Institut für funktionale Gen-Analytik (IFGA)
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- ENaC (13)
- cytokine-induced killer cells (10)
- apoptosis (9)
- immunotherapy (7)
- Organic aciduria (5)
- CD21 (4)
- Inborn error of metabolism (4)
- Amiloride (3)
- Arthritis (3)
- Bcl-2 (3)
The epithelial sodium channel (ENaC) is essential for osmoregulation in tetrapod vertebrates. There are four ENaC-subunits (α, β, γ, δ) which form αβγ- or δβγ-ENaCs. While αβγ-ENaC is a ‘maintenance protein’ controlling sodium homeostasis, δβγ-ENaC might represent a ‘stress protein’ monitoring high sodium concentrations. The δ-subunit emerged with water-to-land transition of vertebrates. We examined ENaC evolution in Cetartiodactyla, a group including even-toed ungulates and cetaceans (whales, dolphins and porpoises) which returned to marine environments in the Eocene. Genes for α-, β-, and γ-ENaC are intact across Cetartiodactyla. While SCNN1D (δ-ENaC) is intact in terrestrial Artiodactyla, it is a pseudogene in cetaceans. A unique fusion of SCNN1D exons 11 and 12 is observed in the Antilopinae. Transcripts of α-, β-, and γ-ENaC are present in kidney, lung and skin tissues of Bottlenose dolphins, underscoring αβγ-ENaC’s maintenance role. Bottlenose dolphins and Beluga whales do not show behavioural differences between sodium-containing and sodium-free stimuli, supporting a function of δ-ENaC as a sodium sensing protein which might have become obsolete in high-salinity marine environments. Consistently, there is reduced selection pressure or pseudogenisation of SCNN1D in other marine mammals. Erosion of SCNN1D might therefore be a consequence of environmental transition in marine mammals.
Hepatic insulin resistance is an important pathophysiology in type 2 diabetes, and the mechanisms by which high-caloric diets induce insulin resistance are unclear. Among vertebrate animals, mammals have retained a unique molecular change that allows an intracellular arrestin domain-containing protein called Thioredoxin-Interacting Protein (TXNIP) to bind covalently to thioredoxin, allowing TXNIP to "sense" oxidative stress(1). Here, we show that a single cysteine in TXNIP mediates the development of hepatic insulin resistance in the setting of a high-fat diet (HFD). Mice with an exchange of TXNIP Cysteine 247 for Serine (C247S) showed improved whole-body and hepatic insulin sensitivity compared to wild-type (WT) controls following an 8-week HFD. HFD-fed TXNIP C247S mouse livers also showed improved insulin signaling. The Transmembrane 7 superfamily member 2 (Tm7sf2) gene encodes for a sterol reductase involved in the process of cholesterol biosynthesis (2). We identified TM7SF2 as a potential mediator of enhanced insulin signaling in HFD-fed TXNIP C247S mouse livers. TM7SF2 increased Akt phosphorylation and suppressed gluconeogenic markers PCK1 and G6Pc specifically under oxidative-stress-induced conditions in HepG2 cells. We also present data suggesting that a heterozygous variant of TXNIP C247 is well-tolerated in humans. Thus, mammals have a single redox-sensitive amino acid in TXNIP that mediates insulin resistance in the setting of a HFD. Our results reveal an evolutionarily conserved mechanism for hepatic insulin resistance in obesity. Hepatic insulin resistance is an important pathophysiology in type 2 diabetes, and the mechanisms by which high-caloric diets induce insulin resistance are unclear. Among vertebrate animals, mammals have retained a unique molecular change that allows an intracellular arrestin domain-containing protein called Thioredoxin-Interacting Protein (TXNIP) to bind covalently to thioredoxin, allowing TXNIP to "sense" oxidative stress. Here, we show that a single cysteine in TXNIP mediates the development of hepatic insulin resistance in the setting of a high-fat diet (HFD). Mice with an exchange of TXNIP Cysteine 247 for Serine (C247S) showed improved whole-body and hepatic insulin sensitivity compared with WT controls following an 8-week HFD. HFD-fed TXNIP C247S mouse livers also showed improved insulin signaling. The Transmembrane 7 Superfamily Member 2 (Tm7sf2) gene encodes for a sterol reductase involved in the process of cholesterol biosynthesis. We identified TM7SF2 as a potential mediator of enhanced insulin signaling in HFD-fed TXNIP C247S mouse livers. TM7SF2 increased Akt phosphorylation and suppressed gluconeogenic markers PCK1 and G6Pc specifically under oxidative stress-induced conditions in HepG2 cells. We also present data suggesting that a heterozygous variant of TXNIP C247 is well tolerated in humans. Thus, mammals have a single redox-sensitive amino acid in TXNIP that mediates insulin resistance in the setting of an HFD. Our results reveal an evolutionarily conserved mechanism for hepatic insulin resistance in obesity.
