahira, Suzanne M. Cloonan, Mary E. Choi
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