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1.
Cell ; 159(4): 789-99, 2014 Nov 06.
Article in English | MEDLINE | ID: mdl-25417156

ABSTRACT

Host genetics and the gut microbiome can both influence metabolic phenotypes. However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Here, we compared microbiotas across >1,000 fecal samples obtained from the TwinsUK population, including 416 twin pairs. We identified many microbial taxa whose abundances were influenced by host genetics. The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea. Furthermore, Christensenellaceae and its partners were enriched in individuals with low body mass index (BMI). An obese-associated microbiome was amended with Christensenella minuta, a cultured member of the Christensenellaceae, and transplanted to germ-free mice. C. minuta amendment reduced weight gain and altered the microbiome of recipient mice. Our findings indicate that host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism.


Subject(s)
Bacteria/classification , Bacteria/isolation & purification , Feces/microbiology , Microbiota , Animals , Bacteria/metabolism , Body Mass Index , Female , Gastrointestinal Tract/microbiology , Germ-Free Life , Humans , Male , Mice , Obesity/microbiology , Twins, Dizygotic , Twins, Monozygotic
2.
Cell ; 155(1): 21-6, 2013 Sep 26.
Article in English | MEDLINE | ID: mdl-24074858

ABSTRACT

Technologies for genome-wide sequence interrogation have dramatically improved our ability to identify loci associated with complex human disease. However, a chasm remains between correlations and causality that stems, in part, from a limiting theoretical framework derived from Mendelian genetics and an incomplete understanding of disease physiology. Here we propose a set of criteria, akin to Koch's postulates for infectious disease, for assigning causality between genetic variants and human disease phenotypes.


Subject(s)
Disease/genetics , Genomics/methods , Phenotype , Amyotrophic Lateral Sclerosis/genetics , Amyotrophic Lateral Sclerosis/physiopathology , Animals , Causality , Genetic Variation , Humans , Multifactorial Inheritance
3.
Genome Res ; 34(5): 711-724, 2024 06 25.
Article in English | MEDLINE | ID: mdl-38749655

ABSTRACT

The piRNA pathway is a highly conserved mechanism to repress transposable element (TE) activity in the animal germline via a specialized class of small RNAs called piwi-interacting RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). Although the molecular processes by which piCs function are relatively well understood in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster with high-quality long-read genome assemblies. We perform annotations of ovary piCs and genome-wide TE content in each strain. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs. Most TEs inferred to be recently active show an enrichment of insertions into old and large piCs, consistent with the previously proposed "trap" model of piC evolution. In contrast, a small subset of active LTR families is enriched for the formation of new piCs, suggesting that these TEs have higher proclivity to form piCs. Thus, our findings uncover processes leading to the origin of piCs. We propose that piC evolution begins with the emergence of piRNAs from individual insertions of a few select TE families prone to seed new piCs that subsequently expand by accretion of insertions from most other TE families during evolution to form larger "trap" clusters. Our study shows that TEs themselves are the major force driving the rapid evolution of piCs.


Subject(s)
DNA Transposable Elements , Drosophila melanogaster , Evolution, Molecular , Ovary , RNA, Small Interfering , Animals , Drosophila melanogaster/genetics , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Female , Ovary/metabolism , Multigene Family , Piwi-Interacting RNA
4.
PLoS Biol ; 21(9): e3002311, 2023 09.
Article in English | MEDLINE | ID: mdl-37695771

ABSTRACT

Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.