Background: Soluble CD21 (sCD21) is the product of metalloprotease-mediated proteolysis of CD21, a mechanism in which the entire extracellular domain of CD21 is shed from the cell surface. Through its retained ligand-binding ability and presence in human serum, sCD21 joins the growing list of surface proteins shed from the leukocyte cell surface which allows modulation of the immune response. Summary: sCD21 plays a multifaceted role in the body, including the promotion of inflammatory responses through receptor-ligand interactions with monocyte CD23, acting as a decoy receptor during Epstein-Barr virus infection preventing lymphoproliferation, and suppression of IgG and IgE responses by competitively inhibiting cell surface CD21. Clinical studies have shown that in comparison with healthy individuals, levels of sCD21 in serum are significantly altered in various diseases, highlighted by diverse viral infections, B-cell leukemias, and autoimmune disorders. Key Messages: Although findings of prevalence and functionality suggest sCD21 to be a key modulator of cellular and humoral immunity, questions remain about its origins and the regulation of its responses. Here, we aim to clarify and connect the advances in understanding sCD21 over time with emphasis on its generation by surface cleavage, binding partners, and functional roles. We also provide an outlook on its clinical significance and usage as a diagnostic target and therapeutic biomarker to monitor treatment efficacy in the context of chronic autoimmune disorders.
Multiple myeloma (MM) is a clonal hematologic malignancy characterized by low rate of complete remissions. Cytokine-induced killer (CIK) cell therapy has shown promising benefits in MM treatment. In this study, we investigated whether the pro-inflammatory cytokines secreted by macrophages could upregulate MICA/B expression and thus the cytotoxicity of CIK cells. Flow cytometry was used for phenotypic measurement and the cytotoxicity assay of CIK cells. Soluble MICA/B and macrophage-derived cytokines were measured using ELISA assay. CCK-8 assay was applied to evaluate cell viabilities. Gene expression levels were investigated using RT-qPCR. The expression of MICA/B and PD-L1 in MM cells was upregulated by pro-inflammatory cytokines. Pro-inflammatory cytokines enhanced the cytotoxicity of CIK cells against MM cells, with TNF-α exhibiting a more potent effect than IL-1β and IL-6 as it strengthened both components of the NKG2D-MICA/B axis. PD-L1 blockade promoted the cytotoxic ability of CIK cells. Mechanistically, IL-1β, IL-6, and TNF-α enhanced the transcription of MICA/B and PD-L1 genes via the PI3K/AKT, JAK/STAT3, and MKK/p38 MAPK pathways. Pro-inflammatory cytokines upregulated the expression of MICA/B and PD-L1, thereby promoting the cytotoxicity of CIK cells against MM by strengthening the NKG2D pathway, while PD-L1 blockade enhanced the cytotoxicity of CIK cells.
Yeast complementation assays provide limited informationon functional features of K+ channels
(2025)
We investigate to what extent yeast complementation assays, which in principle can provide large amounts of training data for machine learning models, yield quantitative correlations between growth rescue and single channel recordings. If this were the case, yeast complementation results could be used as surrogate data for machine learning-based channel design. Therefore, we mutated position L94 at the cavity entry of the model K+ channel KcvPBCV1 to all proteinogenic amino acids. The function of the WT channel and its mutants was investigated by reconstituting them in planar lipid bilayers and by their ability to rescue the growth of a yeast strain deficient in K+ uptake. The single channel data show a distinct effect of mutations in this critical position on unitary conductance and open probability, with no apparent causal relationship between the two functional parameters. We also found that even conservative amino acid replacements can alter the unitary conductance and/or open probability and that most functional changes show no systematic relationship with the physicochemical nature of the amino acids. This emphasizes that the functional influence of an amino acid on channel function cannot be reduced to a single chemical property. Mutual comparison of single channel data and yeast complementation results exhibit only a partial correlation between their electrical parameters and their potency of rescuing growth. Hence complementation data alone are not sufficient for enabling functional channel design; they need to be complemented by additional parameters like the number of channels in the plasma membrane.
Amide synthases catalyze the formation of macrolactam rings from aniline-containing polyketide-derived seco-acids as found in the important class of ansamycin antibiotics. One of these amide synthases is the geldanamycin amide synthase GdmF, which we recombinantly expressed, purified and studied in detail both functionally as well as structurally. Here we show that purified GdmF catalyzes the amide formation using synthetically derived substrates. The atomic structures of the ligand-free enzyme and in complex with simplified substrates reveal distinct structural features of the substrate binding site and a putative role of the flexible interdomain region for the catalysis reaction.
