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Infant microbiome assembly is intensely studied in infants from industrialized nations, but little is known about this process in populations living non-industrialized lifestyles. In this study we deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with over twenty percent of genomes detected in the Hadza infant gut representing phylogenetically diverse novel species. Industrialized infants, even those who are breastfed, have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early-life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.Recognition of work on indigenous communitiesResearch involving indigenous communities is needed for a variety of reasons including to ensure that scientific discoveries and understanding appropriately represent all populations and do not only benefit those living in industrialized nations. Special considerations must be made to ensure that this research is conducted ethically and in a non-exploitative manner. In this study we performed deep metagenomic sequencing on fecal samples that were collected from Hadza hunter-gatherers in 2013/2014 and were analyzed in previous publications using different methods (1, 2). A material transfer agreement with the National Institute for Medical Research in Tanzania ensures that stool samples collected are used solely for academic purposes, permission for the study was obtained from the National Institute of Medical Research (MR/53i 100/83, NIMR/HQ/R.8a/Vol.IX/1542) and the Tanzania Commission for Science and Technology, and verbal consent was obtained from the Hadza after the study’s intent and scope was described with the help of a translator. The publications that first described these samples included several scientists and Tanzanian field-guides as co-authors for the critical roles they played in sample collection, but as no new samples were collected in this study, only scientists who contributed to the analyses described here were included as co-authors in this publication. It is currently not possible for us to travel to Tanzania and present our results to the Hadza people, however we intend to do so once the conditions of the COVID-19 pandemic allow it.

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, most avian gut microbiome studies have focused on birds of economic importance while the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 samples from fourFalcospecies including hybrid birds— raptors of historic importance —in the context of avian evolution by sequencing the 16S rDNA V4 region. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and consists ofSalmonellaat appreciable levels.Salmonellapresence may potentially alter the functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut and presents a potential risk to human health.Author Summary in Arabic

Background Probiotics have been demonstrated to ameliorate clinical signs of gastrointestinal diseases in dogs in various studies. However, the effect of probiotics in a healthy population, as well as factors contributing individualized responses, remain largely unknown. This trial examined gut microbiota (GM) and health outcomes in household dogs after synbiotic (SN) supplementation containing probiotics and inulin (a prebiotic). Healthy dogs were randomized to receive SN (50 mg/d inulin and 20 billion total CFU/d of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples for GM profiling (shotgun metagenomic sequencing) at baseline and week 4 in both groups, and at week 6 in the SN group. Results A significant shift (p n = 24), but not PL group (n = 19), at week 4 relative to baseline. Forty-five bacterial species, 43 (96%) of which were Lactobacillales, showed an increase in the relative abundances (≥2 fold change, adjusted p E. coli also decreased at week 4 in the SN group (2.8-fold, adjusted p Proteobacteria and lower Lactobacillales responded more robustly to supplementation in terms of the change in β-diversity. Dogs fed SN tended to have lower diarrhea incidence (0% vs 16%, p = 0.08). Conclusions SN supplement had a short-term impact on the gut microbiota in healthy household dogs as characterized by shotgun metagenomic sequencing. Findings warrant further investigation with longer duration and populations at risk of gastrointestinal diseases. The magnitude of response to the supplement was associated with microbial profile at baseline. To our knowledge, this is the first study documenting such association and may provide a basis for personalized nutrition in companion dogs.

Background The gut microbiota (GM) is associated with canine health and can be impacted by diet. Dog owners in the U.S. have increasingly shown an interest in feeding their dogs a mildly cooked (MC) diet. However, its impact on canine GM and health remains largely unknown. Methods Healthy household dogs were tracked upon switching from various brands of extruded to MC diets for four weeks. A health assessment was completed and stool samples were collected by each owner before (day 0) and after the diet transition (day 28). Shotgun metagenomic sequencing was performed at both time points to characterize the GM. Results Dogs completed the study by either completing the health assessments (n = 31) or providing stool samples at both time points (n = 28). All owners reported either better or no change in overall health at the end of the study (61% and 39%, respectively), and none reported worse overall health. Defecation frequency was also reported to be lower (58%) or about the same (35%). Principal coordinate (PCo) analysis showed a significant shift (p = 0.004) in the β-diversity of the GM upon diet transition (34.2% and 10.3% explained by the first two axes). The abundances of 70 species increased after the diet change (adjusted p < 0.05), 67% and 24% of which belonged to the Lactobacillales and the Enterobacterales orders respectively. The abundances of 28 species decreased (adjusted p < 0.05), 46%, 18%, and 11% of which belonged to the Clostridiales, Bacillales, and Bacteroidales orders, respectively. Lower Lactobacillales and Enterobacterales, and higher Bacteroidales at baseline were associated with a greater shift along the PCo1 axis. Protein content of the baseline diet was correlated with the shift along the PCo1 axis (ρ = 0.67, p = 0.006). Conclusion Owners reported either improvement or no change in health in dogs transitioning from extruded kibble to MC diets for 4 weeks, but this report of health perception requires further exploration in a controlled trial. Diet change also led to a significant shift in the GM profile of healthy dogs. The magnitude of shift was associated with baseline GM and dietary protein, and warrants further examination of individualized responses and personalized nutrition in companion dogs. These results also support future investigation of the impact of a MC diet on health maintenance given its increasing popularity.