Subject(s)
Cardiovascular Diseases , Diabetes Mellitus, Type 2 , Humans , Disease Susceptibility , Diabetes Mellitus, Type 2/genetics , Biological Evolution , Genomics
5.
Proc Natl Acad Sci U S A ; 120(5): e2214883120, 2023 01 31.
Article in English | MEDLINE | ID: mdl-36706221

ABSTRACT

Sex peptide (SP), a seminal fluid protein of Drosophila melanogaster males, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses including increased egg laying, activity, and food intake and a decreased remating rate. While it is known that SP achieves this, at least in part, by altering neuronal signaling in females, the genetic architecture and temporal dynamics of the female's response to SP remain elusive. We used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 h after mating to learn about the genetic architecture, at the gene and exon levels, of the female's response to SP. We find that SP is not essential to trigger early aspects of a virgin-to-mated transcriptional switch, which includes changes in a metabolic gene regulatory network. However, SP is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that SP alters rhythmic gene expression in females and suggests that SP's disruption of the female's circadian rhythm might be key to its widespread effects.


Subject(s)
Circadian Clocks , Drosophila Proteins , Animals , Male , Female , Drosophila melanogaster/metabolism , Drosophila Proteins/metabolism , Spermatozoa/metabolism , Circadian Clocks/genetics , Time Factors , Peptides/metabolism , Gene Expression Profiling , Sexual Behavior, Animal/physiology
6.
N Engl J Med ; 387(15): 1351-1360, 2022 10 13.
Article in English | MEDLINE | ID: mdl-36027563

ABSTRACT

BACKGROUND: Whether revascularization by percutaneous coronary intervention (PCI) can improve event-free survival and left ventricular function in patients with severe ischemic left ventricular systolic dysfunction, as compared with optimal medical therapy (i.e., individually adjusted pharmacologic and device therapy for heart failure) alone, is unknown. METHODS: We randomly assigned patients with a left ventricular ejection fraction of 35% or less, extensive coronary artery disease amenable to PCI, and demonstrable myocardial viability to a strategy of either PCI plus optimal medical therapy (PCI group) or optimal medical therapy alone (optimal-medical-therapy group). The primary composite outcome was death from any cause or hospitalization for heart failure. Major secondary outcomes were left ventricular ejection fraction at 6 and 12 months and quality-of-life scores. RESULTS: A total of 700 patients underwent randomization - 347 were assigned to the PCI group and 353 to the optimal-medical-therapy group. Over a median of 41 months, a primary-outcome event occurred in 129 patients (37.2%) in the PCI group and in 134 patients (38.0%) in the optimal-medical-therapy group (hazard ratio, 0.99; 95% confidence interval [CI], 0.78 to 1.27; P = 0.96). The left ventricular ejection fraction was similar in the two groups at 6 months (mean difference, -1.6 percentage points; 95% CI, -3.7 to 0.5) and at 12 months (mean difference, 0.9 percentage points; 95% CI, -1.7 to 3.4). Quality-of-life scores at 6 and 12 months appeared to favor the PCI group, but the difference had diminished at 24 months. CONCLUSIONS: Among patients with severe ischemic left ventricular systolic dysfunction who received optimal medical therapy, revascularization by PCI did not result in a lower incidence of death from any cause or hospitalization for heart failure. (Funded by the National Institute for Health and Care Research Health Technology Assessment Program; REVIVED-BCIS2 ClinicalTrials.gov number, NCT01920048.).


Subject(s)
Coronary Artery Disease , Heart Failure , Percutaneous Coronary Intervention , Ventricular Dysfunction, Left , Humans , Heart Failure/etiology , Heart Failure/therapy , Stroke Volume , Treatment Outcome , Ventricular Dysfunction, Left/drug therapy , Ventricular Dysfunction, Left/etiology , Ventricular Dysfunction, Left/mortality , Ventricular Dysfunction, Left/surgery , Ventricular Function, Left , Coronary Artery Disease/complications , Coronary Artery Disease/drug therapy , Coronary Artery Disease/mortality , Coronary Artery Disease/surgery , Cardiovascular Agents/therapeutic use , Myocardial Ischemia/drug therapy , Myocardial Ischemia/etiology , Myocardial Ischemia/mortality , Myocardial Ischemia/surgery
7.
Annu Rev Genet ; 51: 413-433, 2017 11 27.
Article in English | MEDLINE | ID: mdl-28934590

