Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch

Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particularly with respect to the engineering of synthetic gene networks, will require a broader range of tightly performing gene control systems. Here, a generically applicable approach is described that utilizes intronically encoded siRNA on the relevant transregulator construct, and siRNA sequence-specific tags on the reporter construct, to minimize basal gene activity in the off-state of a range of common gene control systems. To demonstrate tight control of residual expression the approach was successfully used to conditionally express the toxic proteins RipDD and Linamarase. The intronic siRNA concept was also extended to create a new generation of compact, single-vector, autoinducible siRNA vectors. Finally, using improved regulation systems a mammalian epigenetic toggle switch was engineered that exhibited superior in vitro and in vivo induction characteristics in mice compared to the equivalent non-intronic system

Diagnostic testing for interstitial lung disease in common variable immunodeficiency: a systematic review

INTRODUCTION: Common variable immunodeficiency related interstitial lung disease (CVID-ILD, also referred to as GLILD) is generally considered a manifestation of systemic immune dysregulation occurring in up to 20% of people with CVID. There is a lack of evidence-based guidelines for the diagnosis and management of CVID-ILD. AIM: To systematically review use of diagnostic tests for assessing patients with CVID for possible ILD, and to evaluate their utility and risks. METHODS: EMBASE, MEDLINE, PubMed and Cochrane databases were searched. Papers reporting information on the diagnosis of ILD in patients with CVID were included. RESULTS: 58 studies were included. Radiology was the investigation modality most commonly used. HRCT was the most reported test, as abnormal radiology often first raised suspicion of CVID-ILD. Lung biopsy was used in 42 (72%) of studies, and surgical lung biopsy had more conclusive results compared to trans-bronchial biopsy (TBB). Analysis of broncho-alveolar lavage was reported in 24 (41%) studies, primarily to exclude infection. Pulmonary function tests, most commonly gas transfer, were widely used. However, results varied from normal to severely impaired, typically with a restrictive pattern and reduced gas transfer. CONCLUSION: Consensus diagnostic criteria are urgently required to support accurate assessment and monitoring in CVID-ILD. ESID and the ERS e-GLILDnet CRC have initiated a diagnostic and management guideline through international collaboration. SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/prospero/, identifier CRD42022276337

Diagnostic testing for interstitial lung disease in common variable immunodeficiency:a systematic review

Introduction: Common variable immunodeficiency related interstitial lung disease (CVID-ILD, also referred to as GLILD) is generally considered a manifestation of systemic immune dysregulation occurring in up to 20% of people with CVID. There is a lack of evidence-based guidelines for the diagnosis and management of CVID-ILD. Aim: To systematically review use of diagnostic tests for assessing patients with CVID for possible ILD, and to evaluate their utility and risks. Methods: EMBASE, MEDLINE, PubMed and Cochrane databases were searched. Papers reporting information on the diagnosis of ILD in patients with CVID were included. Results: 58 studies were included. Radiology was the investigation modality most commonly used. HRCT was the most reported test, as abnormal radiology often first raised suspicion of CVID-ILD. Lung biopsy was used in 42 (72%) of studies, and surgical lung biopsy had more conclusive results compared to trans-bronchial biopsy (TBB). Analysis of broncho-alveolar lavage was reported in 24 (41%) studies, primarily to exclude infection. Pulmonary function tests, most commonly gas transfer, were widely used. However, results varied from normal to severely impaired, typically with a restrictive pattern and reduced gas transfer. Conclusion: Consensus diagnostic criteria are urgently required to support accurate assessment and monitoring in CVID-ILD. ESID and the ERS e-GLILDnet CRC have initiated a diagnostic and management guideline through international collaboration. </p

Comparison of sequential cytomegalovirus isolates in a patient with lymphoma and failing antiviral therapy

BACKGROUND: Long-term anti-cytomegalovirus (CMV) treatments in immunocompromised patients are hampered by resistance to antiviral drugs. Longitudinal changes in the resistance genotype may depend on changes in selective pressure and the complexity of CMV isolates. OBJECTIVE: To evaluate longitudinal changes in the CMV resistance genotype and phenotype along with strain-specific variability in a patient with non-Hodgkin\u27s lymphoma in whom successive anti-CMV treatments failed. STUDY DESIGN: The resistance phenotype and genotype of seven CMV isolates collected from one patient during a 2-year follow-up period were retrospectively analysed. In parallel, we used glycoprotein B (gB) genotyping, and a- and UL10-13-sequence analysis to study CMV interstrain variability. RESULTS: The patient was infected by at least three CMV strains plus variants of the parental strains. Resistance to ganciclovir, cidofovir and foscarnet was successively detected during the follow-up period. UL97 protein kinase changes responsible for resistance to ganciclovir were initially detected at residues 591 and 592, and then at position 594. Decreased sensitivity to foscarnet coincided with the appearance of amino acid substitution N495K in DNA polymerase, whereas cross-resistance to ganciclovir and cidofovir was due to the L501I substitution. CONCLUSIONS: The CMV isolates obtained from our patient were complex mixtures of strains. Changes in resistance genotypes depended on resistance selective pressure and were not linked to interstrain variation

