RESUMO
Thymic epithelial cell differentiation, growth and function depend on the expression of the transcription factor Foxn1; however, its target genes have never been physically identified. Using static and inducible genetic model systems and chromatin studies, we developed a genome-wide map of direct Foxn1 target genes for postnatal thymic epithelia and defined the Foxn1 binding motif. We determined the function of Foxn1 in these cells and found that, in addition to the transcriptional control of genes involved in the attraction and lineage commitment of T cell precursors, Foxn1 regulates the expression of genes involved in antigen processing and thymocyte selection. Thus, critical events in thymic lympho-stromal cross-talk and T cell selection are indispensably choreographed by Foxn1.
Assuntos
Células Epiteliais/fisiologia , Fatores de Transcrição Forkhead/metabolismo , Células Precursoras de Linfócitos T/fisiologia , Linfócitos T/fisiologia , Timo/fisiologia , Animais , Apresentação de Antígeno/genética , Comunicação Celular , Diferenciação Celular/genética , Linhagem da Célula/genética , Células Cultivadas , Seleção Clonal Mediada por Antígeno/genética , Fatores de Transcrição Forkhead/genética , Regulação da Expressão Gênica , Genoma/genética , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Mutantes , Camundongos TransgênicosRESUMO
The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.
Assuntos
Surtos de Doenças/história , Genoma Bacteriano , Peste/microbiologia , Yersinia pestis/genética , Europa (Continente)/epidemiologia , História Medieval , Humanos , Peste/epidemiologia , Peste/história , Yersinia pestis/patogenicidadeRESUMO
BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.
Assuntos
Mycobacterium leprae , Europa (Continente) , Genoma Bacteriano/genética , Humanos , Hanseníase/genética , Mycobacterium leprae/genética , Dinâmica PopulacionalRESUMO
Cenerimod is a potent, selective sphingosine 1-phosphate receptor 1 (S1P1) modulator currently investigated in a Phase IIb study in patients with systemic lupus erythematosus (SLE) (NCT03742037). S1P1 receptor modulators sequester circulating lymphocytes within lymph nodes, thereby reducing pathogenic autoimmune cells (including T and B lymphocytes) in the bloodstream and inflamed tissues, making them an effective therapeutic concept for autoimmune disorders. Although the effect of S1P receptor modulators in reducing circulating lymphocytes is well documented, the precise molecular role of the S1P1 receptor on these cell types is not fully understood. In this study, the mode of action of cenerimod on human primary lymphocytes in different activation states was investigated focusing on their chemotactic behavior towards S1P in real-time, concomitant to S1P1 receptor expression and internalization dynamics. Here, we show that cenerimod effectively prevents T and B cell migration in a concentration-dependent manner. Interestingly, while T cell activation led to strong S1P1 re-expression and enhanced migration; in B cells, an enhanced migration capacity and S1P1 receptor surface expression was observed in an unstimulated state. Importantly, concomitant treatment with glucocorticoids (GCs), a frequently used treatment for autoimmune disorders, had no impact on the inhibitory activity of cenerimod on lymphocytes.