ABSTRACT

The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome. Studies of the heritability of gut microbiotas reveal a subset of microbes whose abundances are partly genetically determined by the host. However, the use of genome-wide association studies (GWASs) to identify human genetic variants associated with microbiome phenotypes has proven challenging. Studies to date are small by GWAS standards, and cross-study comparisons are hampered by differences in analytical approaches. Nevertheless, associations between microbes or microbial genes and human genes have emerged that are consistent between human populations. Most notably, higher levels of beneficial gut bacteria called Bifidobacteria are associated with the human lactase nonpersister genotype, which typically confers lactose intolerance, in several different human populations. It is time for the microbiome to be incorporated into studies that quantify interactions among genotype, environment, and the microbiome in order to predict human disease susceptibility.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Gastrointestinal Microbiome/physiology , Genome, Human , Lactose Intolerance/genetics , Obesity/genetics , Schizophrenia/genetics , Amyotrophic Lateral Sclerosis/metabolism , Amyotrophic Lateral Sclerosis/microbiology , Amyotrophic Lateral Sclerosis/pathology , Bifidobacterium/growth & development , Bifidobacterium/metabolism , Diet/methods , Gastrointestinal Tract/microbiology , Genetic Variation , Genome-Wide Association Study , Genotype , Human Genetics , Humans , Lactose Intolerance/metabolism , Lactose Intolerance/microbiology , Lactose Intolerance/pathology , Obesity/metabolism , Obesity/microbiology , Obesity/pathology , Phenotype , Quantitative Trait, Heritable , Schizophrenia/metabolism , Schizophrenia/microbiology , Schizophrenia/pathology
8.
PLoS Biol ; 20(3): e3001593, 2022 03.
Article in English | MEDLINE | ID: mdl-35324889

ABSTRACT

Actomyosin contractility is a major engine of preimplantation morphogenesis, which starts at the 8-cell stage during mouse embryonic development. Contractility becomes first visible with the appearance of periodic cortical waves of contraction (PeCoWaCo), which travel around blastomeres in an oscillatory fashion. How contractility of the mouse embryo becomes active remains unknown. We have taken advantage of PeCoWaCo to study the awakening of contractility during preimplantation development. We find that PeCoWaCo become detectable in most embryos only after the second cleavage and gradually increase their oscillation frequency with each successive cleavage. To test the influence of cell size reduction during cleavage divisions, we use cell fusion and fragmentation to manipulate cell size across a 20- to 60-µm range. We find that the stepwise reduction in cell size caused by cleavage divisions does not explain the presence of PeCoWaCo or their accelerating rhythm. Instead, we discover that blastomeres gradually decrease their surface tensions until the 8-cell stage and that artificially softening cells enhances PeCoWaCo prematurely. We further identify the programmed down-regulation of the formin Fmnl3 as a required event to soften the cortex and expose PeCoWaCo. Therefore, during cleavage stages, cortical softening, mediated by Fmnl3 down-regulation, awakens zygotic contractility before preimplantation morphogenesis.


Subject(s)
Blastomeres , Embryonic Development , Animals , Blastomeres/metabolism , Embryo, Mammalian , Female , Mice , Morphogenesis , Pregnancy , Zygote
9.
Proc Natl Acad Sci U S A ; 119(35): e2201871119, 2022 08 30.
Article in English | MEDLINE | ID: mdl-35994649

