Membrane association of the ATG8 conjugation machinery emerges as a key regulatory feature for autophagosome biogenesis

Autophagy is a highly conserved intracellular pathway that is essential for survival in all eukaryotes. In healthy cells, autophagy is used to remove damaged intracellular components, which can be as simple as unfolded proteins or as complex as whole mitochondria. Once the damaged component is captured, the autophagosome engulfs it and closes, isolating the content from the cytoplasm. The autophagosome then fuses with the late endosome and/or lysosome to deliver its content to the lysosome for degradation. Formation of the autophagosome, sequestration or capture of content, and closure all require the ATG proteins, which constitute the essential core autophagy protein machinery. This brief 'nutshell' will highlight recent data revealing the importance of small membrane-associated domains in the ATG proteins. In particular, recent findings from two parallel studies reveal the unexpected key role of α-helical structures in the ATG8 conjugation machinery and ATG8s. These studies illustrate how unique membrane association modules can control the formation of autophagosomes.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.

Recent Advances in Metal Complexes for Antimicrobial Photodynamic Therapy

Antimicrobial resistance (AMR) is a growing global problem with more than 1 million deaths due to AMR infection in 2019 alone. New and innovative therapeutics are required to overcome this challenge. Antimicrobial photodynamic therapy (aPDT) is a rapidly growing area of research poised to provide much needed help in the fight against AMR. aPDT works by administering a photosensitizer (PS) that is activated only when irradiated with light, allowing high spatiotemporal control and selectivity. The PS typically generates reactive oxygen species (ROS), which can damage a variety of key biological targets, potentially circumventing existing resistance mechanisms. Metal complexes are well known to display excellent optoelectronic properties, and recent focus has begun to shift towards their application in tackling microbial infections. Herein, we review the last five years of progress in the emerging field of small-molecule metal complex PSs for aPDT.

Particle entity in the Doi-Peliti and response field formalisms

We introduce a procedure to test a theory for point particle entity, that is, whether said theory takes into account the discrete nature of the constituents of the system. We then identify the mechanism whereby particle entity is enforced in the context of two field-theoretic frameworks designed to incorporate the particle nature of the degrees of freedom, namely the Doi-Peliti field theory and the response field theory that derives from Dean's equation. While the Doi-Peliti field theory encodes the particle nature at a very fundamental level that is easily revealed, demonstrating the same for Dean's equation is more involved and results in a number of surprising diagrammatic identities. We derive those and discuss their implications. These results are particularly pertinent in the context of active matter, whose surprising and often counterintuitive phenomenology rests wholly on the particle nature of the agents and their degrees of freedom as particles.

Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a K D <20 μM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.

Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a KD <20 μM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.

Prednisone for the prevention of tuberculosis-associated IRIS (randomized controlled trial): Impact on the health-related quality of life

Background

Tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) is an important complication in patients with HIV-associated tuberculosis (TB) starting antiretroviral treatment (ART) in sub-Saharan Africa. The PredART-trial recently showed that prophylactic prednisone reduces the incidence of paradoxical TB-IRIS by 30% in a population at high risk. This paper reports the impact of the intervention on health-related quality of life (HRQoL), a secondary endpoint of the trial, measured by an amended version of the PROQOL-HIV instrument—the instrument’s validity and reliability is also assessed.

Methods

A total of 240 adult participants (antiretroviral treatment (ART)-naïve, TB-HIV co-infected with CD4 count ≤100 cells/μL) were recruited and randomized (1:1) to (1) a prednisone arm or (2) a placebo arm. In this sub-study of the PredART-trial we evaluated (1) the performance of an HIV-specific HR-QoL instrument amended for TB-IRIS, i.e., the PROQOL-HIV/TB in patients with HIV-associated TB starting ART (reliability, internal and external construct validity and invariance across time) and (2) the impact of prednisone on self-reported HR-QoL in this population through mixed models.

Results

The PROQOL-HIV/TB scale displayed acceptable internal reliability and good internal and external validity. This instrument, including the factor structure with the eight sub-dimensions, can thus be applied for measuring HR-QoL among HIV-TB patients at high risk for TB-IRIS. Prophylactic prednisone was statistically significantly associated only with the ‘Physical Health and Symptoms’-subscale: a four-week course of prednisone resulted in an earlier improvement in the physical dimension of HR-QoL compared to placebo.

Conclusion

We demonstrated that the PROQOL-HIV/TB scale adequately measures different aspects of self-reported HR-QoL in HIV-TB patients. Although more research is needed to understand how other domains related to HR-QoL can be improved, targeting patients at high risk for developing TB-IRIS with a four-week course of prednisone has a beneficial effect on the physical aspects of patient-reported quality of life.

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa

OBJECTIVES

The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.

METHODS

In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.

RESULTS

We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).

CONCLUSIONS

In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.

