RESUMEN
Multiple myeloma (MM) is an incurable malignancy of plasma cells. Epidemiological studies indicate a substantial heritable component, but the underlying mechanisms remain unclear. Here, in a genome-wide association study totaling 10,906 cases and 366,221 controls, we identify 35 MM risk loci, 12 of which are novel. Through functional fine-mapping and Mendelian randomization, we uncover two causal mechanisms for inherited MM risk: longer telomeres; and elevated levels of B-cell maturation antigen (BCMA) and interleukin-5 receptor alpha (IL5RA) in plasma. The largest increase in BCMA and IL5RA levels is mediated by the risk variant rs34562254-A at TNFRSF13B. While individuals with loss-of-function variants in TNFRSF13B develop B-cell immunodeficiency, rs34562254-A exerts a gain-of-function effect, increasing MM risk through amplified B-cell responses. Our results represent an analysis of genetic MM predisposition, highlighting causal mechanisms contributing to MM development.
Asunto(s)
Antígeno de Maduración de Linfocitos B , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Mieloma Múltiple , Polimorfismo de Nucleótido Simple , Mieloma Múltiple/genética , Humanos , Antígeno de Maduración de Linfocitos B/genética , Análisis de la Aleatorización Mendeliana , Linfocitos B/inmunología , Linfocitos B/metabolismo , Estudios de Casos y Controles , Proteína Activadora Transmembrana y Interactiva del CAML/genética , Masculino , Telómero/genéticaRESUMEN
Motivation: AliGater is an open-source framework to accelerate the development of bioinformatic pipelines for the analysis of large-scale, high-dimensional flow cytometry data. AliGater provides a Python package for automatic feature extraction workflows, as well as building blocks to construct analysis pipelines. Results: We illustrate the use of AliGater in a high-resolution flow cytometry-based genome-wide association study on 46 immune cell populations in 14 288 individuals. Availability and implementation: Source code and documentation at https://github.com/LudvigEk/aligater and https://aligater.readthedocs.io.
RESUMEN
Stem cell transplantation is a cornerstone in the treatment of blood malignancies. The most common method to harvest stem cells for transplantation is by leukapheresis, requiring mobilization of CD34+ hematopoietic stem and progenitor cells (HSPCs) from the bone marrow into the blood. Identifying the genetic factors that control blood CD34+ cell levels could reveal new drug targets for HSPC mobilization. Here we report the first large-scale, genome-wide association study on blood CD34+ cell levels. Across 13 167 individuals, we identify 9 significant and 2 suggestive associations, accounted for by 8 loci (PPM1H, CXCR4, ENO1-RERE, ITGA9, ARHGAP45, CEBPA, TERT, and MYC). Notably, 4 of the identified associations map to CXCR4, showing that bona fide regulators of blood CD34+ cell levels can be identified through genetic variation. Further, the most significant association maps to PPM1H, encoding a serine/threonine phosphatase never previously implicated in HSPC biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. Through functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates an MYB transcription factor-binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, PPM1H knockdown increases the proportion of CD34+ and CD34+90+ cells in cord blood assays. Our results provide the first large-scale analysis of the genetic architecture of blood CD34+ cell levels and warrant further investigation of PPM1H as a potential inhibition target for stem cell mobilization.
Asunto(s)
Estudio de Asociación del Genoma Completo , Células Madre Hematopoyéticas , Antígenos CD34/metabolismo , Movilización de Célula Madre Hematopoyética , Células Madre Hematopoyéticas/metabolismo , HumanosRESUMEN
Thousands of non-coding variants have been associated with increased risk of human diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an integrative study combining massively parallel reporter assays (MPRA), expression analyses (eQTL, meQTL, PCHiC) and chromatin accessibility analyses in primary cells (caQTL), we investigate 1,039 variants associated with multiple myeloma (MM). We demonstrate that MM susceptibility is mediated by gene-regulatory changes in plasma cells and B-cells, and identify putative causal variants at six risk loci (SMARCD3, WAC, ELL2, CDCA7L, CEP120, and PREX1). Notably, three of these variants co-localize with significant plasma cell caQTLs, signaling the presence of causal activity at these precise genomic positions in an endogenous chromosomal context in vivo. Our results provide a systematic functional dissection of risk loci for a hematologic malignancy.