Understanding the interactions between the cervico-vaginal microbiome, immune responses, and sexually transmitted infections (STIs) is crucial for developing targeted diagnostic and therapeutic strategies. Although microbiome analyses are not yet standard practice, integrating them into routine diagnostics could enhance personalized medicine and therapies. We investigated the extent to which partial 16S short-read amplicon microbiome analyses could inform on the presence of six commonly encountered STI-causing pathogens in a patient cohort referred for colposcopy, and whether relevant taxonomic or diagnostic discrepancies occur when using vaginal rather than cervical swabs. The study cohort included cervical and vaginal samples collected from women referred for colposcopy at the University Hospital Bonn between November 2021 and February 2022, due to an abnormal PAP smear or positive hrHPV results. 16S rRNA gene sequencing libraries were prepared targeting the V1–V2 and V4 regions of the 16S RNA gene and sequenced on the Illumina MiSeq. PCR diagnostics for common STI-causing pathogens were conducted using the Allplex STI Essential Assay Kit (Seegene, Seoul, Republic of Korea). Concerning the bacterial microbiome, no significant differences were found between vaginal and cervical samples in terms of prevalence of taxa present or diversity. A total of 95 patients and 171 samples tested positive for at least one among Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis, Mycoplasma genitalium, Chlamydophila trachomatis or Neisseria gonorrhoeae. Sequencing the V1–V2 region enabled detection of one-third to half of the PCR-positive samples, with the detection likelihood increasing at lower cycle threshold (Ct) values. In contrast, sequencing the V4 region was less effective overall, yielding fewer species-level identifications and a higher proportion of undetermined taxa. We demonstrate that the vaginal microbiome closely mirrors the cervical microbiome, a relationship that has not been explored previously, but which broadens the possibilities for microbiome analysis and pathogen detection and establishes vaginal swabs as a reliable method for detecting the investigated pathogens, with sensitivities comparable with or superior to endocervical swabs. On the other hand, the sensitivity of partial 16S amplicon sequencing appears insufficient for effective STI diagnostics, as it fails to reliably identify or even detect pathogens at higher Ct values.
Transmembrane protein 175 (TMEM175) is an endolysosomal cation channel, which has attracted much attention recently from academics and the pharmaceutical industry alike since human mutations in TMEM175 were found to be associated with the development of Parkinson's disease (PD). Thus, gain-of-function mutations were identified, which reduce and loss-of-function mutations, which increase the risk of developing PD. After having been characterized as an endolysosomal potassium channel initially, soon after TMEM175 was claimed to act as a proton channel. In fact, recent evidence suggests that depending on the conditions, TMEM175 can act as either a potassium or proton channel, without acting as an antiporter or exchanger. A recent work has now identified amino acid H57 to be directly involved in gating, increasing proton conductance of the channel while leaving the potassium conductance unaffected. We review here the current knowledge of TMEM175 function, pharmacology, physiology, and pathophysiology. We discuss the potential of this ion channel as a novel drug target for the treatment of neurodegenerative diseases such as PD, and we discuss the discovery of H57 as proton sensor.
Illegal wildlife trade is a growing problem internationally. Poaching of animals not only leads to the extinction of populations and species but also has serious consequences for ecosystems and economies. This study introduces a molecular marker system that authorities can use to detect and substantiate wildlife trafficking. SNPSTR markers combine short tandem repeats with single nucleotide polymorphisms within an amplicon to increase discriminatory power. Within the FOGS (Forensic Genetics for Species Protection) project, we have established SNPSTR marker sets for 74 vertebrate species. On average, each set consists of 19 SNPSTR markers with 82 SNPs per set. More than 1300 SNPSTR markers and over 300 STR markers were identified. Also, through its biobanking pipeline, the FOGS project enabled the cryopreservation of somatic cells from 91 vertebrate species as well as viable tissues for later cell initiation from a further 109 species, providing future strategies for ex situ conservation. In addition, many more fixed tissues and DNA samples of endangered species were biobanked. Therefore, FOGS was an interdisciplinary study, combining molecular wildlife forensics and conservation tools. The SNPSTR sets and cell culture information are accessible through the FOGS database (https://fogs-portal.de/data) that is open to scientists, researchers, breeders and authorities worldwide to protect wildlife from illegal trade.
Aberrant Ras homologous (Rho) GTPase signalling is a major driver of cancer metastasis, and GTPase-activating proteins (GAPs), the negative regulators of RhoGTPases, are considered promising targets for suppressing metastasis, yet drug discovery efforts have remained elusive. Here, we report the identification and characterization of adhibin, a synthetic allosteric inhibitor of RhoGAP class-IX myosins that abrogates ATPase and motor function, suppressing RhoGTPase-mediated modes of cancer cell metastasis. In human and murine adenocarcinoma and melanoma cell models, including three-dimensional spheroid cultures, we reveal anti-migratory and anti-adhesive properties of adhibin that originate from local disturbances in RhoA/ROCK-regulated signalling, affecting actin-dynamics and actomyosin-based cell-contractility. Adhibin blocks membrane protrusion formation, disturbs remodelling of cell-matrix adhesions, affects contractile ring formation, and disrupts epithelial junction stability; processes severely impairing single/collective cell migration and cytokinesis. Combined with the non-toxic, non-pathological signatures of adhibin validated in organoids, mouse and Drosophila models, this mechanism of action provides the basis for developing anti-metastatic cancer therapies.