ABSTRACT

The stability of widespread methane hydrates in shallow subsurface sediments of the marine continental margins is sensitive to temperature increases experienced by upper intermediate waters. Destabilization of methane hydrates and ensuing release of methane would produce climatic feedbacks amplifying and accelerating global warming. Hence, improved assessment of ongoing intermediate water warming is crucially important, especially that resulting from a weakening of Atlantic meridional overturning circulation (AMOC). Our study provides an independent paleoclimatic perspective by reconstructing the thermal structure and imprint of methane oxidation throughout a water column of 1,300 m. We studied a sediment sequence from the eastern equatorial Atlantic (Gulf of Guinea), a region containing abundant shallow subsurface methane hydrates. We focused on the early part of the penultimate interglacial and present a hitherto undocumented and remarkably large intermediate water warming of 6.8 °C in response to a brief episode of meltwater-induced, modest AMOC weakening centered at 126,000 to 125,000 y ago. The warming of intermediate waters to 14 °C significantly exceeds the stability field of methane hydrates. In conjunction with this warming, our study reveals an anomalously low δ13C spike throughout the entire water column, recorded as primary signatures in single and pooled shells of multitaxa foraminifers. This extremely negative δ13C excursion was almost certainly the result of massive destabilization of methane hydrates. This study documents and connects a sequence of climatic events and climatic feedback processes associated with and triggered by the penultimate climate warming that can serve as a paleoanalog for modern ongoing warming.


Subject(s)
Global Warming , Ice Cover , Methane , Ice Cover/chemistry , Methane/chemistry , Oxidation-Reduction , Water/chemistry
10.
Proc Natl Acad Sci U S A ; 119(44): e2210258119, 2022 11.
Article in English | MEDLINE | ID: mdl-36279430

ABSTRACT

The paleomagnetic record is an archive of Earth's geophysical history, informing reconstructions of ancient plate motions and probing the core via the geodynamo. We report a robust 3.25-billion-year-old (Ga) paleomagnetic pole from the East Pilbara Craton, Western Australia. Together with previous results from the East Pilbara between 3.34 and 3.18 Ga, this pole enables the oldest reconstruction of time-resolved lithospheric motions, documenting 160 My of both latitudinal drift and rotation at rates of at least 0.55°/My. Motions of this style, rate, and duration are difficult to reconcile with true polar wander or stagnant-lid geodynamics, arguing strongly for mobile-lid geodynamics by 3.25 Ga. Additionally, this pole includes the oldest documented geomagnetic reversal, reflecting a stably dipolar, core-generated Archean dynamo.


Subject(s)
Geological Phenomena , Western Australia
11.
Eur Heart J ; 45(16): 1410-1426, 2024 Apr 21.
Article in English | MEDLINE | ID: mdl-38446126

ABSTRACT

BACKGROUND AND AIMS: What is the relationship between blood tests for iron deficiency, including anaemia, and the response to intravenous iron in patients with heart failure? METHODS: In the IRONMAN trial, 1137 patients with heart failure, ejection fraction ≤ 45%, and either serum ferritin < 100 µg/L or transferrin saturation (TSAT) < 20% were randomized to intravenous ferric derisomaltose (FDI) or usual care. Relationships were investigated between baseline anaemia severity, ferritin and TSAT, to changes in haemoglobin from baseline to 4 months, Minnesota Living with Heart Failure (MLwHF) score and 6-minute walk distance achieved at 4 months, and clinical events, including heart failure hospitalization (recurrent) or cardiovascular death. RESULTS: The rise in haemoglobin after administering FDI, adjusted for usual care, was greater for lower baseline TSAT (Pinteraction < .0001) and ferritin (Pinteraction = .028) and more severe anaemia (Pinteraction = .014). MLwHF scores at 4 months were somewhat lower (better) with FDI for more anaemic patients (overall Pinteraction = .14; physical Pinteraction = .085; emotional Pinteraction = .043) but were not related to baseline TSAT or ferritin. Blood tests did not predict difference in achieved walking distance for those randomized to FDI compared to control. The absence of anaemia or a TSAT ≥ 20% was associated with lower event rates and little evidence of benefit from FDI. More severe anaemia or TSAT < 20%, especially when ferritin was ≥100 µg/L, was associated with higher event rates and greater absolute reductions in events with FDI, albeit not statistically significant. CONCLUSIONS: This hypothesis-generating analysis suggests that anaemia or TSAT < 20% with ferritin > 100 µg/L might identify patients with heart failure who obtain greater benefit from intravenous iron. This interpretation requires confirmation.