Asunto(s)
Linfocitos B/patología , ADN Intergénico/genética , Predisposición Genética a la Enfermedad , Mieloma Múltiple/genética , Proteínas de Neoplasias/genética , Células Plasmáticas/patología , Proteínas Adaptadoras Transductoras de Señales/genética , Proteínas Adaptadoras Transductoras de Señales/inmunología , Protocolos de Quimioterapia Combinada Antineoplásica , Linfocitos B/inmunología , Secuencia de Bases , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/inmunología , Cromatina/química , Cromatina/inmunología , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/inmunología , ADN Intergénico/inmunología , Regulación Neoplásica de la Expresión Génica , Factores de Intercambio de Guanina Nucleótido/genética , Factores de Intercambio de Guanina Nucleótido/inmunología , Humanos , Patrón de Herencia , Mieloma Múltiple/tratamiento farmacológico , Mieloma Múltiple/inmunología , Mieloma Múltiple/patología , Proteínas de Neoplasias/inmunología , Células Plasmáticas/inmunología , Polimorfismo Genético , Cultivo Primario de Células , Sitios de Carácter Cuantitativo , Proteínas Represoras/genética , Proteínas Represoras/inmunología , Medición de Riesgo , Factores de Elongación Transcripcional/genética , Factores de Elongación Transcripcional/inmunologíaRESUMEN
Multiple myeloma (MM) is caused by the uncontrolled, clonal expansion of plasma cells. While there is epidemiological evidence for inherited susceptibility, the molecular basis remains incompletely understood. We report a genome-wide association study totalling 5,320 cases and 422,289 controls from four Nordic populations, and find a novel MM risk variant at SOHLH2 at 13q13.3 (risk allele frequency = 3.5%; odds ratio = 1.38; P = 2.2 × 10-14). This gene encodes a transcription factor involved in gametogenesis that is normally only weakly expressed in plasma cells. The association is represented by 14 variants in linkage disequilibrium. Among these, rs75712673 maps to a genomic region with open chromatin in plasma cells, and upregulates SOHLH2 in this cell type. Moreover, rs75712673 influences transcriptional activity in luciferase assays, and shows a chromatin looping interaction with the SOHLH2 promoter. Our work provides novel insight into MM susceptibility.
Asunto(s)
Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Mieloma Múltiple/genética , Anciano , Femenino , Frecuencia de los Genes , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Células Germinativas/metabolismo , Mutación de Línea Germinal , Humanos , Desequilibrio de Ligamiento , Masculino , Polimorfismo de Nucleótido SimpleRESUMEN
Is the oncogene MYC upregulated or hyperactive? In the majority of human cancers, finding agents that target c-MYC has proved difficult. Here we report specific bacterial effector molecules that inhibit cellular MYC (c-MYC) in human cells. We show that uropathogenic Escherichia coli (UPEC) degrade the c-MYC protein and attenuate MYC expression in both human cells and animal tissues. c-MYC protein was rapidly degraded by both cell-free bacterial lysates and the purified bacterial protease Lon. In mice, intravesical or peroral delivery of Lon protease delayed tumor progression and increased survival in MYC-dependent bladder and colon cancer models, respectively. These results suggest that bacteria have evolved strategies to control c-MYC tissue levels in the host and that the Lon protease shows promise for therapeutic targeting of c-MYC in cancer.
Asunto(s)
Neoplasias del Colon/patología , Genes myc , Neoplasias de la Vejiga Urinaria/patología , Escherichia coli Uropatógena/enzimología , Enfermedad Aguda , Animales , Modelos Animales de Enfermedad , Infecciones por Escherichia coli/patología , Eliminación de Gen , Ratones , Nefritis/genéticaRESUMEN
The nervous system is engaged by infection, indirectly through inflammatory cascades or directly, by bacterial attack on nerve cells. Here we identify a neuro-epithelial activation loop that participates in the control of mucosal inflammation and pain in acute cystitis. We show that infection activates Neurokinin-1 receptor (NK1R) and Substance P (SP) expression in nerve cells and bladder epithelial cells in vitro and in vivo in the urinary bladder mucosa. Specific innate immune response genes regulated this mucosal response, and single gene deletions resulted either in protection (Tlr4-/- and Il1b-/- mice) or in accentuated bladder pathology (Asc-/- and Nlrp3-/- mice), compared to controls. NK1R/SP expression was lower in Tlr4-/- and Il1b-/- mice than in C56BL/6WT controls but in Asc-/- and Nlrp3-/- mice, NK1R over-activation accompanied the exaggerated disease phenotype, due, in part to transcriptional de-repression of Tacr1. Pharmacologic NK1R inhibitors attenuated acute cystitis in susceptible mice, supporting a role in disease pathogenesis. Clinical relevance was suggested by elevated urine SP levels in patients with acute cystitis, compared to patients with asymptomatic bacteriuria identifying NK1R/SP as potential therapeutic targets. We propose that NK1R and SP influence the severity of acute cystitis through a neuro-epithelial activation loop that controls pain and mucosal inflammation.