Managing granulomatous-lymphocytic interstitial lung disease in common variable immunodeficiency disorders : e-GLILDnet International Clinicians Survey

Background Granulomatous-lymphocytic interstitial lung disease (GLILD) is a rare, potentially severe pulmonary complication of common variable immunodeficiency disorders (CVID). Informative clinical trials and consensus on management are lacking. Aims The European GLILD network (e-GLILDnet) aims to describe how GLILD is currently managed in clinical practice and to determine the main uncertainties and unmet needs regarding diagnosis, treatment and follow-up. Methods The e-GLILDnet collaborators developed and conducted an online survey facilitated by the European Society for Immunodeficiencies (ESID) and the European Respiratory Society (ERS) between February-April 2020. Results were analyzed using SPSS. Results One hundred and sixty-one responses from adult and pediatric pulmonologists and immunologists from 47 countries were analyzed. Respondents treated a median of 27 (interquartile range, IQR 82-maximum 500) CVID patients, of which a median of 5 (IQR 8-max 200) had GLILD. Most respondents experienced difficulties in establishing the diagnosis of GLILD and only 31 (19%) had access to a standardized protocol. There was little uniformity in diagnostic or therapeutic interventions. Fewer than 40% of respondents saw a definite need for biopsy in all cases or performed bronchoalveolar lavage for diagnostics. Sixty-six percent used glucocorticosteroids for remission-induction and 47% for maintenance therapy; azathioprine, rituximab and mycophenolate mofetil were the most frequently prescribed steroid-sparing agents. Pulmonary function tests were the preferred modality for monitoring patients during follow-up. Conclusions These data demonstrate an urgent need for clinical studies to provide more evidence for an international consensus regarding management of GLILD. These studies will need to address optimal procedures for definite diagnosis and a better understanding of the pathogenesis of GLILD in order to provide individualized treatment options. Non-availability of well-established standardized protocols risks endangering patients

Granulomatous-lymphocytic interstitial lung disease: an international research prioritisation

The first ever research prioritisation exercise in GLILD: this survey identified areas of interest in the diagnosis, treatment and management of GLILD, which can be used as a roadmap for future research

Granulomatous-lymphocytic interstitial lung disease: an international research prioritisation

The first ever research prioritisation exercise in GLILD: this survey identified areas of interest in the diagnosis, treatment and management of GLILD, which can be used as a roadmap for future research