Additional file 11: Table S10A. Gut bacteria from samples collected at baseline that were significantly different in the differential abundance analysis (|fold change| ≥ 2 and p

Additional file 6: Table S5. Relative abundances (as % of reads in the synbiotic supplement) for species with significantly increased abundances in the stool at week 4 in the synbiotic group. Only species not added to the supplement are reported and relative abundances were averaged from two samples.

Additional file 8: Table S7. Median (IQR) of gut microbial evenness, richness, and α-diversity indices among tertiles of responders (n = 23) at sequencing coverage of 380,000 reads.

Additional file 5: Table S4A. Species of gut bacteria with significant increase or decrease in the differential abundance analysis (|fold change| ≥ 2 and adjusted p

Additional file 2: Table S1. Guaranteed analysis and ingredients of the 4 cooked diet recipes.

Additional file 4: Table S3. Breeds and diet of study participants (placebo n = 19, synbiotic n = 24).

Additional file 9: Table S8A. Bacterial species that were significantly different in the differential abundance analysis (|fold change| ≥ 2 and p

Additional file 7: Table S6. Baseline subject characteristics of high- (HR), mid- (MR), and low-responders (LR) in the synbiotics group.

Background: Probiotics ameliorate gastrointestinal symptoms in dogs. However, the effect of probiotics in a healthy population, as well as factors contributing individualized responses, remains largely unknown. This trial examined gut microbiota (GM) and health outcomes in household dogs after synbiotic (SN) supplementation containing probiotics and inulin. Healthy dogs were randomized to receive SN (50 mg/d inulin and 20 billion total CFU/d of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples for GM profiling (metagenomic sequencing) at baseline and week 4 in both groups, and at week 6 in the SN group.Results: A significant shift (p

OBJECTIVES: Dogs share similar gut microbiome (GM) with humans, making them a great model for investigating the effects of probiotics (PR) on GM and health. This randomized control trial examined changes in MB and health outcomes in household dogs after PR supplementation. METHODS: All dogs recruited were fed human grade cooked food ≥ 1 mo, not fed any cultured food, PR, prebiotics, or on antibiotics ≥ 3 mo, and absent of major diseases. Dogs were randomized to receive a daily dose of PR (20 billion CFU of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples at baseline and 4 weeks after the intervention in both groups. Additional stool samples were collected 2 weeks after stopping the PR in the PR group. GM profiling was performed with metagenomic sequencing. RESULTS: Twenty three dogs in the PR and 19 dogs in the PL group completed the trial (5.6 ± 3.0 y, 69% male). PR had no effect on α-diversity. As compared to baseline, changes in β-diversity at the species level in 4.3% of GM were significantly affected by PR at week 4 (P

BackgroundOverweightness and obesity in dogs are associated with negative health outcomes. A better understanding of risk factors associated with canine weight is fundamental to identifying preventative interventions and treatments. In this cross-sectional study, we used a direct to consumer approach to collect body condition scores (BCS), as well as demographic, diet, and lifestyle data on 4,446 dogs. BCS was assessed by owners using a 9-point system and categorized as ideal (BCS 4-5), overweight (BCS 6), and obese (BCS 7+). Following univariate analyses, a stepwise procedure was used to select variables which were included in multivariate logistic regression models. One model was created to compare ideal to all overweight and obese dogs, and another was created to compare ideal to obese dogs only. We then used Elastic Net selection and XGBoost variable importance measures to validate these results.ResultsOverall, 1,480 (33%) of dogs were reported to be overweight or obese, of which 356 (8% total) of dogs were reported to be obese. Seven factors were significantly associated with both overweightness/obesity and obesity alone in all three analyses (stepwise, Elastic Net, and XGBoost): diet composition, probiotic supplementation, treat quantity, exercise, age, food motivation level, and pet appetite. Neutering was also associated with overweightness/obesity in all analyses.ConclusionsThis study recapitulated established risk factors associated with BCS (age, exercise, neutering). Moreover, we elucidated associations between previously examined risk factors and BCS (diet composition, treat consumption, and temperament) and identified a novel factor (probiotic supplementation). Specifically, relative to dogs on fresh food diets, BCS was higher in dogs eating dry food both alone and in combination with other foods. Furthermore, dogs receiving probiotics, but not other forms of supplementation, were more likely to have an ideal BCS. Future studies should corroborate these findings with experimental manipulations.

The role of gut microbiomes as important regulators of mammalian health is increasingly recognized, although feline and canine gut microbiomes remain poorly characterized. In this proof-of-concept study, we assessed the utility of a direct-to-consumer approach to executing pet microbiome studies. We characterized the gut microbiomes of 238 pets (46 cats and 192 dogs) by generating ~11 million merged reads that were mapped to the V4 region of 16S ribosomal RNA gene at a sequencing depth of 45,806 (±22,325) reads per sample. Analyses of these reads revealed that both feline and canine gut microbiomes are dominated by three major phyla, namely Firmicutes, Proteobacteria, and Bacteroides and that alpha diversity is higher in the feline gut. In addition to interspecies differences between the feline and canine gut, we also detected appreciable intraspecies bacterial variation within the canine population. While the dogs in this dataset could be assigned to three distinct clusters based on their gut microbiome, no clustering was observed within the feline population. Integration of additional data obtained from survey questionnaires revealed that geography and body weight may be associated with canine gut microbiome composition. Furthermore, we found that both the inter and intraspecies differences are more pronounced at finer taxonomic levels, indicating that strain-level investigations may be necessary in the future. This study demonstrates that the direct-to-consumer approach overcomes existing limitations in pet microbiome research, for example, it allows collection of large numbers of pet samples. The direct-to-consumer approach has proven successful in human genomics as well as human microbiomics and this study demonstrates that by building partnerships with an engaged general public this approach can also propel the field of pet microbiomics forward.