Subject(s)
Anemia, Iron-Deficiency , Anemia , Heart Failure , Iron Deficiencies , Humans , Iron/therapeutic use , Anemia, Iron-Deficiency/drug therapy , Ferritins/therapeutic use , Ferric Compounds/therapeutic use , Hemoglobins , Heart Failure/drug therapy
12.
Pharmacol Rev ; 74(1): 48-118, 2022 01.
Article in English | MEDLINE | ID: mdl-34987088

ABSTRACT

The purpose of this review is to summarize essential pharmacological, pharmaceutical, and clinical aspects in the field of orally inhaled therapies that may help scientists seeking to develop new products. After general comments on the rationale for inhaled therapies for respiratory disease, the focus is on products approved approximately over the last half a century. The organization of these sections reflects the key pharmacological categories. Products for asthma and chronic obstructive pulmonary disease include ß -2 receptor agonists, muscarinic acetylcholine receptor antagonists, glucocorticosteroids, and cromones as well as their combinations. The antiviral and antibacterial inhaled products to treat respiratory tract infections are then presented. Two "mucoactive" products-dornase α and mannitol, which are both approved for patients with cystic fibrosis-are reviewed. These are followed by sections on inhaled prostacyclins for pulmonary arterial hypertension and the challenging field of aerosol surfactant inhalation delivery, especially for prematurely born infants on ventilation support. The approved products for systemic delivery via the lungs for diseases of the central nervous system and insulin for diabetes are also discussed. New technologies for drug delivery by inhalation are analyzed, with the emphasis on those that would likely yield significant improvements over the technologies in current use or would expand the range of drugs and diseases treatable by this route of administration. SIGNIFICANCE STATEMENT: This review of the key aspects of approved orally inhaled drug products for a variety of respiratory diseases and for systemic administration should be helpful in making judicious decisions about the development of new or improved inhaled drugs. These aspects include the choices of the active ingredients, formulations, delivery systems suitable for the target patient populations, and, to some extent, meaningful safety and efficacy endpoints in clinical trials.


Subject(s)
Pharmaceutical Preparations , Pulmonary Disease, Chronic Obstructive , Administration, Inhalation , Drug Compounding , Drug Delivery Systems , Humans
13.
J Allergy Clin Immunol ; 153(6): 1621-1633, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38597862

ABSTRACT

BACKGROUND: Despite the promise of oral immunotherapy (OIT) to treat food allergies, this procedure is associated with potential risk. There is no current agreement about what elements should be included in the preparatory or consent process. OBJECTIVE: We developed consensus recommendations about the OIT process considerations and patient-specific factors that should be addressed before initiating OIT and developed a consensus OIT consent process and information form. METHODS: We convened a 36-member Preparing Patients for Oral Immunotherapy (PPOINT) panel of allergy experts to develop a consensus OIT patient preparation, informed consent process, and framework form. Consensus for themes and statements was reached using Delphi methodology, and the consent information form was developed. RESULTS: The expert panel reached consensus for 4 themes and 103 statements specific to OIT preparatory procedures, of which 76 statements reached consensus for inclusion specific to the following themes: general considerations for counseling patients about OIT; patient- and family-specific factors that should be addressed before initiating OIT and during OIT; indications for initiating OIT; and potential contraindications and precautions for OIT. The panel reached consensus on 9 OIT consent form themes: benefits, risks, outcomes, alternatives, risk mitigation, difficulties/challenges, discontinuation, office policies, and long-term management. From these themes, 219 statements were proposed, of which 189 reached consensus, and 71 were included on the consent information form. CONCLUSION: We developed consensus recommendations to prepare and counsel patients for safe and effective OIT in clinical practice with evidence-based risk mitigation. Adoption of these recommendations may help standardize clinical care and improve patient outcomes and quality of life.