Assuntos
Linfócitos B/fisiologia , Movimento Celular , Lisofosfolipídeos/metabolismo , Oxidiazóis/farmacologia , Propilenoglicóis/farmacologia , Receptores de Esfingosina-1-Fosfato/antagonistas & inibidores , Esfingosina/análogos & derivados , Linfócitos T/fisiologia , Linfócitos B/efeitos dos fármacos , Humanos , Transdução de Sinais , Esfingosina/metabolismo , Receptores de Esfingosina-1-Fosfato/metabolismo , Linfócitos T/efeitos dos fármacosRESUMO
OBJECTIVES: Warfare is assumed to be one of the defining cultural characteristics of steppe nomads in Eastern Eurasia. For the first-centuries CE, a period of political turmoil in Northern China and Southern Siberia, relatively few data are, however, available about the degree and variability of violence in these communities. Here, we provide new data on violence among steppe nomads during the first-centuries CE by analyzing the type, anatomical distribution, and demographic distribution of perimortem trauma at Tunnug1 (Tuva, Southern Siberia-second to fourth c. CE). MATERIALS AND METHODS: Perimortem traumas were assessed on 87 individuals representing both sexes and different age classes. The timing of the lesions was assessed based on morphological criteria, including the absence and presence of bone reactive processes and the relative plasticity of the bone at the moment of impact. The distribution by age, sex, and anatomical location of trauma was analyzed by means of logistic models, Fisher's exact tests, and 3D visualizations. RESULTS: A total of 130 perimortem traumas, including chop marks, slice marks, penetrating lesions, and blunt traumas were identified on 22 individuals. Chop marks were mostly at the level of the skull and vertebrae and were likely caused by bladed weapons. Slice marks were found on the cervical vertebrae and cranium and may be the result of throat slitting and scalping by means of smaller bladed implements. Traumas were more frequent in males, and their presence is not correlated with age. DISCUSSION: This study adds new data to the few available regarding violence among steppe nomadic cultures and provides new insights about the effects of political instability on the life of the people inhabiting Eastern Eurasia during the early centuries CE.
Assuntos
Povo Asiático/história , Violência/história , Ferimentos Penetrantes/história , Adolescente , Adulto , Antropologia Física , Osso e Ossos/lesões , Osso e Ossos/patologia , Sepultamento/história , Criança , Pré-Escolar , Decapitação/história , Feminino , História Antiga , Humanos , Lactente , Recém-Nascido , Masculino , Sibéria , Migrantes , Guerra/história , Adulto JovemRESUMO
One of the most important advantages of mass spectrometry is the ability to quantify proteins and their modifications in parallel to obtain a holistic picture of the protein of interest. Here, we present a hybrid immunoaffinity targeted mass spectrometry (MS) method that combines efficient pan-antibody enrichment of a specific protein from plasma with the selectivity of high-resolution targeted MS analysis to quantitate specific proteoforms of interest. We used this approach to quantify plasma levels of the chemokine CXCL10 that has been associated with many immunological disorders such as systemic lupus erythematosus and primary Sjögren's Syndrome (pSS). The hybrid approach enabled sensitive, specific, and simultaneous quantification of total, full-length (active) CXCL101-77 and DPP4-truncated (inactive) CXCL103-77 in human plasma down to the low pg/mL level, reaching ELISA sensitivities. Samples from 30 control subjects and 34 pSS patients (n = 64) were analyzed. The ratio of CXCL101-77 to truncated CXCL103-77 was significantly increased in patients with pSS and provided the highest correlation with pSS disease activity. Therefore, this CXCL10 proteoform ratio represents an interesting exploratory disease activity biomarker to further investigate. As this strategy can be readily adapted to other plasma proteins and proteoforms of interest, we are convinced that it will lead to a more detailed understanding of proteoforms in physiology and pathology yielding more relevant biomarkers and drug targets.
Assuntos
Lúpus Eritematoso Sistêmico , Síndrome de Sjogren , Biomarcadores , Quimiocina CXCL10/genética , Ensaio de Imunoadsorção Enzimática , Humanos , Espectrometria de Massas , Síndrome de Sjogren/diagnóstico , Síndrome de Sjogren/genéticaRESUMO
The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.