// Mark A. Applebaum 1, 2, * , Aashish R. Jha 3, 4, * , Clara Kao 4 , Kyle M. Hernandez 5 , Gillian DeWane 1 , Helen R. Salwen 1 , Alexandre Chlenski 1 , Marija Dobratic 1 , Christopher J. Mariani 6 , Lucy A. Godley 6 , Nanduri Prabhakar 6 , Kevin White 4 , Barbara E. Stranger 3, 6, 7 , Susan L. Cohn 1, 2 1 Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America 2 Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, 60637, United States of America 3 Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, 60637, United States of America 4 Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America 5 Center for Research Informatics, University of Chicago, Chicago, Illinois, 60637, United States of America 6 Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America 7 Center for Data Intensive Science, University of Chicago, Chicago, Illinois, 60637, United States of America * These authors contributed equally to this work Correspondence to: Susan L. Cohn, email: scohn@peds.bsd.uchicago.edu Keywords: neuroblastoma, hypoxia, metabolism, RNA expression, pathway analysis Received: August 02, 2016 Accepted: October 12, 2016 Published: October 17, 2016 ABSTRACT Neuroblastoma is notable for its broad spectrum of clinical behavior ranging from spontaneous regression to rapidly progressive disease. Hypoxia is well known to confer a more aggressive phenotype in neuroblastoma. We analyzed transcriptome data from diagnostic neuroblastoma tumors and hypoxic neuroblastoma cell lines to identify genes whose expression levels correlate with poor patient outcome and are involved in the hypoxia response. By integrating a diverse set of transcriptome datasets, including those from neuroblastoma patients and neuroblastoma derived cell lines, we identified nine genes ( SLCO4A1, ENO1, HK2, PGK1, MTFP1, HILPDA, VKORC1, TPI1, and HIST1H1C ) that are up-regulated in hypoxia and whose expression levels are correlated with poor patient outcome in three independent neuroblastoma cohorts. Analysis of 5-hydroxymethylcytosine and ENCODE data indicate that at least five of these nine genes have an increase in 5-hydroxymethylcytosine and a more open chromatin structure in hypoxia versus normoxia and are putative targets of hypoxia inducible factor (HIF) as they contain HIF binding sites in their regulatory regions. Four of these genes are key components of the glycolytic pathway and another three are directly involved in cellular metabolism. We experimentally validated our computational findings demonstrating that seven of the nine genes are significantly up-regulated in response to hypoxia in the four neuroblastoma cell lines tested. This compact and robustly validated group of genes, is associated with the hypoxia response in aggressive neuroblastoma and may represent a novel target for biomarker and therapeutic development.

Background: In cancer, hypoxia leads to a clinically aggressive phenotype by inducing angiogenesis, altering metabolism, and promoting cell infiltration, invasion and metastasis. Hypoxia also results in specific adaptive genetic changes in Drosophila melanogaster and many other species. We hypothesized that an evolutionarily conserved transcriptional program exists in Drosophila, neuroblastoma cell lines, and primary neuroblastoma tumors conferring both a survival advantage in Drosophila bred in hypoxia and aggressive tumor behavior. Methods: RNA-seq data from neuroblastoma cells grown in normoxia or hypoxia were analyzed to identify differentially expressed genes (DEG). These data were compared to previously identified human orthologous DEG from Drospohila bred in normoxia or hypoxia. The analysis was validated using public microarray expression data from 11 additional neuroblastoma cell lines cultured in normal or hypoxic conditions (GEO accession GSE17714). In order to evaluate these genes in patients, gene expression microarray data from 479 primary neuroblastoma tumors (EMBL accession E-MTAB-179) were analyzed with respect to patient survival status. Results: Pathway analysis of genes differentially expressed in Drosophila bred in hypoxia revealed enrichment for genes of the citric acid cycle (p = 13.1x10-17), pyruvate metabolism (p = 5.4x10-10), and glycolysis (p = 4.1x10-7). Analysis of neuroblastoma cells grown in hypoxia identified DEG in steroid biosynthesis (p = 1.3x10-13), HIF-1α transcription network (p = 3.3x10-13), and glycolysis (p = 3.2x10-6). 222 common DEG in neuroblastoma cells and Drosophila were enriched for glycolysis (p = 2.1x10-8), gluconeogenesis (p = 1.2x10-5) and the HIF-1α transcription network (p = 7.2x10-5). Up-regulation of glycolysis genes was also detected in the 11 additional neuroblastoma cell lines cultured in hypoxia. These cell lines showed additional differential expression in Ataxia telangiectasia and Rad3 (ATR) DNA damage sensing genes and general cell cycle related genes (p = 2.9x10-9 and p = 1.5x10-5, respectively). Of the 479 primary tumor samples with median follow up time of 3.75 years, there were 119 stage 1, 80 stage 2, 69 stage 3, 148 stage 4, and 62 stage 4S patients of whom 91 are deceased. In the analysis of primary tumors, decreased expression of cell cycle and metabolism genes (p = 4.8x10-13 and p = 1.6x10-12, respectively) was associated with survival. Thirty-nine of the DEG from patients, including multiple metabolism genes such as PGK1, GPI, and ACSS2, were common for both Drosophila and cell lines exposed to hypoxic conditions. Conclusions: Hypoxia alters metabolism in Drosophila, and neuroblastoma cell lines, and similar changes are associated with clinically aggressive phenotype in primary neuroblastoma tumors. Changes in cell cycle gene expression were also common in neuroblastoma cell lines grown in hypoxia and in clinically aggressive primary tumors. Further analysis of these pathways and their regulation will allow us to identify patients at high risk and provide insight to personalize therapy. Citation Format: Mark A. Applebaum, Aashish R. Jha, Alexandre Chlenski, Kyle Hernandez, Christopher J. Mariani, Barbara E. Stranger, Susan L. Cohn. Identification of evolutionarily conserved hypoxia-induced genomic pathways responsible for aggressive neuroblastoma phenotypes. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-55.