Functions of Stress-Induced Lipid Droplets in the Nervous System

Lipid droplets are highly dynamic intracellular organelles that store neutral lipids such as cholesteryl esters and triacylglycerols. They have recently emerged as key stress response components in many different cell types. Lipid droplets in the nervous system are mostly observed in vivo in glia, ependymal cells and microglia. They tend to become more numerous in these cell types and can also form in neurons as a consequence of ageing or stresses involving redox imbalance and lipotoxicity. Abundant lipid droplets are also a characteristic feature of several neurodegenerative diseases. In this minireview, we take a cell-type perspective on recent advances in our understanding of lipid droplet metabolism in glia, neurons and neural stem cells during health and disease. We highlight that a given lipid droplet subfunction, such as triacylglycerol lipolysis, can be physiologically beneficial or harmful to the functions of the nervous system depending upon cellular context. The mechanistic understanding of context-dependent lipid droplet functions in the nervous system is progressing apace, aided by new technologies for probing the lipid droplet proteome and lipidome with single-cell type precision.

The Properties and Functions of Glial Cell Types of the Hypothalamic Median Eminence

The median eminence (ME) is part of the neuroendocrine system (NES) that functions as a crucial interface between the hypothalamus and pituitary gland. The ME contains many non-neuronal cell types, including oligodendrocytes, oligodendrocyte precursor cells (OPCs), tanycytes, astrocytes, pericytes, microglia and other immune cells, which may be involved in the regulation of NES function. For example, in mice, ablation of tanycytes (a special class of ependymal glia with stem cell-like functions) results in weight gain, feeding, insulin insensitivity and increased visceral adipose, consistent with the demonstrated ability of these cells to sense and transport both glucose and leptin, and to differentiate into neurons that control feeding and metabolism in the hypothalamus. To give a further example, OPCs in the ME of mice have been shown to rapidly respond to dietary signals, in turn controlling composition of the extracellular matrix in the ME, derived from oligodendrocyte-lineage cells, which may contribute to the previously described role of these cells in actively maintaining leptin-receptor-expressing dendrites in the ME. In this review, we explore and discuss recent advances such as these, that have developed our understanding of how the various cell types of the ME contribute to its function in the NES as the interface between the hypothalamus and pituitary gland. We also highlight avenues of future research which promise to uncover additional functions of the ME and the glia, stem and progenitor cells it contains.

Application of direct stochastic optical reconstruction microscopy (dSTORM) to the histological analysis of human glomerular disease

Electron microscopy (EM) following immunofluorescence (IF) imaging is a vital tool for the diagnosis of human glomerular diseases, but the implementation of EM is limited to specialised institutions and it is not available in many countries. Recent progress in fluorescence microscopy now enables conventional widefield fluorescence microscopes to be adapted at modest cost to provide resolution below 50 nm in biological specimens. We show that stochastically switched single-molecule localisation microscopy can be applied to clinical histological sections stained with standard IF techniques and that such super-resolved IF may provide an alternative means to resolve ultrastructure to aid the diagnosis of kidney disease where EM is not available. We have implemented the direct stochastic optical reconstruction microscopy technique with human kidney biopsy frozen sections stained with clinically approved immunofluorescent probes for the basal laminae and immunoglobulin G deposits. Using cases of membranous glomerulonephritis, thin basement membrane lesion, and lupus nephritis, we compare this approach to clinical EM images and demonstrate enhanced imaging compared to conventional IF microscopy. With minor modifications in established IF protocols of clinical frozen renal biopsies, we believe the cost-effective adaptation of conventional widefield microscopes can be widely implemented to provide super-resolved image information to aid diagnosis of human glomerular disease.

Pathogenic ACVR1R206H activation by Activin A-induced receptor clustering and autophosphorylation

Fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG) are debilitating diseases that share causal mutations in ACVR1, a TGF-β family type I receptor. ACVR1R206H is a frequent mutation in both diseases. Pathogenic signaling via the SMAD1/5 pathway is mediated by Activin A, but how the mutation triggers aberrant signaling is not known. We show that ACVR1 is essential for Activin A-mediated SMAD1/5 phosphorylation and is activated by two distinct mechanisms. Wild-type ACVR1 is activated by the Activin type I receptors, ACVR1B/C. In contrast, ACVR1R206H activation does not require upstream kinases, but is predominantly activated via Activin A-dependent receptor clustering, which induces its auto-activation. We use optogenetics and live-imaging approaches to demonstrate Activin A-induced receptor clustering and show it requires the type II receptors ACVR2A/B. Our data provide molecular mechanistic insight into the pathogenesis of FOP and DIPG by linking the causal activating genetic mutation to disrupted signaling.

A molecular perspective of mammalian autophagosome biogenesis

Autophagy is a highly conserved process and is essential for the maintenance of cellular homeostasis. Autophagy occurs at a basal level in all cells, but it can be up-regulated during stress, starvation, or infection. Misregulation of autophagy has been linked to various disorders, including cancer, neurodegeneration, and immune diseases. Here, we discuss the essential proteins acting in the formation of an autophagosome, with a focus on the ULK and VPS34 kinase complexes, phosphatidylinositol 3-phosphate effector proteins, and the transmembrane autophagy-related protein ATG9. The function and regulation of these and other autophagy-related proteins acting during formation will be addressed, in particular during amino acid starvation.