Assuntos
DNA Antigo/análise , Peste/microbiologia , Yersinia pestis/genética , Sequência de Bases , DNA Bacteriano/genética , Variação Genética , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Pandemias , Virulência/genéticaRESUMO
Regulatory T (Treg) cells are pivotal for the maintenance of peripheral tolerance by controlling self-reactive, chronic, and homeostatic T-cell responses. Here, we report that the increase in Treg-cell suppressive function observed in lymphopenic mice correlates with the degree of lymphopenia and is caused by a higher frequency of a novel subpopulation of CD103(pos) ICOS(pos) Treg cells. Though present in the thymus, CD103(pos) ICOS(pos) Treg cells are not generated there but recirculate from the periphery to that site. The acquisition and maintenance of this distinctive phenotype requires the LN microenvironment and the in situ availability of antigen. Contrary to conventional effector and other Treg cells, the cellularity of CD103(pos) ICOS(pos) Treg cells is not affected by the absence of IL-7 and thymic stroma lymphopoetin. Given their increased frequency in lymphopenia, the absolute number of CD103(pos) ICOS(pos) Treg cells remains unchanged in the periphery irrespective of a paucity of total Treg cells. We furthermore demonstrate, with cell transfers in mice, that the CD103(pos) ICOS(pos) phenotype represents a LN-specific differentiation stage arrived at by several other Treg-cell subsets. Thus, tissue-specific cues determine the overall potency of the peripheral Treg-cell pool by shaping its subset composition.
Assuntos
Antígenos CD/metabolismo , Proteína Coestimuladora de Linfócitos T Induzíveis/metabolismo , Cadeias alfa de Integrinas/metabolismo , Linfonodos/imunologia , Linfopenia/sangue , Linfopenia/imunologia , Linfócitos T Reguladores/imunologia , Linfócitos T Reguladores/metabolismo , Animais , Diferenciação Celular/imunologia , Microambiente Celular , Análise por Conglomerados , Citocinas/metabolismo , Perfilação da Expressão Gênica , Homeostase , Interleucina-7/metabolismo , Contagem de Linfócitos , Linfopenia/metabolismo , Camundongos , Transdução de Sinais , Subpopulações de Linfócitos T/citologia , Subpopulações de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo , Linfócitos T Reguladores/citologia , Linfopoietina do Estroma do TimoRESUMO
OBJECTIVES: Straight next to a segment of the outer ditch of the Late Neolithic Michelsberg Culture earthwork of Bruchsal-Aue in SW-Germany (ca. 4250-3650 calBC), a multiple burial of eight individuals (two male adults and six children) plus a subsequent child burial was excavated. In this study, we applied a multidisciplinary approach to elucidate interpersonal relationships and life histories within this collective. MATERIALS AND METHODS: To determine the identity of this collective, we performed aDNA analyses in addition to osteological examination using HVR I plus Y-chromosomal and autosomal STR profiling to find evidence for kinship relations. Strontium isotopic analyses were used to reconsider migrational behavior. To find evidence for a specific social affiliation, the individual diet was reconstructed by performing nitrogen and carbon isotopic analyses. Furthermore, radiocarbon-dating was carried out to integrate the burial context into an absolute timeframe. Two nearby single burials were included in the analyses for comparison. RESULTS: Because of a shared HVR I haplotype, three pairs of individuals were most likely linked by kinship, and statistical testing on autosomal STR profiles shows a high probability for the pair of two men being brothers. Although it cannot be excluded, isotopic data gave no clear proof for migration. A rather poor health status is indicated by skeletal stress markers even though the isotope data attest to a diet rich in meat and fish. DISCUSSION: Although clear kinship relations among the infants remain unconfirmed, a relationship could also be indicated by the positioning of the bodies in the burial pit. Whereas a common cause of death might have been the presupposition for their special treatment, interpersonal relationships were likely the decisive factor for the multiple burial.
Assuntos
Osso e Ossos/química , Cromossomos Humanos Y/genética , DNA Mitocondrial/genética , Repetições de Microssatélites/genética , Adulto , Antropologia Física , Arqueologia , Criança , Pré-Escolar , DNA Mitocondrial/análise , Feminino , Alemanha , Humanos , Lactente , Isótopos/análise , Masculino , Pessoa de Meia-IdadeRESUMO
Migration of immune cells to sites of inflammation is a critical step in the body's response to infections but also during autoimmune flares. Chemokine receptors, members of the GPCR receptors, are instrumental in directing specific cell types to their target organs. Herein, we describe a highly potent small molecule antagonist of the chemokine receptor CCR6, which came out of fine-tuned structural elaborations from a proprietary HTS hit. Three main issues in the parent chemical series-cytotoxicity, phototoxicity, and hERG, were successfully solved. Biological characterization demonstrated that compound 45 (IDOR-1117-2520) is a selective and insurmountable antagonist of CCR6. In vivo proof-of-mechanism studies in a mouse lung inflammation model using a representative compound from the chemical class of 45 confirmed that the targeted CCR6+ cells were efficiently inhibited from migrating into the bronchoalveoli. Finally, ADMET and physicochemical properties were well balanced and the preclinical package warranted progress in the clinic.