Background: In cancer, hypoxia leads to a clinically aggressive phenotype by inducing angiogenesis, altering metabolism, and promoting cell infiltration, invasion and metastasis. Hypoxia also results in specific adaptive genetic changes in Drosophila melanogaster and many other species. We hypothesized that an evolutionarily conserved transcriptional program exists in Drosophila, neuroblastoma cell lines, and primary neuroblastoma tumors conferring both a survival advantage in Drosophila bred in hypoxia and aggressive tumor behavior. Methods: RNA-seq data from neuroblastoma cells grown in normoxia or hypoxia were analyzed to identify differentially expressed genes (DEG). These data were compared to previously identified human orthologous DEG from Drospohila bred in normoxia or hypoxia. The analysis was validated using public microarray expression data from 11 additional neuroblastoma cell lines cultured in normal or hypoxic conditions (GEO accession GSE17714). In order to evaluate these genes in patients, gene expression microarray data from 479 primary neuroblastoma tumors (EMBL accession E-MTAB-179) were analyzed with respect to patient survival status. Results: Pathway analysis of genes differentially expressed in Drosophila bred in hypoxia revealed enrichment for genes of the citric acid cycle (p = 13.1x10-17), pyruvate metabolism (p = 5.4x10-10), and glycolysis (p = 4.1x10-7). Analysis of neuroblastoma cells grown in hypoxia identified DEG in steroid biosynthesis (p = 1.3x10-13), HIF-1α transcription network (p = 3.3x10-13), and glycolysis (p = 3.2x10-6). 222 common DEG in neuroblastoma cells and Drosophila were enriched for glycolysis (p = 2.1x10-8), gluconeogenesis (p = 1.2x10-5) and the HIF-1α transcription network (p = 7.2x10-5). Up-regulation of glycolysis genes was also detected in the 11 additional neuroblastoma cell lines cultured in hypoxia. These cell lines showed additional differential expression in Ataxia telangiectasia and Rad3 (ATR) DNA damage sensing genes and general cell cycle related genes (p = 2.9x10-9 and p = 1.5x10-5, respectively). Of the 479 primary tumor samples with median follow up time of 3.75 years, there were 119 stage 1, 80 stage 2, 69 stage 3, 148 stage 4, and 62 stage 4S patients of whom 91 are deceased. In the analysis of primary tumors, decreased expression of cell cycle and metabolism genes (p = 4.8x10-13 and p = 1.6x10-12, respectively) was associated with survival. Thirty-nine of the DEG from patients, including multiple metabolism genes such as PGK1, GPI, and ACSS2, were common for both Drosophila and cell lines exposed to hypoxic conditions. Conclusions: Hypoxia alters metabolism in Drosophila, and neuroblastoma cell lines, and similar changes are associated with clinically aggressive phenotype in primary neuroblastoma tumors. Changes in cell cycle gene expression were also common in neuroblastoma cell lines grown in hypoxia and in clinically aggressive primary tumors. Further analysis of these pathways and their regulation will allow us to identify patients at high risk and provide insight to personalize therapy. Citation Format: Mark A. Aplebaum, Aashish R. Jha, Alexandre Chlenski, Kyle Hernandez, Christopher J. Mariani, Barbara E. Stranger, Susan L. Cohn. Identification of evolutionarily conserved hypoxia-induced genomic pathways responsible for aggressive neuroblastoma phenotypes. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-15.