Asunto(s)
Cistitis/patología , Células Neuroepiteliales/fisiología , Receptores de Neuroquinina-1/metabolismo , Adulto , Animales , Cistitis/inmunología , Femenino , Expresión Génica/efectos de los fármacos , Humanos , Inmunidad Mucosa/fisiología , Inflamación/patología , Interleucina-1beta/genética , Macrófagos , Masculino , Ratones , Ratones Endogámicos C57BL , Mucositis/patología , Músculo Liso/metabolismo , Células Neuroepiteliales/metabolismo , Neutrófilos , Dolor/patología , Sustancia P/metabolismo , Receptor Toll-Like 4/genética , Vejiga Urinaria/metabolismo , Vejiga Urinaria/patologíaRESUMEN
Tissue damage is usually regarded as a necessary price to pay for successful elimination of pathogens by the innate immune defense. Yet, it is possible to distinguish protective from destructive effects of innate immune activation and selectively attenuate molecular nodes that create pathology. Here, we identify acute cystitis as an Interleukin-1 beta (IL-1ß)-driven, hyper-inflammatory condition of the infected urinary bladder and IL-1 receptor blockade as a novel therapeutic strategy. Disease severity was controlled by the mechanism of IL-1ß processing and mice with intact inflammasome function developed a moderate, self-limiting form of cystitis. The most severe form of acute cystitis was detected in mice lacking the inflammasome constituents ASC or NLRP-3. IL-1ß processing was hyperactive in these mice, due to a new, non-canonical mechanism involving the matrix metalloproteinase 7- (MMP-7). ASC and NLRP-3 served as transcriptional repressors of MMP7 and as a result, Mmp7 was markedly overexpressed in the bladder epithelium of Asc-/- and Nlrp3-/- mice. The resulting IL-1ß hyper-activation loop included a large number of IL-1ß-dependent pro-inflammatory genes and the IL-1 receptor antagonist Anakinra inhibited their expression and rescued susceptible Asc-/- mice from bladder pathology. An MMP inhibitor had a similar therapeutic effect. Finally, elevated levels of IL-1ß and MMP-7 were detected in patients with acute cystitis, suggesting a potential role as biomarkers and immunotherapeutic targets. The results reproduce important aspects of human acute cystitis in the murine model and provide a comprehensive molecular framework for the pathogenesis and immunotherapy of acute cystitis, one of the most common infections in man. TRIAL REGISTRATION: The clinical studies were approved by the Human Ethics Committee at Lund University (approval numbers LU106-02, LU236-99 and Clinical Trial Registration RTP-A2003, International Committee of Medical Journal Editors, www.clinicaltrials.gov).
Asunto(s)
Cistitis/genética , Cistitis/inmunología , Interleucina-1beta/inmunología , Metaloproteinasa 7 de la Matriz/inmunología , Enfermedad Aguda , Animales , Western Blotting , Modelos Animales de Enfermedad , Ensayo de Cambio de Movilidad Electroforética , Ensayo de Inmunoadsorción Enzimática , Femenino , Humanos , Inmunohistoquímica , Inmunoprecipitación , Interleucina-1beta/genética , Masculino , Metaloproteinasa 7 de la Matriz/genética , Ratones , Ratones Endogámicos C57BL , Microscopía Confocal , Reacción en Cadena de la Polimerasa , Transcriptoma , TransfecciónRESUMEN
Boosting innate immunity represents an important therapeutic alternative to antibiotics. However, the molecular selectivity of this approach is a major concern because innate immune responses often cause collateral tissue damage. We identify the transcription factor interferon regulatory factor 7 (IRF-7), a heterodimer partner of IRF-3, as a target for non-antibiotics-based therapy of bacterial infections. We found that the efficient and self-limiting innate immune response to bacterial infection relies on a tight balance between IRF-3 and IRF-7. Deletion of Irf3 resulted in overexpression of Irf7 and led to an IRF-7-driven hyperinflammatory phenotype, which was entirely prevented if Irf7 was deleted. We then identified a network of strongly up-regulated, IRF-7-dependent genes in Irf3(-/-) mice with kidney pathology, which was absent in Irf7(-/-) mice. IRF-3 and IRF-7 from infected kidney cell nuclear extracts were shown to bind OAS1, CCL5, and IFNB1 promoter oligonucleotides. These data are consistent in children with low IRF7 expression in the blood: attenuating IRF7 promoter polymorphisms (rs3758650-T and rs10902179-G) negatively associated with recurrent pyelonephritis. Finally, we identified IRF-7 as a target for immunomodulatory therapy. Administering liposomal Irf7 siRNA to Irf3(-/-) mice suppressed mucosal IRF-7 expression, and the mice were protected against infection and renal tissue damage. These findings offer a response to the classical but unresolved question of "good versus bad inflammation" and identify IRF7 as a therapeutic target for protection against bacterial infection.
