Single cell tracking of gadolinium labeled CD4(+) T cells by laser ablation inductively coupled plasma mass spectrometry

Cellular therapy is emerging as a promising alternative to conventional immunosuppression in the fields of haematopoietic stem cell (HSC) transplantation, autoimmune disease and solid organ transplantation. Determining the persistence of cell-based therapies in vivo is crucial to understanding their regulatory function and requires the combination of an extremely sensitive detection technique and a stable, long-lifetime cell labelling agent. This paper reports the first application of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to perform single cell detection of T cell populations relevant to cellular immunotherapy. Purified human CD4+ T cells were labelled with commercially available Gd-based MRI contrast agents, Omniscan® and Dotarem®, which enabled passive loading of up to 108 Gd atoms per cell. In mixed preparations of labelled and unlabelled cells, LA-ICP-MS was capable of enumerating labelled cells at close to the predicted ratio. More importantly, LA-ICP-MS single cell analysis demonstrated that the cells retained sufficient label to remain detectable for up to 10 days post-labelling both in vitro and in vivo in an immunodeficient mouse model

Trajectories of alcohol-induced blackouts in adolescence: early risk factors and alcohol use disorder outcomes in early adulthood

Background and aims: Experience of alcohol-induced memory blackouts in adolescence may be an important risk factor for later harms. This longitudinal study (i) modelled trajectories of alcohol-related blackouts throughout adolescence, (ii) explored early-adolescent predictors of blackout trajectories and (iii) examined the association between blackout trajectories and alcohol use disorder (AUD) symptoms. Design: Longitudinal study in which data from six annual surveys of a longitudinal cohort of Australian adolescents were used to model latent class growth trajectories of blackouts, adjusting for alcohol consumption frequency and typical quantity. Regression models were used to determine whether parent, child and peer factors at baseline (mean age = 12.9) predicted profiles of blackout trajectory membership and whether blackout trajectories predicted meeting criteria for AUD in early adulthood (mean age = 19.8). Setting and participants: Australian adolescents (n = 1821; mean age = 13.9–18.8 years). Measurements: Alcohol-related blackouts, alcohol consumption frequency, typical consumption quantity and DSM-5 AUD in early adulthood were all self-reported. Findings: We identified a three-class solution: delayed alcohol initiation, rare blackouts (n = 701; 38.5%); early initiation, rare blackouts (n = 869; 47.7%); and early initiation, increasing blackouts (n = 251; 13.8%). Female sex was associated with increased risk of early initiation, increasing blackouts relative to delayed initiation, rare blackouts [relative risk ratio (RRR) = 3.90; 99.5% confidence interval (CI) = 1.96, 7.76] and relative to early initiation, rare blackouts (RRR = 2.89; 99.5% CI = 1.42, 5.87). Early initiation, rare blackouts [odds ratio (OR) = 1.96; 99.5% CI = 1.17, 3.29] and early initiation, increasing blackouts (OR = 4.93; 99.5% CI = 2.32, 10.48) were each associated with increased odds of meeting criteria for AUD in early adulthood relative to delayed initiation, rare blackouts. Early initiation, increasing blackouts was associated with increased odds of meeting criteria for AUD in early adulthood relative to early initiation, rare blackouts (OR = 2.51; 99.5% CI = 1.18, 5.38). Conclusions: Females in Australia appear to be at higher risk of adolescent alcohol-related blackouts independent of alcohol consumption levels and age of initiation. Alcohol-related blackouts may be associated with later alcohol use disorder

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set

Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^>0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations

The experience of physiological and psychosocial alcohol-related harms across adolescence and its association with alcohol use disorder in early adulthood: A prospective cohort study