Assuntos
Doenças Autoimunes , Receptores CCR6 , Receptores CCR6/antagonistas & inibidores , Receptores CCR6/metabolismo , Animais , Humanos , Doenças Autoimunes/tratamento farmacológico , Camundongos , Relação Estrutura-Atividade , Descoberta de DrogasRESUMO
Genomic information is increasingly used to inform medical treatments and manage future disease risks. However, any personal and societal gains must be carefully balanced against the risk to individuals contributing their genomic data. Expanding our understanding of actionable genomic insights requires researchers to access large global datasets to capture the complexity of genomic contribution to diseases. Similarly, clinicians need efficient access to a patient's genome as well as population-representative historical records for evidence-based decisions. Both researchers and clinicians hence rely on participants to consent to the use of their genomic data, which in turn requires trust in the professional and ethical handling of this information. Here, we review existing and emerging solutions for secure and effective genomic information management, including storage, encryption, consent, and authorization that are needed to build participant trust. We discuss recent innovations in cloud computing, quantum-computing-proof encryption, and self-sovereign identity. These innovations can augment key developments from within the genomics community, notably GA4GH Passports and the Crypt4GH file container standard. We also explore how decentralized storage as well as the digital consenting process can offer culturally acceptable processes to encourage data contributions from ethnic minorities. We conclude that the individual and their right for self-determination needs to be put at the center of any genomics framework, because only on an individual level can the received benefits be accurately balanced against the risk of exposing private information.
Assuntos
Genômica , Humanos , Genômica/métodos , Genômica/ética , Segurança Computacional , Computação em Nuvem , Consentimento Livre e EsclarecidoRESUMO
In many cases of machine learning, research suggests that the development of training data might have a higher relevance than the choice and modelling of classifiers themselves. Thus, data augmentation methods have been developed to improve classifiers by artificially created training data. In NLP, there is the challenge of establishing universal rules for text transformations which provide new linguistic patterns. In this paper, we present and evaluate a text generation method suitable to increase the performance of classifiers for long and short texts. We achieved promising improvements when evaluating short as well as long text tasks with the enhancement by our text generation method. Especially with regard to small data analytics, additive accuracy gains of up to 15.53% and 3.56% are achieved within a constructed low data regime, compared to the no augmentation baseline and another data augmentation technique. As the current track of these constructed regimes is not universally applicable, we also show major improvements in several real world low data tasks (up to +4.84 F1-score). Since we are evaluating the method from many perspectives (in total 11 datasets), we also observe situations where the method might not be suitable. We discuss implications and patterns for the successful application of our approach on different types of datasets.
RESUMO
The CXCR3 chemokine receptor is a G protein-coupled receptor mainly expressed on immune cells from the lymphoid lineage, including activated T cells. Binding of its inducible chemokine ligands CXCL9, CXCL10, and CXCL11 leads to downstream signaling events and the migration of activated T cells to sites of inflammation. Herein, we report the third part of our CXCR3 antagonist program in the field of autoimmunity, culminating in the discovery of the clinical compound ACT-777991 (8a). A previously disclosed advanced molecule was exclusively metabolized by the CYP2D6 enzyme, and options to address the issue are described. ACT-777991 is a highly potent, insurmountable, and selective CXCR3 antagonist that showed dose-dependent efficacy and target engagement in a mouse model of acute lung inflammation. The excellent properties and safety profile warranted progress in the clinics.