Asunto(s)
Infecciones Bacterianas/inmunología , Inmunidad Innata/fisiología , Factor 7 Regulador del Interferón/metabolismo , Animales , Infecciones Bacterianas/metabolismo , Femenino , Regulación de la Expresión Génica/genética , Regulación de la Expresión Génica/fisiología , Humanos , Inmunidad Innata/genética , Factor 3 Regulador del Interferón/genética , Factor 3 Regulador del Interferón/metabolismo , Factor 7 Regulador del Interferón/genética , Riñón/metabolismo , Ratones , Ratones Endogámicos C57BL , Pielonefritis/genética , Pielonefritis/metabolismo , Transducción de Señal/genética , Transducción de Señal/fisiologíaRESUMEN
The aim of this study was a reliable intra-species discrimination and strain biodiversity in Oenococcus oeni populations of two different Aglianico wineries by molecular, biochemical, and physiological characterization. Pulsed field gel electrophoresis (PFGE) analysis revealed a high polymorphism related to the origin (winery) of strains, while differential display PCR (DD-PCR) allowed a further discrimination of strains from the same winery. Moreover, the heterogeneity of these natural populations was investigated by capillary electrophoresis and enzymatic assays. A variability related to a different surface charge distribution was observed among strains, linked to their origin. Malolactic activity study evidenced strain-specific differences in malic acid degradation, and then, only the presence of L(-)-malic acid in the medium induced the mle gene. This study provided evidences on the importance of intra-species biodiversity of malolactic bacterial populations in wine ecosystems, as each wine possess peculiar winemaking conditions and physical-chemical properties which make specific the bacterial survival and growth. This study highlighted a great biodiversity among O. oeni strains that can be also winery specific. Such biodiversity within a certain winery and winemaking area is important for selecting malolactic starters, and strain-specific trait identification is especially important to match individual strains to specific industrial process.
Asunto(s)
Biodiversidad , Oenococcus/clasificación , Oenococcus/aislamiento & purificación , Polimorfismo Genético , Vino/microbiología , Malatos/metabolismo , Tipificación Molecular , Oenococcus/genética , Oenococcus/fisiologíaRESUMEN
Twenty-two Brevibacterium linens strains isolated from 'Pecorino di Filiano' cheese ripened in two different environments (natural cave and storeroom) were characterized and differentiated for features of technological interest and by genotypic methods, in order to select strains with specific features to be used as surface starter cultures. Results showed significant differences among strains on the basis of physiological and technological features, indicating heterogeneity within the species. A middle-low level of proteolytic activity was observed in 27.3 % of strains, while a small group (9.1 %) showed a high ability. Lipolytic activity was observed at three different temperatures and the highest value was detected at 20 °C with 13.6 % of strains, while an increase in temperature produced a slightly lower lipolysis in all strains. The evaluation of diacetyl production revealed that only 22.8 % of strains showed this ability, and most of them were isolated from product ripened in the natural cave. All strains exhibited only leu-aminopeptidase activity, with values more elevated in strains coming from the natural cave product. The combined analysis of genotypic results with the data obtained by the features of technological interest study established that the random amplified polymorphic DNA (RAPD) clusters obtained were composed not only of different genotypes but of different profiles based on technological properties too. This study demonstrated the importance of the ripening environment that affects the typical features of the artisanal product, leading to the selection of a specific surface microflora. Characterized strains could be associated within surface starters to standardize the production process of cheese, but preserving its typical organoleptic and sensory characteristics and improving the quality of the final product.
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Brevibacterium/metabolismo , Queso/microbiología , Microbiología de Alimentos , Leche/microbiología , Animales , Proteínas Bacterianas/metabolismo , Brevibacterium/enzimología , Brevibacterium/genética , Brevibacterium/aislamiento & purificación , Bovinos , Ambiente , Microbiología Ambiental , Fermentación , Microbiología de Alimentos/instrumentación , Microbiología de Alimentos/métodos , GenotipoRESUMEN
In this study, we compared different total protein extraction protocols to achieve highly efficient isolation and purification of total proteins for the specific protein profiling of Oenococcus oeni. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis patterns obtained for the different extraction protocols revealed not only a qualitative similar protein pattern but also quantitative variations with different intensity bands depending on the extraction method used. The selected extraction method added with sonication proved to work extremely well and efficiently and was able to obtain a high-resolution 2-D electrophoresis (2-DE) map. Prominent spots were successfully identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry and corresponded to 76 different proteins involved in the main metabolic pathways. The approach allowed to achieve a protein profiling specific for O. oeni from Aglianico wine with numerous characterized protein products corresponding to many different O. oeni genes and associated with main cellular pathways. Further investigations of the 2-DE protein expression profile will provide useful and interesting information on the molecular mechanisms at the protein level responsible for growth and survival of O. oeni in wine.