Background: Different forms of alcohol-related harm (e.g., hangovers, fighting) may confer differential risk of clinically relevant alcohol problems. We examine: (i) patterns of transition in experiencing alcohol-related harms across adolescence; (ii) whether factors in early adolescence predict transition patterns; and (iii) whether transition patterns predict later alcohol use disorder (AUD) symptoms. Methods: We used a longitudinal Australian cohort (n = 1828) to model latent class transition patterns of alcohol-related harms across three timepoints (Mage = 13.9, 16.8, 18.8 years). Regression models assessed whether child, peer, and parent factors in early adolescence (Mage = 12.9) predicted harms transition patterns and whether these patterns predicted AUD symptoms in early adulthood (Mage = 19.8). Results: Five transition patterns characterized most of the cohort (n ≈ 1609, 88.0%): (i) minimal harms (n ≈ 381, 20.8%); (ii) late physiological harms (n ≈ 702, 38.4%); (iii) early physiological harms (n ≈ 226, 12.4%); (iv) late all harms (n ≈ 131, 7.2%); and (v) gradual all harms (n ≈ 169, 9.2%). With late physiological harms as the reference, females had increased risk of experiencing early physiological harms (relative risk [RR]: 2.15; 99.5% CI: 1.19, 3.90). Late all harms (RR: 1.71; CI: 1.19, 2.47) and gradual all harms (RR: 1.84; CI: 1.37, 2.47) were each associated with increased odds of meeting criteria for AUD, even when patterns of alcohol consumption are considered. Conclusions: Adolescents display heterogeneous transition patterns across physiological and psychosocial alcohol-related harms. Females are at greater risk of experiencing early physiological harms. Experience of both physiological and psychosocial harms in late adolescence is an important and potentially modifiable precursor to clinically relevant alcohol problems in early adulthood

Common single nucleotide polymorphisms in genes related to immune function and risk of papillary thyroid cancer

Accumulating evidence suggests that alterations in immune function may be important in the etiology of papillary thyroid cancer (PTC). To identify genetic markers in immune-related pathways, we evaluated 3,985 tag single nucleotide polymorphisms (SNPs) in 230 candidate gene regions (adhesion-extravasation-migration, arachidonic acid metabolism/eicosanoid signaling, complement and coagulation cascade, cytokine signaling, innate pathogen detection and antimicrobials, leukocyte signaling, TNF/NF-kB pathway or other) in a case-control study of 344 PTC cases and 452 controls. We used logistic regression models to estimate odds ratios (OR) and calculate one degree of freedom P values of linear trend (P(SNP-trend)) for the association between genotype (common homozygous, heterozygous, variant homozygous) and risk of PTC. To correct for multiple comparisons, we applied the false discovery rate method (FDR). Gene region- and pathway-level associations (P(Region) and P(Pathway)) were assessed by combining individual P(SNP-trend) values using the adaptive rank truncated product method. Two SNPs (rs6115, rs6112) in the SERPINA5 gene were significantly associated with risk of PTC (P(SNP-FDR)/P(SNP-trend) = 0.02/6×10(−6) and P(SNP-FDR)/P(SNP-trend) = 0.04/2×10(−5), respectively). These associations were independent of a history of autoimmune thyroiditis (OR = 6.4; 95% confidence interval: 3.0–13.4). At the gene region level, SERPINA5 was suggestively associated with risk of PTC (P(Region-FDR)/P(Region = )0.07/0.0003). Overall, the complement and coagulation cascade pathway was the most significant pathway (P(Pathway) = 0.02) associated with PTC risk largely due to the strong effect of SERPINA5. Our results require replication but suggest that the SERPINA5 gene, which codes for the protein C inhibitor involved in many biological processes including inflammation, may be a new susceptibility locus for PTC

On the Interplay of Telomeres, Nevi and the Risk of Melanoma

The relationship between telomeres, nevi and melanoma is complex. Shorter telomeres have been found to be associated with many cancers and with number of nevi, a known risk factor for melanoma. However, shorter telomeres have also been found to decrease melanoma risk. We performed a systematic analysis of telomere-related genes and tagSNPs within these genes, in relation to the risk of melanoma, dysplastic nevi, and nevus count combining data from four studies conducted in Italy. In addition, we examined whether telomere length measured in peripheral blood leukocytes is related to the risk of melanoma, dysplastic nevi, number of nevi, or telomere-related SNPs. A total of 796 cases and 770 controls were genotyped for 517 SNPs in 39 telomere-related genes genotyped with a custom-made array. Replication of the top SNPs was conducted in two American populations consisting of 488 subjects from 53 melanoma-prone families and 1,086 cases and 1,024 controls from a case-control study. We estimated odds ratios for associations with SNPs and combined SNP P-values to compute gene region-specific, functional group-specific, and overall P-value using an adaptive rank-truncated product algorithm. In the Mediterranean population, we found suggestive evidence that RECQL4, a gene involved in genome stability, RTEL1, a gene regulating telomere elongation, and TERF2, a gene implicated in the protection of telomeres, were associated with melanoma, the presence of dysplastic nevi and number of nevi, respectively. However, these associations were not found in the American samples, suggesting variable melanoma susceptibility for these genes across populations or chance findings in our discovery sample. Larger studies across different populations are necessary to clarify these associations