The ability to withstand low oxygen (hypoxia tolerance) is a polygenic and mechanistically conserved trait that has important implications for both human health and evolution. However, little is known about the diversity of genetic mechanisms involved in hypoxia adaptation in evolving populations. We used experimental evolution and whole-genome sequencing in Drosophila melanogaster to investigate the role of natural variation in adaptation to hypoxia. Using a generalized linear mixed model we identified significant allele frequency differences between three independently evolved hypoxia-tolerant populations and normoxic control populations for approximately 3,800 single nucleotide polymorphisms. Around 50% of these variants are clustered in 66 distinct genomic regions. These regions contain genes that are differentially expressed between hypoxia-tolerant and normoxic populations and several of the differentially expressed genes are associated with metabolic processes. Additional genes associated with respiratory and open tracheal system development also show evidence of directional selection. RNAi-mediated knockdown of several candidate genes' expression significantly enhanced survival in severe hypoxia. Using genomewide single nucleotide polymorphism data from four high-altitude human populations-Sherpas, Tibetans, Ethiopians, and Andeans, we found that several human orthologs of the genes under selection in flies are also likely under positive selection in all four high-altitude human populations. Thus, our results indicate that selection for hypoxia tolerance can act on standing genetic variation in similar genes and pathways present in organisms diverged by hundreds of millions of years.

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle/modernization. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut microbiota and find that the gut microbiome composition is significantly associated with lifestyle. The Chepang foragers harbor elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. For example, our results show that drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across populations. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of isolating dietary effects from other factors that change during modernization.

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity’s past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting–gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250–300 years ago, the Raute and Raji transitioned 30–40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across lifestyles. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of determining how large-scale gut microbiome reconfiguration impacts human biology., Author summary Although much of humanity’s history has been spent foraging in the forests, the advent of agriculture approximately 10,000 years ago and industrialization approximately 250 years ago mark major shifts in human lifestyle. Several studies have investigated the effect of industrialization on the human gut microbiome—a collection of microbes that inhabit the human gut. However, little is known about whether the gut microbiome changed as humans shifted away from foraging. To investigate how the gut community changes in response to shifts in traditional human lifestyles, we characterized the gut microbial community from four Himalayan populations representing diverse subsistence strategies. We show that the divergence of the gut microbiome from the foraging population is strongly correlated with agricultural dependence in these populations. Many of the taxa that differ across lifestyles are known to be influenced by diet, but we also demonstrate that environmental factors, such as sources of drinking water, are strongly associated with the human gut microbiome. Our findings show that both diet and environment play key roles in shaping the human gut microbiome.

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans., Facultad de Ciencias Naturales y Museo

Progressive loss of T cell functionality is a hallmark of chronic infection with human immunodeficiency virus 1 (HIV-1). We have identified a novel population of dysfunctional T cells marked by surface expression of the glycoprotein Tim-3. The frequency of this population was increased in HIV-1–infected individuals to a mean of 49.4 ± SD 12.9% of CD8+ T cells expressing Tim-3 in HIV-1–infected chronic progressors versus 28.5 ± 6.8% in HIV-1–uninfected individuals. Levels of Tim-3 expression on T cells from HIV-1–infected inviduals correlated positively with HIV-1 viral load and CD38 expression and inversely with CD4+ T cell count. In progressive HIV-1 infection, Tim-3 expression was up-regulated on HIV-1–specific CD8+ T cells. Tim-3–expressing T cells failed to produce cytokine or proliferate in response to antigen and exhibited impaired Stat5, Erk1/2, and p38 signaling. Blocking the Tim-3 signaling pathway restored proliferation and enhanced cytokine production in HIV-1–specific T cells. Thus, Tim-3 represents a novel target for the therapeutic reversal of HIV-1–associated T cell dysfunction.

Sudmant, Peter H. et al., In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide–variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load., This project has been funded in part with federal funds from the National Cancer Institute, NIH, under contract HHSN26120080001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does the mention of trade names, commercial products, or organizations imply endorsement by the U.S. government. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. This work was also partly supported by NIH grant 2R01HG002385 and a grant (11631) from the Paul G. Allen Family Foundation to E.E.E. The sequencing for this study was supported by a grant from the Simons Foundation to D.R. (SFARI 280376) and by a HOMINID grant from the NSF to D.R. (BCS-1032255). T.K. is supported by a European Research Council Starting Investigator grant (FP7 - 26213). R.S. and S.D. received support from the Ministry of Education and Science, Russian Federation (14.Z50.31.0010). H.S., E.M., R.V., and M.M. are supported by Institutional Research Funding from the Estonian Research Council IUT24-1 and by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu. S.A.T. is supported by NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01. C.T.-S. is supported by Wellcome Trust grant 098051. C.M.B. is supported by the NSF (award numbers 0924726 and 1153911). E.E.E. and D.R. are investigators of the Howard Hughes Medical Institute. Data are deposited into ENA (PRJEB9586 or ERP010710), and variant calls are deposited in dbVar (PRJNA285786). E.E.E. is on the scientific advisory board of DNAnexus, Incorporated, and is a consultant for Kunming University of Science and Technology (KUST) as part of the 1000 China Talent Program.

Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size.