The epithelial sodium channel (ENaC) plays a key role in osmoregulation in tetrapod vertebrates and is a candidate receptor for salt taste sensation. There are four ENaC subunits (alpha, beta, gamma, & delta) which form alpha beta gamma or delta beta gamma-ENaCs. While alpha beta gamma-ENaC is a maintenance protein controlling sodium and potassium homeostasis, delta beta gamma-ENaC might represent a stress protein monitoring high sodium concentrations. The delta-subunit emerged with water-to-land transition of tetrapod vertebrate ancestors. We investigated the evolutionary path of ENaC-coding genes in Cetartiodactyla, a group comprising even-toed ungulates and the cetaceans (whales/dolphins) which transitioned from terrestrial to marine environments in the Eocene. The genes SCNN1A (alpha-ENaC), SCNN1B (beta-ENaC) and SCNN1G (gamma-ENaC) are intact in all 22 investigated cetartiodactylan families. While SCNN1D (delta-ENaC) is intact in terrestrial Artiodactyla, it is a pseudogene in 12 cetacean families. A fusion of SCNN1D exons 11 and 12 under preservation of the open reading frame was observed in the Antilopinae, representing a new feature of this clade. Transcripts of SCNN1A, SCNN1B and SCNN1G were present in kidney and lung tissues of Bottlenose dolphins, highlighting alpha beta gamma-ENaC's role as a maintenance protein. Consistent with SCNN1D loss, Bottlenose dolphins and Beluga whales did not show behavioural differences to stimuli with or without sodium in seawater-equivalent concentrations. These data suggest a function of delta-ENaC as a sodium sensing protein which might have become obsolete in cetaceans after the migration to high-salinity marine environments. Consistently, there is reduced selection pressure or pseudogenisation of SCNN1D in other marine mammals, including sirenians, pinnipeds and sea otter.
The lysosomal cation channel TMEM175 is crucial for maintaining lysosomal function and pH homeostasis, and its aberrant function is linked to Parkinson’s disease (PD). While TMEM175 activity was first interpreted in the context of its potassium (K+) selective conductance, subsequent studies revealed also a substantial permeability to protons (H+). Here we dissect the complex changes in TMEM175 conductance and current reversal voltages in response to pH jumps on the luminal side of the channel protein. In whole-cell patch clamp experiments with plasma membrane redistributed TMEM175 we show that a pH jump from symmetrical pH 7.4 to pH 4.7 on the luminal side triggers a continuous rise in inward and outward current, concomitant with a transient positive excursion of the reversal voltage (Erev). The peak Erev shift remains almost 100 mV below the estimated equilibrium voltage for protons and shows little sensitivity to the K+ gradient. The data are consistent with a scenario in which a TMEM175 mediated proton flux elicits a fast collapse of the pH gradient. In MD simulations we identify the luminal H57 as titratable partner for the formation of intra- and inter-subunit salt bridges with D279 and E282 for stabilizing the channel open state. This presumed gating function is confirmed by mutational studies and lysosomal patch-clamp experiments in which a H57Y mutant exhibits a reduced pH dependency of activation. Our findings contribute to a better comprehension of TMEM175’s complex electrophysiological properties and foster understanding of TMEM175 as a pharmacological target for neurodegenerative disease therapy.
Funktionale Gen-Analytik
(2022)
Modern forensic DNA quantitation assays provide information on the suitability of a DNA extract for a particular type of analysis, on the amount of sample to put into the analysis in order to yield an optimal (or best possible) result, and on the requirement for optional steps to improve the analysis. To achieve a high sensitivity and specificity, these assays are based on quantitative PCR (qPCR) and analyze target DNA loci that are present in multiple copies distributed across the genome. These target loci allow the determination of the amount of DNA, the degree of DNA degradation, and the proportion of DNA from male contributors. In addition, internal control DNA of a known amount is analyzed in order to inform about the presence of PCR inhibitors. These assays are nowadays provided as commercial kits that have been technically validated and are compatible with common qPCR instruments. In this review, the principles of forensic qPCR assays will be explained, followed by information on the nature of DNA loci targeted by modern forensic qPCR assays. Finally, we critically draw attention to the current trend of manufacturers not to disclose the exact nature of the target loci of their commercial kits.
Sulfite intoxication is the hallmark of four ultrarare disorders that are caused by impaired sulfite oxidase activity due to genetic defects in the synthesis of the molybdenum cofactor or of the apoenzyme sulfite oxidase. Delays on the diagnosis of these disorders are common and have been caused by their unspecific presentation of acute neonatal encephalopathy with high early mortality, followed by the evolution of dystonic cerebral palsy and also by the lack of easily available and reliable diagnostic tests. There is significant variation in survival and in the quality of symptomatic management of affected children. One of the four disorders, molybdenum cofactor deficiency type A (MoCD-A) has recently become amenable to causal treatment with synthetic cPMP (fosdenopterin). The evidence base for the rational use of cPMP is very limited. This prompted the formulation of these clinical guidelines to facilitate diagnosis and support the management of patients. The guidelines were developed by experts in diagnosis and treatment of sulfite intoxication disorders. It reflects expert consensus opinion and evidence from a systematic literature search.