Campylobacter infection in adult patients with primary antibody deficiency

International audienceNo abstract availabl

Campylobacter infection in adult patients with primary antibody deficiency

International audiencePrimary antibody deficiency (PAD) is characterized by a defective immunoglobulin production and recurrent infections, mostly involving respiratory and gastrointestinal tracts. Chronic or recurrent diarrhea is reported in up to 23%. Campylobacter infection is a common cause of infectious diarrhea, reported in 1.2% to 7.5% of patients with common variable immunodefi-ciency (CVID), the most frequent PAD. The aim of this study was to describe Campylobacter infection in patients with PAD included in a large nationwide study and analyze factors associ-ated with susceptibility to this pathogen. The DEFI (DEFicit Immunitaire) study is an ongoing large cross-sectional French multicentric study of adults with PAD, with retrospective collection of clinical data. All patients with a history of bacteriologically documented Campylobacter infection were identified, and clinical data were collected for each episode. Factors associated with recurrent infection were assessed as oddsratio (OR) and 95% confidence interval (CI), calculated by means of simple regression analysis. In patients with available material, strains of each episode were characterized using molecular analysis and compared (Table E1, available in this article’s Online Repository at www.jaci-inpractice.org). A com-parison of immunodeficiency-related characteristics of patients with and without Campylobacter infection was performed in the homogeneous group of patients with CVID. The control group included patients with CVID from DEFI centers who confirmed that patients did not develop Campylobacter infection after enrollment (Figure E1, available in this article’s Online Repository at www.jaci-inpractice.org). After correction for multiple comparisons, P<.016 was considered significant. Since 2004, 790 patients with PAD were included in the DEFI study, and 51 presented with Campylobacter infection (6.5%). Medical chart was available for review in 45 patients. Characteristics of these patients at the time of enrollment in the DEFI study are detailed in Table E2 (available in this article’s Online Repository at www.jaci-inpractice.org). A total of 97 episodes were recorded (Table I). The overall distribution of Campylobacter species was unremarkable. Antimicrobial susceptibility testing revealed a higher resistance rate than in the general population for each antibiotic tested (see Figure E2, available in this article’s Online Repository at www.jaci-inpractice.org). A comorbidity was present in 55% of Campylobacter episodes, and a coinfection by other enteropathogens in 10%. Most patients were receiving concomitant therapy at the time of episode. One patient with end-stage cirrhosis died with Campylobacter bacteremia. Overall, bacteremia was observed in 24 episodes (13 patients) and was associated with extraintestinal complication in 10 episodes. Nineteen patients (42%) presented with recurrent (2-11) episodes. Factors associated with recurrent episodes were the presence of comorbidity (OR, 3.7 [95% CI, 1.1-13.1]) and undetectable serum IgA (OR, 8.6 [95% CI, 1.1-21.2]). None of these factors remain significant in multivariate analysis. A mo- lecular study of a subset of 18 strains from 5 patients with recurrent infections demonstrated that all strains were different, even when the antimicrobial susceptibility testing was similar and when the episodes occurred closely over time (Figure E3, available in this article’s Online Repository at www.jaci-inpractice.org). Compared with 288 patients with CVID without Campylobacter infection, patients with CVID with Campylo-bacter infection presented a higher prevalence of consanguinity and a more severe CVID phenotype, with more frequent disease- related complications, lower serum immunoglobulin levels, lower B and natural killer (NK) cells, and a trend for lower naive CD4þT cell at the time of enrollment in the DEFI study (Table II). This study is the first description of a large series of patients with PAD and Campylobacter infection. The 6.5% prevalence was probably underestimated because of the retrospective nature of the clinical data collection. In this population, symptoms were mostly restricted to an isolated, frequently severe, chronic watery diarrhea, with associated malnutrition, leading to repeated hospitalizations and impaired quality of life. Other digestive symptoms and fever were less frequent than those observed in the general population. In contrast, bacteremia and extra- digestive localizations were more frequent (25% vs 0.15% to 2%, and 22% vs 7%, respectively). Despite frequent hospitalizations, the overall prognosis was good. Recurrence rate was high (42%) compared with 1.2% in the general population, and was associated with extraintestinal comorbidity and unde- tectable IgA level in univariate analysis. Although limited by the number of available strains, molecular profiles of strains from patients with recurrent infections were all different. Thus, we could hypothesize that reinfection is more likely than persistent colonization, although colonization with multiple strains cannot be excluded. Conditions associated with the occurrence of Campylobacter infection were described in an analysis restricted to a large ho- mogeneous group of 325 patients with CVID. The present data suggest that hypochlorhydria, either proton pump inhibitor (PPI)-induced or associated with autoimmune gastritis, might play an important role in the pathogenesis of this infection. Almost all CVID-associated complications, particularly liver and gastrointestinal disease, were more frequent in patients with Campylobacter infection. A more severe immune deficiency at CVID diagnosis, with a lower serum immunoglobulin level, was also observed. Even in patients with immunoglobulin replacement therapy, IgM and IgA levels remain very low. IgA and IgM, almost absent in immunoglobulin batches, are more important than IgG in Campylobacter immunity. B-cell and specifically switch memory B-cell deficiency was also more severe in patients with CVID with Campylobacter infection than in patients without Campylobacter infection. This is in line with the high prevalence of Campylobacter infection observed in Good syndrome and X-linked agammaglobulinemia, 2 conditions associated with no circulating B cells (Figure E1, available in this article’s Online Repository at www.jaci-inpractice.org). B cells are also known to be important for the dialogue between the immune system and gut microbiota, whose composition is important for Campylobacter immunity. T cells may also play an important role, with a trend for decreased naive T cells. Indeed, 15 patients (40%) presented with a severe associated T-cell defect and could be considered as late-onset combined im-munodeficiency (data not shown). In patients with PAD, Campylobacter infection is quite frequent and seems to be related to various factors adding up together: severity of the immune deficiency, PAD complication, and associated antibiotics, immunosuppressive therapies, and PPI. It is characterized by a high frequency of recurrence and bacteremia. Recurrence is associated with the presence of comorbidity and IgA defect, and turned out to be due to rein- fection more than to persistent colonization, suggesting a specific susceptibility despite immunoglobulin substitution

Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells

Abstract Optogenetic switches are emerging molecular tools for studying cellular processes as they offer higher spatiotemporal and quantitative precision than classical, chemical-based switches. Light-controllable gene expression systems designed to upregulate protein expression levels meanwhile show performances superior to their chemical-based counterparts. However, systems to reduce protein levels with similar efficiency are lagging behind. Here, we present a novel two-component, blue light-responsive optogenetic OFF switch (‘Blue-OFF’), which enables a rapid and quantitative down-regulation of a protein upon illumination. Blue-OFF combines the first light responsive repressor KRAB-EL222 with the protein degradation module B-LID (blue light-inducible degradation domain) to simultaneously control gene expression and protein stability with a single wavelength. Blue-OFF thus outperforms current optogenetic systems for controlling protein levels. The system is described by a mathematical model which aids in the choice of experimental conditions such as light intensity and illumination regime to obtain the desired outcome. This approach represents an advancement of dual-controlled optogenetic systems in which multiple photosensory modules operate synergistically. As exemplified here for the control of apoptosis in mammalian cell culture, the approach opens up novel perspectives in fundamental research and applications such as tissue engineering