Subject(s)
Consensus , Delphi Technique , Desensitization, Immunologic , Food Hypersensitivity , Informed Consent , Humans , Desensitization, Immunologic/methods , Administration, Oral , Food Hypersensitivity/therapy , Food Hypersensitivity/immunology
14.
J Infect Dis ; 229(3): 763-774, 2024 Mar 14.
Article in English | MEDLINE | ID: mdl-38035854

ABSTRACT

BACKGROUND: Chronic inflammation persists in some people living with human immunodeficiency virus (HIV) during antiretroviral therapy and is associated with premature aging. The glycoprotein 120 (gp120) subunit of HIV-1 envelope sheds and can be detected in plasma, showing immunomodulatory properties even in the absence of detectable viremia. We evaluated whether plasma soluble gp120 (sgp120) and a family of gp120-specific anti-cluster A antibodies, linked to CD4 depletion in vitro, contribute to chronic inflammation, immune dysfunction, and subclinical cardiovascular disease in participants of the Canadian HIV and Aging Cohort Study with undetectable viremia. METHODS: Cross-sectional assessment of sgp120 and anti-cluster A antibodies was performed in 386 individuals from the cohort. Their association with proinflammatory cytokines and subclinical coronary artery disease was assessed using linear regression models. RESULTS: High levels of sgp120 and anti-cluster A antibodies were inversely correlated with CD4+ T cell count and CD4/CD8 ratio. The presence of sgp120 was associated with increased levels of interleukin 6. In participants with detectable atherosclerotic plaque and detectable sgp120, anti-cluster A antibodies and their combination with sgp120 levels correlated positively with the total volume of atherosclerotic plaques. CONCLUSIONS: This study showed that sgp120 may act as a pan toxin causing immune dysfunction and sustained inflammation in a subset of people living with HIV, contributing to the development of premature comorbid conditions.


Subject(s)
HIV Infections , HIV-1 , Humans , Viremia , Cohort Studies , Cross-Sectional Studies , Canada , HIV Infections/drug therapy , HIV Antibodies , Glycoproteins , HIV Envelope Protein gp120
15.
Mol Biol Evol ; 40(2)2023 02 03.
Article in English | MEDLINE | ID: mdl-36721950

ABSTRACT

Genomic imprinting is a parent-of-origin-specific expression phenomenon that plays fundamental roles in many biological processes. In animals, imprinting is only observed in therian mammals, with ∼200 imprinted genes known in humans and mice. The imprinting pattern in marsupials has been minimally investigated by examining orthologs to known eutherian imprinted genes. To identify marsupial-specific imprinting in an unbiased way, we performed RNA-seq studies on samples of fetal brain and placenta from the reciprocal cross progeny of two laboratory opossum stocks. We inferred allele-specific expression for >3,000 expressed genes and discovered/validated 13 imprinted genes, including three previously known imprinted genes, Igf2r, Peg10, and H19. We estimate that marsupials imprint ∼60 autosomal genes, which is a much smaller set compared with eutherians. Among the nine novel imprinted genes, three noncoding RNAs have no known homologs in eutherian mammals, while the remaining genes have important functions in pluripotency, transcription regulation, nucleolar homeostasis, and neural differentiation. Methylation analyses at promoter CpG islands revealed differentially methylated regions in five of these marsupial-specific imprinted genes, suggesting that differential methylation is a common mechanism in the epigenetic regulation of marsupial imprinting. Clustering and co-regulation were observed at marsupial imprinting loci Pou5f3-Npdc1 and Nkrfl-Ipncr2, but eutherian-type multi-gene imprinting clusters were not detected. Also differing from eutherian mammals, the brain and placenta imprinting profiles are remarkably similar in opossums, presumably due to the shared origin of these organs from the trophectoderm. Our results contribute to a fuller understanding of the origin, evolution, and mechanisms of genomic imprinting in therian mammals.