Introduction: A multitude of findings from cell cultures and animal studies are available to support the anti-cancer properties of cannabidiol (CBD). Since CBD acts on multiple molecular targets, its clinical adaptation, especially in combination with cancer immunotherapy regimen remains a serious concern.
Methods: Considering this, we extensively studied the effect of CBD on the cytokine-induced killer (CIK) cell immunotherapy approach using multiple non-small cell lung cancer (NSCLC) cells harboring diverse genotypes.
Results: Our analysis showed that, a) The Transient Receptor Potential Cation Channel Subfamily V Member 2 (TRPV2) channel was intracellularly expressed both in NSCLC cells and CIK cells. b) A synergistic effect of CIK combined with CBD, resulted in a significant increase in tumor lysis and Interferon gamma (IFN-g) production. c) CBD had a preference to elevate the CD25+CD69+ population and the CD62L_CD45RA+terminal effector memory (EMRA) population in NKT-CIK cells, suggesting early-stage activation and effector memory differentiation in CD3+CD56+ CIK cells. Of interest, we observed that CBD enhanced the calcium influx, which was mediated by the TRPV2 channel and elevated phosphor-Extracellular signal-Regulated Kinase (p-ERK) expression directly in CIK cells, whereas ERK selective inhibitor FR180204 inhibited the increasing cytotoxic CIK ability induced by CBD. Further examinations revealed that CBD induced DNA double-strand breaks via upregulation of histone H2AX phosphorylation in NSCLC cells and the migration and invasion ability of NSCLC cells suppressed by CBD were rescued using the TRPV2 antagonist (Tranilast) in the absence of CIK cells. We further investigated the epigenetic effects of this synergy and found that adding CBD to CIK cells decreased the Long Interspersed Nuclear Element-1 (LINE-1) mRNA expression and the global DNA methylation level in NSCLC cells carrying KRAS mutation. We further investigated the epigenetic effects of this synergy and found that adding CBD to CIK cells decreased the Long Interspersed Nuclear Element-1 (LINE-1) mRNA expression and the global DNA methylation level in NSCLC cells carrying KRAS mutation.
Conclusions: Taken together, CBD holds a great potential for treating NSCLC with CIK cell immunotherapy. In addition, we utilized NSCLC with different driver mutations to investigate the efficacy of CBD. Our findings might provide evidence for CBD-personized treatment with NSCLC patients.
A firm link between endoplasmic reticulum (ER) stress and tumors has been wildly reported. Endoplasmic reticulum oxidoreductase 1 alpha (ERO1α), an ER-resident thiol oxidoreductase, is confirmed to be highly upregulated in various cancer types and associated with a significantly worse prognosis. Of importance, under ER stress, the functional interplay of ERO1α/PDI axis plays a pivotal role to orchestrate proper protein folding and other key processes. Multiple lines of evidence propose ERO1α as an attractive potential target for cancer treatment. However, the unavailability of specific inhibitor for ERO1α, its molecular inter-relatedness with closely related paralog ERO1β and the tightly regulated processes with other members of flavoenzyme family of enzymes, raises several concerns about its clinical translation. Herein, we have provided a detailed description of ERO1α in human cancers and its vulnerability towards the aforementioned concerns. Besides, we have discussed a few key considerations that may improve our understanding about ERO1α in tumors.
Trade of wild-caught animals is illegal for many taxa and in many countries. Common regulatory procedures involve documentation and marking techniques. However, these procedures are subject to fraud and thus should be complemented by routine genetic testing in order to authenticate the captive-bred origin of animals intended for trade. A suitable class of genetic markers are SNPSTRs that combine a short tandem repeat (STR) and single nucleotide polymorphisms (SNPs) within one amplicon. This combined marker type can be used for genetic identification and for parentage analyses and in addition, provides insight into haplotype history. As a proof of principle, this study establishes a set of 20 SNPSTR markers for Athene noctua, one of the most trafficked owls in CITES Appendix II. These markers can be coamplified in a single multiplex reaction. Based on population data, the percentage of observed and expected heterozygosities of the markers ranged from 0.400 to 1.000 and 0.545 to 0.850, respectively. A combined probability of identity of 5.3*10-23 was achieved with the whole set, and combined parentage exclusion probabilities reached over 99.99%, even if the genotype of one parent was missing. A direct comparison of an owl family and an unrelated owl demonstrated the applicability of the SNPSTR set in parentage testing. The established SNPSTR set thus proved to be highly useful for identifying individuals and analysing parentage to determine wild or captive origin. We propose to implement SNPSTR-based routine certification in wildlife trade as a way to reveal animal laundering and misdeclaration of wild-caught animals.