Assuntos
Quimiocina CXCL10 , Receptores de Quimiocinas , Animais , Camundongos , Quimiocina CXCL10/metabolismo , Quimiocina CXCL9 , Receptores de Quimiocinas/metabolismo , Ligantes , Transdução de Sinais , Receptores CXCR3/metabolismoRESUMO
Four dogs with T(2)N(0)M(0) transitional cell carcinoma of the lower urinary tract underwent multimodal treatment consisting of neoadjuvant chemotherapy, external-beam radiotherapy, and adjuvant chemotherapy. No significant toxicity was documented. All dogs showed clinical improvement and reduction of tumor volume based on computed tomography (CT).
RésuméChimiothérapie et radiothérapie comme traitement pour carcinomes à cellules transitionnelles urothéliaux avec infiltration du muscle dans 4 chiens. Quatre chiens avec des carcinomes à cellules transitionnelles du bas tractus urinaire (TNM) ont été traités avec une approche multimodale consistent en chimiothérapie néodjuvante, radiothérapie externe et chimiothérapie adjuvante. Nous n'avons pas observé une toxicité signifiante. Tous les chiens ont répondu à ce traitement multimodale, défini comme amélioration des symptômes cliniques et réduction des dimensions de la tumeur, indiqué au scanner.(Traduit par Julia Buchholz).
Assuntos
Carcinoma de Células de Transição/veterinária , Doenças do Cão/terapia , Neoplasias Musculares/veterinária , Neoplasias Urológicas/veterinária , Animais , Antineoplásicos/uso terapêutico , Carcinoma de Células de Transição/terapia , Quimioterapia Adjuvante/veterinária , Cães , Evolução Fatal , Feminino , Neoplasias Musculares/terapia , Invasividade Neoplásica , Radioterapia/veterinária , Resultado do Tratamento , Neoplasias Urológicas/terapiaRESUMO
The chemokine receptor CXCR3 allows the selective recruitment of innate and adaptive inflammatory immune cells into inflamed tissue. CXCR3 ligands are secreted after exposure to pro-inflammatory cytokines. Upon binding to CXCR3 ligands, CXCR3 expressing T-lymphocytes migrate toward sites of inflammation and can promote tissue damage. Therefore, antagonizing this receptor may provide clinical benefits for patients suffering from autoimmune diseases characterized by high concentrations of CXCR3 ligands. Herein, we report the second part of our CXCR3 discovery program where we explored the benzimidazolo-thiazole core scaffold. The optimization of potency and the mitigation of an hERG liability are described. Further pharmacokinetic considerations led to the identification of the potent CXCR3 antagonist ACT-672125 (29). The compound showed good physicochemical properties and safety profile. In a proof-of-mechanism model of lung inflammation, ACT-672125 inhibited the recruitment of CXCR3 expressing T cells into the inflamed lung in a dose-dependent manner.
Assuntos
Doenças Autoimunes , Tiazóis , Doenças Autoimunes/tratamento farmacológico , Citocinas , Humanos , Ligantes , Receptores CXCR3/metabolismo , Linfócitos T/metabolismo , Tiazóis/farmacologia , Tiazóis/uso terapêuticoRESUMO
The chemokine receptor CXCR3 is a seven-transmembrane G-protein-coupled receptor (GPCR) involved in various pathologies, in particular autoimmune diseases. It is activated by the three chemokine ligands CXCL9, CXCL10, and CXCL11 and enables the recruitment of immune cell subsets leading to damage of inflamed tissues. Starting from a high-throughput screening hit, we describe the iterative optimization of a chemical series culminating in the discovery of the selective CXCR3 antagonist ACT-660602 (9j). The careful structural modifications during the lead optimization phase led to a compound with high biological potency in inhibiting cell migration together with improvements of the metabolic stability and hERG issue. In a LPS-induced lung inflammation model in mice, ACT-660602 led to significantly reduced recruitment of the CXCR3+ CD8+ T cell in the bronchoalveolar lavage compartment when administered orally at a dose of 30 mg/kg.