Subject(s)
Marsupialia , Pregnancy , Humans , Female , Animals , Mice , Marsupialia/genetics , DNA Methylation , Epigenesis, Genetic , Gene Duplication , Genomic Imprinting , Opossums/genetics , Mammals , Eutheria/genetics
16.
Am J Hum Genet ; 108(9): 1752-1764, 2021 09 02.
Article in English | MEDLINE | ID: mdl-34363748

ABSTRACT

An individual's genetics can dramatically influence breast cancer (BC) risk. Although clinical measures for prevention do exist, non-invasive personalized measures for reducing BC risk are limited. Commonly used medications are a promising set of modifiable factors, but no previous study has explored whether a range of widely taken approved drugs modulate BC genetics. In this study, we describe a quantitative framework for exploring the interaction between the genetic susceptibility of BC and medication usage among UK Biobank women. We computed BC polygenic scores (PGSs) that summarize BC genetic risk and find that the PGS explains nearly three-times greater variation in disease risk within corticosteroid users compared to non-users. We map 35 genes significantly interacting with corticosteroid use (FDR < 0.1), highlighting the transcription factor NRF2 as a common regulator of gene-corticosteroid interactions in BC. Finally, we discover a regulatory variant strongly stratifying BC risk according to corticosteroid use. Within risk allele carriers, 18.2% of women taking corticosteroids developed BC, compared to 5.1% of the non-users (with an HR = 3.41 per-allele within corticosteroid users). In comparison, there are no differences in BC risk within the reference allele homozygotes. Overall, this work highlights the clinical relevance of gene-drug interactions in disease risk and provides a roadmap for repurposing biobanks in drug repositioning and precision medicine.


Subject(s)
Adrenal Cortex Hormones/adverse effects , Breast Neoplasms/genetics , Gene-Environment Interaction , Multifactorial Inheritance , NF-E2-Related Factor 2/genetics , Prescription Drugs/adverse effects , Alleles , Biological Specimen Banks , Breast Neoplasms/chemically induced , Breast Neoplasms/diagnosis , Breast Neoplasms/epidemiology , Female , Gene Expression , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Incidence , NF-E2-Related Factor 2/metabolism , Polymorphism, Single Nucleotide , Precision Medicine/methods , Risk Assessment , United Kingdom/epidemiology
17.
Am J Hum Genet ; 108(1): 49-67, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33326753

ABSTRACT

Although thousands of loci have been associated with human phenotypes, the role of gene-environment (GxE) interactions in determining individual risk of human diseases remains unclear. This is partly because of the severe erosion of statistical power resulting from the massive number of statistical tests required to detect such interactions. Here, we focus on improving the power of GxE tests by developing a statistical framework for assessing quantitative trait loci (QTLs) associated with the trait means and/or trait variances. When applying this framework to body mass index (BMI), we find that GxE discovery and replication rates are significantly higher when prioritizing genetic variants associated with the variance of the phenotype (vQTLs) compared to when assessing all genetic variants. Moreover, we find that vQTLs are enriched for associations with other non-BMI phenotypes having strong environmental influences, such as diabetes or ulcerative colitis. We show that GxE effects first identified in quantitative traits such as BMI can be used for GxE discovery in disease phenotypes such as diabetes. A clear conclusion is that strong GxE interactions mediate the genetic contribution to body weight and diabetes risk.