Striated muscle contraction is regulated by the translocation of troponin-tropomyosin strands over the thin filament surface. Relaxation relies partly on highly-favorable, conformation-dependent electrostatic contacts between actin and tropomyosin, which position tropomyosin such that it impedes actomyosin associations. Impaired relaxation and hypercontractile properties are hallmarks of various muscle disorders. The α-cardiac actin M305L hypertrophic cardiomyopathy-causing mutation lies near residues that help confine tropomyosin to an inhibitory position along thin filaments. Here, we investigate M305L actin in vivo, in vitro, and in silico to resolve emergent pathological properties and disease mechanisms. Our data suggest the mutation reduces actin flexibility and distorts the actin-tropomyosin electrostatic energy landscape that, in muscle, result in aberrant contractile inhibition and excessive force. Thus, actin flexibility may be required to establish and maintain interfacial contacts with tropomyosin as well as facilitate its movement over distinct actin surface features and is, therefore, likely necessary for proper regulation of contraction.
The French–Italian Concordia Research Station, situated on the Antarctic Polar Plateau at an elevation of 3233 m above sea level, offers a unique opportunity to study the presence and variation of microbes introduced by abiotic or biotic vectors and, consequently, appraise the amplitude of human impact in such a pristine environment. This research built upon a previous work, which explored microbial diversity in the surface snow surrounding the Concordia Research Station. While that study successfully characterized the bacterial assemblage, detecting fungal diversity was hampered by the low DNA content. To address this knowledge gap, in the present study, we optimized the sampling by increasing ice/snow collected to leverage the final DNA yield. The V4 variable region of the 16S rDNA and Internal Transcribed Spacer (ITS1) rDNA was used to evaluate bacterial and fungal diversity. From the sequencing, we obtained 3,352,661 and 4,433,595 reads clustered in 930 and 3182 amplicon sequence variants (ASVs) for fungi and bacteria, respectively. Amplicon sequencing revealed a predominance of Basidiomycota (49%) and Ascomycota (42%) in the fungal component; Bacteroidota (65.8%) is the main representative among the bacterial phyla. Basidiomycetes are almost exclusively represented by yeast-like fungi. Our findings provide the first comprehensive overview of both fungal and bacterial diversity in the Antarctic Polar Plateau’s surface snow/ice near Concordia Station and to identify seasonality as the main driver of microbial diversity; we also detected the most sensitive microorganisms to these factors, which could serve as indicators of human impact in this pristine environment and aid in planetary protection for future exploration missions.
Nitrosamines have been identified as a probable human carcinogen and thus are of high concern in many manufacturing industries and various matrices (for example pharmaceutical, cosmetic and food products, workplace air or potable- and wastewater). This study aims to analyse nine nitrosamines relevant in the field of occupational safety using a gas chromatography-drift tube ion mobility spectrometry (GC-DT-IMS) system. To do this, single nitrosamine standards as well as a standard mix, each at 0.1 g/L, were introduced via liquid injection. A GC-DT-IMS method capable of separating the nitrosamine signals according to retention time (first dimension) and drift time (second dimension) in 10 min was developed. The system shows excellent selectivity as each nitrosamine gives two signals pertaining to monomer and dimer in the second dimension. For the first time, reduced ion mobility values for nitrosamines were determined, ranging from 1.18 to 2.03 cm2s−1V−1. The high selectivity of the GC-DT-IMS method could provide a definite advantage for monitoring nitrosamines in different manufacturing industries and consumer products.
The non-filarial and non-communicable disease podoconiosis affects around 4 million people and is characterized by severe leg lymphedema accompanied with painful intermittent acute inflammatory episodes, called acute dermatolymphangioadenitis (ADLA) attacks. Risk factors have been associated with the disease but the mechanisms of pathophysiology remain uncertain. Lymphedema can lead to skin lesions, which can serve as entry points for bacteria that may cause ADLA attacks leading to progression of the lymphedema. However, the microbiome of the skin of affected legs from podoconiosis individuals remains unclear. Thus, we analysed the skin microbiome of podoconiosis legs using next generation sequencing. We revealed a positive correlation between increasing lymphedema severity and non-commensal anaerobic bacteria, especially Anaerococcus provencensis, as well as a negative correlation with the presence of Corynebacterium, a constituent of normal skin flora. Disease symptoms were generally linked to higher microbial diversity and richness, which deviated from the normal composition of the skin. These findings show an association of distinct bacterial taxa with lymphedema stages, highlighting the important role of bacteria for the pathogenesis of podoconiosis and might enable a selection of better treatment regimens to manage ADLA attacks and disease progression.