Human endogenous retroviruses are found throughout the genome, and most insertions predate human divergence from other primates. A small number are unique to humans and unfixed in the human genome. Much scientific interest has centered on the human endogenous retroviruses (HERV)-K113 and HERV-K115 insertions. The evolutionary history of these two endogenous proviruses is complex, and the estimates of both of their insertion times have recently been revised. HERV-K113 inserted into the genome sometime between 0.8 and 1.3 million years ago (Ma), while HERV-K115 was inserted into the genome sometime between 1.1 and 1.9 Ma. Both insertions occurred during a time when Homo erectus is believed to have been the dominant hominin species. Key Concepts: HERV-K113 and HERV-K115 are members of the HML-2 group of endogenous retroviruses and neither insertion is fixed in the modern human genome. Despite their unfixed state, HERV-K113 and HERV-K115 are not recent insertions into the human genome. HERV-K113 inserted into the genome sometime between 0.8 and 1.3 Ma. HERV-K115 inserted into the genome sometime between 1.1 and 1.9 Ma. Despite a possibly wide separation in their insertion times, HERV-K113 and HERV-K115 are highly similar in sequence. Both insertions occurred during a time when Homo erectus is believed to have been the dominant hominin species. Keywords: endogenous retrovirus; HERV-K113; HERV-K115; hominin

We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1,2,3,4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ∼44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages., Instituto Multidisciplinario de Biología Celular

IL-17 is proinflammatory cytokine secreted by a unique CD4+ T (Th17) cell subset and proposed to play a role in host defense. We hypothesized that Th17 cells are lost in HIV-1 infection. HIV-1-infected children with plasma viremia below 50 copies/ml had IL-17 production, whereas those with detectable viremia had minimal secretion. These results imply viral-mediated destruction or impairment of Th17 cells and argue for complete suppression of viremia for reconstitution of Th17 cells.

Although metabolic adaptation is a cornerstone of the hypoxia response, very little is known about hypoxia-induced metabolic changes in neuroblastoma or how the metabolome influences phenotype. Identifying genes that regulate neuroblastoma metabolism and also influence clinical behavior may provide clues for novel therapeutic targets. Mixed linear models were used to identify differentially expressed genes between neuroblastoma cells grown in hypoxia or normoxia in two independent experiments (GEO accessions GSE17714 and GSE55391). Linear models were also used in to identify differentially expressed genes from tumors of two independent cohorts of neuroblastoma patients (GEO accession GSE16254 and EMBL accession E-MTAB-179) who survived compared to those that did not. We utilized a false discovery rate of 0.01 and fold change in the top or bottom 10% of all genes as a significance cutoff. qPCR was used to validate expression differences in multiple neuroblastoma cell lines. 157 genes, significantly exceeding chance (p < 1x10-6) on permutation testing, were present in both neuroblastoma cell line data sets, all but five of which showed consistent directionality of expression change from normoxia to hypoxia, including 44 involved in metabolism. These genes were enriched for hypoxia and metabolic pathways: HIF-1α transcription factor network (p = 1.3x10-11), glycolysis (p = 1.9x10-8) and fructose metabolism (p = 1.0x10-3). 826 genes, significantly exceeding chance (p < 1x10-6) were differentially expressed in both patient cohorts of 478 and 88 patients. These genes were enriched for cell cycle pathways (p = 4.5x10-7). Of these genes, nine of them were also differentially expressed in hypoxia compared to normoxia with consistent directionality, again more than expected by chance (p < 1x10-6). High expression in eight of the nine genes was also significantly associated with poor outcome in a Kaplan-Meier analysis of both of the patient cohorts evaluated. Three of these genes are part of the glycolytic pathway and three more are directly involved in cellular metabolism. In the SK-N-BE2 cell line, all eight of our identified genes are up-regulated in hypoxia (p < 0.05). Analysis of the LAN-5, La1-55n, SK-N-DZ cell lines and show similar results. MTT assays of proliferation show the expected decreased proliferation for all of these cell lines in 48 hours of hypoxia compared to normoxia (p < 0.05). Analysis of cell cycle by flow cytometry in SK-N-BE2 cells shows an increase of cells in G0/G1 in normoxia compared to hypoxia (58.3% vs. 71.5% p = 0.04) and decrease of cells in S phase (24.5% vs. 13.6%, p = 0.001). We have identified eight genes with increased expression in hypoxia and are associated with poor survival in patients. Efforts to use shRNA to alter cellular phenotype are ongoing. Citation Format: Mark A. Aplebaum, Aashish Jha, Alexandre Chlenski, Christopher Mariani, Clara Kao, Mildred Nelson, Kyle Hernandez, Helen Salwen, Marija Dobratic, Kevin White, Barbara Stranger, Susan L. Cohn. Evaluation of hypoxia adaptation in neuroblastoma identifies reproducible transcriptional and phenotypic responses. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A01.

Natural killer (NK) cells are innate lymphocytes that play an important role against viral infections and cancer. This effect is achieved through a complex mosaic of inhibitory and activating receptors expressed by NK cells that ultimately determine the magnitude of the NK-cell response. The T-cell immunoglobulin– and mucin domain–containing (Tim)–3 receptor was initially identified as a T-helper 1–specific type I membrane protein involved in regulating T-cell responses. Human NK cells transcribe the highest amounts of Tim-3 among lymphocytes. Tim-3 protein is expressed on essentially all mature CD56dimCD16+ NK cells and is expressed heterogeneously in the immature CD56brightCD16– NK-cell subset in blood from healthy adults and in cord blood. Tim-3 expression was induced on CD56brightCD16− NK cells after stimulation with IL-15 or IL-12 and IL-18 in vitro, suggesting that Tim-3 is a maturation marker on NK cells. Whereas Tim-3 has been used to identify dysfunctional T cells, NK cells expressing high amounts of Tim-3 are fully responsive with respect to cytokine production and cytotoxicity. However, when Tim-3 was cross-linked with antibodies it suppressed NK cell–mediated cytotoxicity. These findings suggest that NK-cell responses may be negatively regulated when NK cells encounter target cells expressing cognate ligands of Tim-3.