Assuntos
Doenças Autoimunes , Quimiocina CXCL10 , Animais , Doenças Autoimunes/tratamento farmacológico , Linfócitos T CD8-Positivos/metabolismo , Quimiocina CXCL9/metabolismo , Ligantes , Camundongos , Receptores CXCR3/metabolismoRESUMO
BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available. RESULTS: We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill. CONCLUSIONS: Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases.
Assuntos
Vacinas Anti-Haemophilus , Peste , Criança , Haemophilus influenzae/genética , Humanos , Lactente , Filogenia , SorogrupoRESUMO
DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
Assuntos
DNA Antigo , RNA , Animais , Automação , Cavalos/genética , RNA/genética , Sondas RNA , Análise de Sequência de DNA/métodosRESUMO
BACKGROUND: Autoimmune polyendocrine syndrome type 1 (APS-1) is a multiorgan autoimmune disorder caused by mutations in AIRE, the autoimmune regulator gene. Though recent studies concerning AIRE deficiency have begun to elucidate the molecular pathogenesis of organ-specific autoimmunity in patients with APS-1, the autoantigen responsible for hypoparathyroidism, a hallmark of APS-1 and its most common autoimmune endocrinopathy, has not yet been identified. METHODS: We performed immunoscreening of a human parathyroid complementary DNA library, using serum samples from patients with APS-1 and hypoparathyroidism, to identify patients with reactivity to the NACHT leucine-rich-repeat protein 5 (NALP5). Subsequently, serum samples from 87 patients with APS-1 and 293 controls, including patients with other autoimmune disorders, were used to determine the frequency and specificity of autoantibodies against NALP5. In addition, the expression of NALP5 was investigated in various tissues. RESULTS: NALP5-specific autoantibodies were detected in 49% of the patients with APS-1 and hypoparathyroidism but were absent in all patients with APS-1 but without hypoparathyroidism, in all patients with other autoimmune endocrine disorders, and in all healthy controls. NALP5 was predominantly expressed in the cytoplasm of parathyroid chief cells. CONCLUSIONS: NALP5 appears to be a tissue-specific autoantigen involved in hypoparathyroidism in patients with APS-1. Autoantibodies against NALP5 appear to be highly specific and may be diagnostic for this prominent component of APS-1.
Assuntos
Autoanticorpos/sangue , Autoantígenos/imunologia , Hipoparatireoidismo/diagnóstico , Glândulas Paratireoides/imunologia , Poliendocrinopatias Autoimunes/imunologia , Autoanticorpos/análise , Autoantígenos/genética , Biomarcadores/análise , Biomarcadores/sangue , DNA Complementar/análise , Biblioteca Gênica , Humanos , Hipoparatireoidismo/etiologia , Hipoparatireoidismo/imunologia , Proteínas Mitocondriais , Proteínas Nucleares , Glândulas Paratireoides/química , Poliendocrinopatias Autoimunes/complicações , RNA Mensageiro/análiseRESUMO
Thymic T cell development is dependent on a specialized epithelial microenvironment mainly composed of cortical and medullary thymic epithelial cells (TECs). The molecular programs governing the differentiation and maintenance of TECs remain largely unknown. Wnt signaling is central to the development and maintenance of several organ systems but a specific role of this pathway for thymus organogenesis has not yet been ascertained. In this report, we demonstrate that activation of the canonical Wnt signaling pathway by a stabilizing mutation of beta-catenin targeted exclusively to TECs changes the initial commitment of endodermal epithelia to a thymic cell fate. Consequently, the formation of a correctly composed and organized thymic microenvironment is prevented, thymic immigration of hematopoietic precursors is restricted, and intrathymic T cell differentiation is arrested at a very early developmental stage causing severe immunodeficiency. These results suggest that a precise regulation of canonical Wnt signaling in thymic epithelia is essential for normal thymus development and function.