Host-derived succinate accumulates in the airways during bacterial infection. Here, we show that luminal succinate activates murine tracheal brush (tuft) cells through a signaling cascade involving the succinate receptor 1 (SUCNR1), phospholipase Cβ2, and the cation channel transient receptor potential channel subfamily M member 5 (TRPM5). Stimulated brush cells then trigger a long-range Ca2+ wave spreading radially over the tracheal epithelium through a sequential signaling process. First, brush cells release acetylcholine, which excites nearby cells via muscarinic acetylcholine receptors. From there, the Ca2+ wave propagates through gap junction signaling, reaching also distant ciliated and secretory cells. These effector cells translate activation into enhanced ciliary activity and Cl- secretion, which are synergistic in boosting mucociliary clearance, the major innate defense mechanism of the airways. Our data establish tracheal brush cells as a central hub in triggering a global epithelial defense program in response to a danger-associated metabolite.
RELA haploinsufficiency is a recently described autoinflammatory condition presenting with intermittent fevers and mucocutaneous ulcerations. The RELA gene encodes the p65 protein, one of five NF-κB family transcription factors. As RELA is an essential regulator of mucosal homeostasis, haploinsufficiency leads to decreased NF-κB signaling which promotes TNF-driven mucosal apoptosis with impaired epithelial recovery. Thus far, only eight cases have been reported in the literature. Here, we report four families with three novel and one previously described pathogenic variant in RELA. These four families included 23 affected individuals for which genetic testing was available in 16. Almost half of these patients had been previously diagnosed with more common rheumatologic entities (such as Behcet's Disease; BD) prior to the discovery of their pathogenic RELA variants. The most common clinical features were orogenital ulcers, rash, joint inflammation, and fever. The least common were conjunctivitis and recurrent infections. Clinical variability was remarkable even among familial cases, and incomplete penetrance was observed. Patients in our series were treated with a variety of medications, and benefit was observed with glucocorticoids, colchicine, and TNF inhibitors. Altogether, our work adds to the current literature and doubles the number of reported cases with RELA-Associated Inflammatory Disease (RAID). It reaffirms the central importance of the NF-κB pathway in immunity and inflammation, as well as the important regulatory role of RELA in mucosal homeostasis. RELA associated inflammatory disease should be considered in all patients with BD, particularly those with early onset and/or with a strong family history.
The deficiency of adenosine deaminase 2 (DADA2) is an autosomal recessively inherited disease that has undergone extensive phenotypic expansion since being first described in patients with fevers, recurrent strokes, livedo racemosa, and polyarteritis nodosa in 2014. It is now recognized that patients may develop multisystem disease that spans multiple medical subspecialties. Here, we describe the findings from a large single center longitudinal cohort of 60 patients, the broad phenotypic presentation, as well as highlight the cohort's experience with hematopoietic cell transplantation and COVID-19. Disease manifestations could be separated into three major phenotypes: inflammatory/vascular, immune dysregulatory, and hematologic, however, most patients presented with significant overlap between these three phenotype groups. The cardinal features of the inflammatory/vascular group included cutaneous manifestations and stroke. Evidence of immune dysregulation was commonly observed, including hypogammaglobulinemia, absent to low class-switched memory B cells, and inadequate response to vaccination. Despite these findings, infectious complications were exceedingly rare in this cohort. Hematologic findings including pure red cell aplasia (PRCA), immune-mediated neutropenia, and pancytopenia were observed in half of patients. We significantly extended our experience using anti-TNF agents, with no strokes observed in 2026 patient months on TNF inhibitors. Meanwhile, hematologic and immune features had a more varied response to anti-TNF therapy. Six patients received a total of 10 allogeneic hematopoietic cell transplant (HCT) procedures, with secondary graft failure necessitating repeat HCTs in three patients, as well as unplanned donor cell infusions to avoid graft rejection. All transplanted patients had been on anti-TNF agents prior to HCT and received varying degrees of reduced-intensity or non-myeloablative conditioning. All transplanted patients are still alive and have discontinued anti-TNF therapy. The long-term follow up afforded by this large single-center study underscores the clinical heterogeneity of DADA2 and the potential for phenotypes to evolve in any individual patient.
Somatic Mutations in UBA1 Define a Distinct Subset of Relapsing Polychondritis Patients With VEXAS
(2021)
BACKGROUND
Biallelic loss-of-function variants in NCF1 lead to reactive oxygen species deficiency and chronic granulomatous disease (CGD). Heterozygosity for the p.Arg90His variant in NCF1 has been associated with susceptibility to systemic lupus erythematosus, rheumatoid arthritis, and Sjögren's syndrome in adult patients. This study demonstrates the association of the homozygous p.Arg90His variant with interferonopathy with features of autoinflammation and autoimmunity in a pediatric patient.
CASE PRESENTATION
A 5-year old female of Indian ancestry with early-onset recurrent fever and headache, and persistently elevated antinuclear, anti-Ro, and anti-La antibodies was found to carry the homozygous p.Arg90His variant in NCF1 through exome sequencing. Her unaffected parents and three other siblings were carriers for the mutant allele. Because the presence of two NCF1 pseudogenes, this variant was confirmed by independent genotyping methods. Her intracellular neutrophil oxidative burst and NCF1 expression levels were normal, and no clinical features of CGD were apparent. Gene expression analysis in peripheral blood detected an interferon gene expression signature, which was further supported by cytokine analyses of supernatants of cultured patient's cells. These findings suggested that her inflammatory disease is at least in part mediated by type I interferons. While her fever episodes responded well to systemic steroids, treatment with the JAK inhibitor tofacitinib resulted in decreased serum ferritin levels and reduced frequency of fevers.