Background: Antibodies are important in the control of blood stage Plasmodium falciparum infection. It is unclear which antibody responses are responsible for, or even associated with protection, partly due to confounding by heterogeneous exposure. Assessment of response to partially effective antimalarial therapy, which requires the host to assist in clearing parasites, offers an opportunity to measure protection independent of exposure. Methods: A cohort of children aged 1–10 years in Kampala, Uganda were treated with amodiaquine+sulfadoxinepyrimethamine for uncomplicated malaria. Serum samples from the time of malaria diagnosis and 14 days later were analyzed for total IgG to 8 P. falciparum antigens using a quantitative indirect ELISA. Associations between antibody levels and risk of treatment failure were estimated using Cox proportional hazard regression. Results: Higher levels of antibodies to apical membrane antigen 1 (AMA-1), but to none of the other 7 antigens were significantly associated with protection against treatment failure (HR 0.57 per 10-fold increase in antibody level, CI 0.41– 0.79, p=0.001). Protection increased consistently across the entire range of antibody levels. Conclusions: Measurement of antibody levels to AMA-1 at the time of malaria may offer a quantitative biomarker of blood stage immunity to P. falciparum, a tool which is currently lacking.

HERV-K113 and HERV-K115 have been considered to be among the youngest HERVs because they are the only known full-length proviruses that are insertionally polymorphic and maintain the open reading frames of their coding genes. However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older. A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking. Therefore, we sought to determine how recently HERVs were exogenous and infectious by examining sequence variation in the long terminal repeat (LTR) regions of all full-length HERV-K loci. We used the traditional method of inter-LTR comparison to analyze all full length HERV-Ks and determined that two insertions, HERV-K106 and HERV-K116 have no differences between their 5' and 3' LTR sequences, suggesting that these insertions were endogenized in the recent evolutionary past. Among these insertions with no sequence differences between their LTR regions, HERV-K106 had the most intact viral sequence structure. Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

Little is known about the manipulation of IL-17 producing CD4+ T cells (TH17) on a per-cell basis in humans in vivo. Previous studies on the effects of IL-2 on IL-17 secretion in non-HIV models have shown divergent results. We hypothesized that IL-2 would mediate changes in IL-17 levels among recently HIV-1-infected adults receiving anti-retroviral therapy. We measured cytokine T cell responses to CD3/CD28, HIV-1 Gag, and CMV pp65 stimulation, and changes in multiple CD4+ T cell subsets. Those who received IL-2 showed a robust expansion of naive and total CD4+ T cell counts and T-reg counts. However, after IL-2 treatment, the frequency of TH17 cells declined, while counts of TH17 cells did not change due to an expansion of the CD4+ naïve T cell population (CD27+CD45RA+). Counts of HIV-1 Gag-specific T cells declined modestly, but CMV pp65 and CD3/CD28 stimulated populations did not change. Hence, in contrast with recent studies, our results suggest IL-2 is not a potent in vivo regulator of TH17 cell populations in HIV-1 disease. However, IL-2-mediated T-reg expansions may selectively reduce responses to certain antigen-specific populations, such as HIV-1 Gag. Electronic supplementary material The online version of this article (doi:10.1007/s10875-010-9432-3) contains supplementary material, which is available to authorized users.

The complexity of immunoregulation has focused attention on the CD4+ T “suppressor” regulatory cell (Treg), which helps maintain balance between immunity and tolerance. An immunoregulatory T cell population that upon activation amplifies cellular immune responses was described in murine models more than thirty years ago. However, no study has yet identified a naturally occurring T “inducer” cell type. Here, we report that the ectoenzyme CD39/NTPDase1 (ecto-nucleoside triphosphate diphosphohydrolase 1) helps to delineate a novel population of human “inducer” CD4+ T cells (TInd) that significantly increases the proliferation and cytokine production of responder T cells in a dose-dependent manner. Furthermore, this unique TInd cell subset produces a distinct repertoire of cytokines in comparison to the other CD4+ T cell subsets. We propose that this novel CD4+ T cell population counterbalances the suppressive activity of suppressor Treg cells in peripheral blood and serves as a calibrator of immunoregulation.

Summary Human T lymphotropic virus type 1 (HTLV-1) infects 10–20 million people worldwide. The majority of infected individuals are asymptomatic; however, approximately 3% develop the debilitating neurological disease HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). There is also currently no cure, vaccine or effective therapy for HTLV-1 infection, and the mechanisms for progression to HAM/TSP remain unclear. NK T cells are an immunoregulatory T cell subset whose frequencies and effector functions are associated critically with immunity against infectious diseases. We hypothesized that NK T cells are associated with HAM/TSP progression. We measured NK T cell frequencies and absolute numbers in individuals with HAM/TSP infection from two cohorts on two continents: São Paulo, Brazil and San Francisco, CA, USA, and found significantly lower levels when compared with healthy subjects and/or asymptomatic carriers. Also, the circulating NK T cell compartment in HAM/TSP subjects is comprised of significantly more CD4+ and fewer CD8+ cells than healthy controls. These findings suggest that lower numbers of circulating NK T cells and enrichment of the CD4+ NK T subset are associated with HTLV-1 disease progression.