Subject(s)
Biological Variation, Population/genetics , Genome-Wide Association Study/methods , Gene-Environment Interaction , Genotype , Humans , Phenotype , Quantitative Trait Loci/genetics , Quantitative Trait, Heritable
18.
Br J Haematol ; 204(6): 2365-2377, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38577874

ABSTRACT

Allogeneic haematopoietic cell transplantation (allo-HCT) remains an option for tyrosine kinase inhibitor-resistant chronic myeloid leukaemia (CML) in first chronic phase (CP1) and high-risk patients with advanced disease phases. In this European Society for Blood and Marrow Transplantation (EBMT) registry-based study of 1686 CML patients undergoing first allo-HCT between 2012 and 2019, outcomes were evaluated according to donor type, particularly focusing on mismatched related donors (MMRDs). Median age at allo-HCT was 46 years (IQR 36-55). Disease status was CP1 in 43%, second CP (CP2) or later in 27%, accelerated phase in 12% and blast crisis in 18%. Donor type was matched related (MRD) in 39.2%, MMRD in 8.1%, matched unrelated (MUD) in 40.2%, and mismatched unrelated (MMUD) in 12.6%. In 4 years, overall survival (OS) for MRD, MMRD, MUD and MMUD was 61%, 56%, 63% and 59% (p = 0.21); relapse-free survival (RFS) was 48%, 42%, 52% and 46% (p = 0.03); cumulative incidence of relapse (CIR) was 33%, 37%, 27% and 30% (p = 0.07); non-relapse mortality (NRM) was 19%, 21%, 21% and 24% (p = 0.21); and graft-versus-host disease (GvHD)-free/relapse-free survival (GRFS) was 16%, 18%, 22% and 15% (p = 0.05) respectively. On multivariate analysis, MMRD use associated with longer engraftment times and higher risk of graft failure compared to MRD or MUD. There was no statistical evidence that MMRD use associated with different OS, RFS and incidence of GvHD compared to other donor types.


Subject(s)
Hematopoietic Stem Cell Transplantation , Leukemia, Myelogenous, Chronic, BCR-ABL Positive , Humans , Hematopoietic Stem Cell Transplantation/methods , Middle Aged , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality , Adult , Male , Female , Retrospective Studies , Graft vs Host Disease/etiology , Transplantation, Homologous , Registries , Tissue Donors , Unrelated Donors
19.
HIV Med ; 2024 Aug 25.
Article in English | MEDLINE | ID: mdl-39183479

ABSTRACT

OBJECTIVES: Fostemsavir is a novel attachment inhibitor used with other antiretrovirals in heavily treatment-experienced (HTE) adults with multidrug-resistant HIV-1. Real-world immunological and virological responses were assessed in individuals starting fostemsavir in the OPERA cohort. METHODS: Among adults with HIV-1 starting fostemsavir between 2 July 2020 and 1 September 2022, 6-month and 12-month changes in CD4 T-cell count and CD4%, and maintenance/achievement of viral load (VL) <50 copies/mL were described and stratified by baseline VL (suppressed: <50 copies/mL; viraemic: ≥50 copies/mL) and CD4 count (high: ≥350 cells/µL; low: <350 cells/µL). RESULTS: Of 182 individuals starting fostemsavir, 64% were viraemic (34% low CD4, 30% high CD4) and 36% were suppressed (16% low CD4, 20% high CD4). The suppressed/low CD4 group had the largest median increases in CD4 count (6-month: 30 cells/µL [interquartile range {IQR} 9-66], 12-month: 66 cells/µL [IQR 17-125]), and CD4% (6-month: 1.0% [IQR -0.3-2.8], 12-month: 1.9% [IQR 1.3-3.9]). Regardless of baseline VL, those with a high baseline CD4 count experienced a greater variability in immunological response than those with low CD4 counts (12-month standard deviation range 172-231 cells/µL vs. 69-90 cells/µL). VL <50 copies/mL was maintained in most suppressed individuals; nearly half of the viraemic/high CD4 group and a third of the viraemic/low CD4 group achieved a VL <50 copies/mL at either timepoint. CONCLUSIONS: After 6 or 12 months of fostemsavir use, virological response was low in viraemic individuals, although most suppressed individuals did maintain suppression. While immunological response varied across individuals, virologically suppressed HTE individuals with low CD4 counts may benefit from immunological improvements with fostemsavir.

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