CONCLUSION
Homozygosity for p.Arg90His in NCF1 should be considered contributory in young patients with an atypical systemic inflammatory antecedent phenotype that may evolve into autoimmunity later in life. The complex genomic organization of NCF1 poses a difficulty for high-throughput genotyping techniques and variants in this gene should be carefully evaluated when using the next generation and Sanger sequencing technologies. The p.Arg90His variant is found at a variable allele frequency in different populations, and is higher in people of South East Asian ancestry. In complex genetic diseases such as SLE, other rare and common susceptibility alleles might be necessary for the full disease expressivity.
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL), defined primarily by developmental delay/intellectual disability, speech delay, postnatal microcephaly, and dysmorphic features, is a syndrome resulting from heterozygous variants in the dosage-sensitive bromodomain PHD finger chromatin remodeler transcription factor BPTF gene. To date, only 11 individuals with NEDDFL due to de novo BPTF variants have been described. To expand the NEDDFL phenotypic spectrum, we describe the clinical features in 25 novel individuals with 20 distinct, clinically relevant variants in BPTF, including four individuals with inherited changes in BPTF. In addition to the previously described features, individuals in this cohort exhibited mild brain abnormalities, seizures, scoliosis, and a variety of ophthalmologic complications. These results further support the broad and multi-faceted complications due to haploinsufficiency of BPTF.
Mendelian diseases of dysregulated canonical NF-κB signaling: From immunodeficiency to inflammation
(2020)
Systemic autoinflammatory diseases (SAIDs) are a group of inflammatory disorders caused by dysregulation in the innate immune system that leads to enhanced immune responses. The clinical diagnosis of SAIDs can be difficult since individually these are rare diseases with considerable phenotypic overlap. Most SAIDs have a strong genetic background, but environmental and epigenetic influences can modulate the clinical phenotype. Molecular diagnosis has become essential for confirmation of clinical diagnosis. To date there are over 30 genes and a variety of modes of inheritance that have been associated with monogenic SAIDs. Mutations in the same gene can lead to very distinct phenotypes and can have different inheritance patterns. In addition, somatic mutations have been reported in several of these conditions. New genetic testing methods and databases are being developed to facilitate the molecular diagnosis of SAIDs, which is of major importance for treatment, prognosis and genetic counselling. The aim of this review is to summarize the latest advances in genetic testing for SAIDs and discuss potential obstacles that might arise during the molecular diagnosis of SAIDs.
The pyrin inflammasome has evolved as an innate immune sensor to detect bacterial toxin-induced Rho guanosine triphosphatase (Rho GTPase)-inactivation, a process that is similar to the "guard" mechanism in plants. Rho GTPases act as molecular switches to regulate a variety of signal transduction pathways including cytoskeletal organization. Pathogens can modulate Rho GTPase activity to suppress host immune responses such as phagocytosis. Pyrin is encoded by MEFV, the gene that is mutated in patients with familial Mediterranean fever (FMF). FMF is the prototypic autoinflammatory disease characterized by recurring short episodes of systemic inflammation and is a common disorder in many populations in the Mediterranean basin. Pyrin specifically senses modifications in the activity of the small GTPase RhoA, which binds to many effector proteins including the serine/threonine-protein kinases PKN1 and PKN2 and actin-binding proteins. RhoA activation leads to PKN-mediated phosphorylation-dependent pyrin inhibition. Conversely, pathogen virulence factors downregulate RhoA activity in a variety of ways, and these changes are detected by the pyrin inflammasome irrespective of the type of modifications. MEFV pathogenic variants favor the active state of pyrin and elicit proinflammatory cytokine release and pyroptosis. They can be inherited either as a dominant or recessive trait depending on the variant's location and effect on the protein function. Mutations in the C-terminal B30.2 domain are usually considered recessive, although heterozygotes may manifest a biochemical or even a clinical phenotype. These variants are hypomorphic in regard to their effect on intramolecular interactions, but ultimately accentuate pyrin activity. Heterozygous mutations in other domains of pyrin affect residues critical for inhibition or protein oligomerization, and lead to constitutively active inflammasome. In healthy carriers of FMF mutations who have the subclinical inflammatory phenotype, the increased activity of pyrin might have been protective against endemic infections over human history. This finding is supported by the observation of high carrier frequencies of FMF-mutations in multiple populations. The pyrin inflammasome also plays a role in mediating inflammation in other autoinflammatory diseases linked to dysregulation in the actin polymerization pathway. Therefore, the assembly of the pyrin inflammasome is initiated in response to fluctuations in cytoplasmic homeostasis and perturbations in cytoskeletal dynamics.