The human genome, human endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full-length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population; to date, there has been no report on their prevalence in the United States population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1+ subjects from the United States, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in African Americans compared with Caucasians (K113 9% and K115 6%) within the United States. We also report the presence of three single nucleotide polymorphism sites in the K113 5' long terminal repeats (LTRs) and four in the K115 5' LTR that together constituted four haplotypes for K113 and five haplotypes for K115. HERV insertion times can be estimated from the sequence differences between the 5' and 3' LTR of each insertion, but this dating method cannot be used with HERV-K115. We developed a method to estimate insertion times by applying coalescent inference to 5' LTR sequences within our study population and validated this approach using an independent estimate derived from the genetic distance between K113 5' and 3' LTR sequences. Using our method, we estimated the insertion dates of K113 and K115 to be a minimum of 800,000 and 1.1 million years ago, respectively. Both these insertion dates predate the emergence of anatomically modern Homo sapiens.

Recent studies have indicated that regulatory T cells contribute to the human immunodeficiency virus type 1 (HIV-1)-related immune pathogenesis. However, it is not clear whether T cells with suppressive properties reside within the HIV-1-specific T-cell population. Here, peripheral blood mononuclear cells from HIV-1-infected individuals were stimulated with a 15-mer Gag peptide pool, and HIV-1-specific T cells were enriched by virtue of their secretion of interleukin (IL)-10 or interferon (IFN)-γ using immunomagnetic cell-sorting. Neither the IL-10-secreting cells nor the IFN-γ-secreting cells expressed the regulatory T-cell marker forkhead box P3 (FOXP3), yet the IL-10-secreting cells potently suppressed anti-CD3/CD28-induced CD4+ as well as CD8+ T-cell proliferative responses. As shown by intracellular cytokine staining, IL-10- and IFN-γ-producing T cells represent distinct subsets of the HIV-1-specific T cells. Our data collectively suggest that functionally defined HIV-1-specific T-cell subsets harbor potent immunoregulatory properties that may contribute to HIV-1-associated T-cell dysfunction.

The T cell immunoglobulin mucin 3 (Tim-3) receptor is highly expressed on HIV-1-specific T cells, rendering them partially “exhausted” and unable to contribute to the effective immune mediated control of viral replication. To elucidate novel mechanisms contributing to the HTLV-1 neurological complex and its classic neurological presentation called HAM/TSP (HTLV-1 associated myelopathy/tropical spastic paraparesis), we investigated the expression of the Tim-3 receptor on CD8+ T cells from a cohort of HTLV-1 seropositive asymptomatic and symptomatic patients. Patients diagnosed with HAM/TSP down-regulated Tim-3 expression on both CD8+ and CD4+ T cells compared to asymptomatic patients and HTLV-1 seronegative controls. HTLV-1 Tax-specific, HLA-A*02 restricted CD8+ T cells among HAM/TSP individuals expressed markedly lower levels of Tim-3. We observed Tax expressing cells in both Tim-3+ and Tim-3− fractions. Taken together, these data indicate that there is a systematic downregulation of Tim-3 levels on T cells in HTLV-1 infection, sustaining a profoundly highly active population of potentially pathogenic T cells that may allow for the development of HTLV-1 complications., Author Summary The retrovirus, Human T lymphotropic virus type 1 (HTLV-1) infects 10–20 million people worldwide. The majority of infected individuals are asymptomatic; however, approximately 3% develop the debilitating neurological disease, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). There is also currently no cure, vaccine or effective therapy for HTLV-1 infection. The precise role of CD8+ killer T cells in the control or contribution of HTLV-1 disease progression remains unclear. The T-cell immunoglobulin mucin domain-containing (Tim) proteins are type 1 transmembrane proteins. Three human Tim proteins (Tim-1, -3, and -4) exist and display markedly diverse expression patterns and functions. Tim-3 is upregulated on CD8+ T cells during chronic viral infections leading to a population of poorly functioning T cells. We investigated the expression of Tim-3 on T cells from patients with asymptomatic and symptomatic HTLV-1 infection and compared this with HTLV-1 uninfected donors. Patients diagnosed with HAM/TSP down-regulated Tim-3 expression on T cells when compared to asymptomatic patients and uninfected controls. Our study provides evidence of a novel mechanism for the persistent inflammation observed in HTLV-1 infected patients with neurological deficits and significantly advances our understanding of how the Tim-3 pathway functions.

SummaryGene expression has to withstand stochastic, environmental, and genomic perturbations. For example, in the latter case, 0.5%–1% of the human genome is typically variable between any two unrelated individuals. Such diversity might create problematic variability in the activity of gene regulatory networks and, ultimately, in cell behaviors. Using multigenerational selection experiments, we find that for the Drosophila proneural network, the effect of genomic diversity is dampened by miR-9a-mediated regulation of senseless expression. Reducing miR-9a regulation of the Senseless transcription factor frees the genomic landscape to exert greater phenotypic influence. Whole-genome sequencing identified genomic loci that potentially exert such effects. A larger set of sequence variants, including variants within proneural network genes, exhibits these characteristics when miR-9a concentration is reduced. These findings reveal that microRNA-target interactions may be a key mechanism by which the impact of genomic diversity on cell behavior is dampened.