Variants in interferon-alpha pathway genes and response to pegylated interferon-Alpha2a plus ribavirin for treatment of chronic hepatitis C virus infection in the hepatitis C antiviral long-term treatment against cirrhosis trial

Combination treatment with pegylated-interferon-alpha (PEG IFN-Α) and ribavirin, the current recommended therapy for chronic hepatitis C virus (HCV) infection, results in a sustained virological response (SVR) in only about half of patients. Because genes involved in the interferon-alpha pathway may affect antiviral responses, we analyzed the relationship between variants in these genes and SVR among participants in the Hepatitis C Antiviral Long-Term treatment Against Cirrhosis (HALT-C) trial. Patients had advanced chronic hepatitis C that had previously failed to respond to interferon-based treatment. Participants were treated with peginterferon-Α2a and ribavirin during the trial. Subjects with undetectable HCV RNA at week 72 were considered to have had an SVR. Subjects with detectable HCV RNA at week 20 were considered nonresponders. We used TaqMan assays to genotype 56 polymorphisms found in 13 genes in the interferon-alpha pathway. This analysis compares genotypes for participants with an SVR to nonresponders. The primary analysis was restricted to European American participants because a priori statistical power was low among the small number (n = 131) of African American patients. We used logistic regression to control the effect of other variables that are associated with treatment response. Among 581 European American patients, SVR was associated with IFNAR1 IVS1-22G (adjusted odds ratio, 0.57; P = 0.02); IFNAR2 Ex2-33C (adjusted odds ratio, 2.09; P = 0.02); JAK1 IVS22+112T (adjusted odds ratio, 1.66; P = 0.04); and ADAR Ex9+14A (adjusted odds ratio, 1.67; P = 0.03). For the TYK2 -2256A promoter region variant, a borderline association was present among European American participants (OR, 1.51; P = 0.05) and a strong relationship among African American patients; all 10 with SVR who were genotyped for TYK2 -2256 carried the A variant compared with 68 of 120 (57%) nonresponders ( P = 0.006). Conclusion: Genetic polymorphisms in the interferon-Α pathway may affect responses to antiviral therapy of chronic hepatitis C. (H EPATOLOGY 2009.)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63061/1/22877_ftp.pd

The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study

The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. A total of 881 women were included (369 breast cancers, 93 nonmalignant cases and 419 population-based controls). The V4 region of the 16S rRNA gene was sequenced from oral and fecal samples. Alpha-diversity (observed amplicon sequence variants [ASVs], Shannon index and Faiths Phylogenetic Diversity) and beta-diversity (Bray-Curtis, Jaccard and weighted and unweighted UniFrac) metrics were computed. MiRKAT and logistic regression models were used to investigate the case-control associations. Oral sample alpha-diversity was inversely associated with breast cancer and nonmalignant breast disease with odds ratios (95% CIs) per every 10 observed ASVs of 0.86 (0.83-0.89) and 0.79 (0.73-0.85), respectively, compared to controls. Beta-diversity was also associated with breast cancer and nonmalignant breast disease compared to controls (P ≤ .001). The relative abundances of Porphyromonas and Fusobacterium were lower for breast cancer cases compared to controls. Alpha-diversity and presence/relative abundance of specific genera from the oral and fecal microbiome were strongly correlated among breast cancer cases, but weakly correlated among controls. Particularly, the relative abundance of oral Porphyromonas was strongly, inversely correlated with fecal Bacteroides among breast cancer cases (r = -.37, P ≤ .001). Many oral microbial metrics were strongly associated with breast cancer and nonmalignant breast disease, and strongly correlated with fecal microbiome among breast cancer cases, but not controls