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Rare coding variants in the triggering receptor expressed on myeloid cells 2 (TREM2) are associated with increased risk for Alzheimer's disease (AD), but how they confer this risk remains uncertain. We assessed binding of TREM2, AD‐associated TREM2 variants to various forms of Aβ and APOE in multiple assays. TREM2 interacts directly with various forms of Aβ, with highest affinity interactions observed between TREM2 and soluble Aβ42 oligomers. High‐affinity binding of TREM2 to Aβ oligomers is characterized by very slow dissociation. Pre‐incubation with Aβ is shown to block the interaction of APOE. In cellular assays, AD‐associated variants of TREM2 reduced the amount of Aβ42 internalized, and in NFAT assay, the R47H and R62H variants decreased NFAT signaling activity in response to Aβ42. These studies demonstrate i) a high‐affinity interaction between TREM2 and Aβ oligomers that can block interaction with another TREM2 ligand and ii) that AD‐associated TREM2 variants bind Aβ with equivalent affinity but show loss of function in terms of signaling and Aβ internalization. Synopsis Rare coding variants of TREM2 (R47H, R62H) are associated with increased risk for Alzheimer's disease (AD), but how they confer this risk remains uncertain. Using BioLayer Interferometry and other biochemical methods, TREM2 and AD‐associated variants binding to Aβ and APOE is examined. High‐affinity binding of TREM2 to Aβ oligomers is characterized by very slow dissociation which is almost “irreversible”. Pre‐incubation of TREM2 with Aβ oligomers is shown to block its interaction with APOE. AD‐associated TREM2 variants bound Aβ with equivalent affinity. AD‐associated TREM2 variants reduced Aβ42 internalization and NFAT signaling activity. AD‐associated TREM2 variants showed a partial loss of function. Graphical Abstract Rare coding variants of TREM2 (R47H, R62H) are associated with increased risk for Alzheimer's disease (AD), but how they confer this risk remains uncertain. Using BioLayer Interferometry and other biochemical methods, TREM2 and AD‐associated variants binding to Aβ and APOE is examined.

Lysosomal storage diseases are a group of metabolic disorders caused by deficiencies of several components of lysosomal function. Most commonly affected are lysosomal hydrolases, which are involved in the breakdown and recycling of a variety of complex molecules and cellular structures. The understanding of lysosomal biology has progressively improved over time. Lysosomes are no longer viewed as organelles exclusively involved in catabolic pathways, but rather as highly dynamic elements of the autophagic‐lysosomal pathway, involved in multiple cellular functions, including signaling, and able to adapt to environmental stimuli. This refined vision of lysosomes has substantially impacted on our understanding of the pathophysiology of lysosomal disorders. It is now clear that substrate accumulation triggers complex pathogenetic cascades that are responsible for disease pathology, such as aberrant vesicle trafficking, impairment of autophagy, dysregulation of signaling pathways, abnormalities of calcium homeostasis, and mitochondrial dysfunction. Novel technologies, in most cases based on high‐throughput approaches, have significantly contributed to the characterization of lysosomal biology or lysosomal dysfunction and have the potential to facilitate diagnostic processes, and to enable the identification of new therapeutic targets. Graphical Abstract In the last decade, our understanding of lysosomal storage diseases immensely improved. The current article comprehensively reviews recent advances in lysosomal storage diseases research and therapy development.

The assessment of variant effect predictor (VEP) performance is fraught with biases introduced by benchmarking against clinical observations. In this study, building on our previous work, we use independently generated measurements of protein function from deep mutational scanning (DMS) experiments for 26 human proteins to benchmark 55 different VEPs, while introducing minimal data circularity. Many top‐performing VEPs are unsupervised methods including EVE, DeepSequence and ESM‐1v, a protein language model that ranked first overall. However, the strong performance of recent supervised VEPs, in particular VARITY, shows that developers are taking data circularity and bias issues seriously. We also assess the performance of DMS and unsupervised VEPs for discriminating between known pathogenic and putatively benign missense variants. Our findings are mixed, demonstrating that some DMS datasets perform exceptionally at variant classification, while others are poor. Notably, we observe a striking correlation between VEP agreement with DMS data and performance in identifying clinically relevant variants, strongly supporting the validity of our rankings and the utility of DMS for independent benchmarking. Synopsis Common sources of bias in variant effect predictor benchmarking are assessed using data from deep mutational scanning experiments. ESM‐1v, EVE and DeepSequence are among the top performers on both functionally validated and clinically observed variants. Deep mutational scanning datasets from 26 human proteins are used to benchmark 55 computational predictors of missense variant effect. The top‐performing methods include several very recent predictors and are based mostly on unsupervised machine learning methodologies. There is a strong correlation between predictor performance when benchmarked against deep mutational scanning data and clinical variants. Graphical Abstract Common sources of bias in variant effect predictor benchmarking are assessed using data from deep mutational scanning experiments. ESM‐1v, EVE and DeepSequence are among the top performers on both functionally validated and clinically observed variants.

Lysosomes are cell organelles that degrade macromolecules to recycle their components. If lysosomal degradative function is impaired, e.g., due to mutations in lysosomal enzymes or membrane proteins, lysosomal storage diseases (LSDs) can develop. LSDs manifest often with neurodegenerative symptoms, typically starting in early childhood, and going along with a strongly reduced life expectancy and quality of life. We show here that small molecule activation of the Ca 2+ ‐permeable endolysosomal two‐pore channel 2 (TPC2) results in an amelioration of cellular phenotypes associated with LSDs such as cholesterol or lipofuscin accumulation, or the formation of abnormal vacuoles seen by electron microscopy. Rescue effects by TPC2 activation, which promotes lysosomal exocytosis and autophagy, were assessed in mucolipidosis type IV (MLIV), Niemann–Pick type C1, and Batten disease patient fibroblasts, and in neurons derived from newly generated isogenic human iPSC models for MLIV and Batten disease. For in vivo proof of concept, we tested TPC2 activation in the MLIV mouse model. In sum, our data suggest that TPC2 is a promising target for the treatment of different types of LSDs, both in vitro and in‐vivo . Synopsis Mutations in proteins of the endolysosomal machinery such as lysosomal enzymes or lysosomal membrane proteins often result in severe neurodegenerative disease, including mucolipidosis type IV, Niemann Pick type C1, or Batten disease. Small molecule activation of the endolysosomal two‐pore channel 2 (TPC2) results in an amelioration of cellular phenotypes associated with lysosomal storage diseases (LSDs), such as the accumulation of cholesterol, lactosylceramide, or lipofuscin, or the formation of abnormal vacuoles. Rescue effects of the TPC2 agonist are demonstrated in LSD patient fibroblasts and neurons derived from newly generated isogenic human iPSC models for MLIV and Batten disease. Mechanistically, the fully preserved capability of TPC2 to promote lysosomal exocytosis and autophagy in these diseases is demonstrated, suggesting rescue effects by clearing intracellular debris. Expression patterns of TPC2 in the brain are examined using a newly engineered TPC2‐GFP reporter mouse model, complemented by qPCR analyses of human and mouse brain samples. In vivo efficacy of the PI(3,5)P2‐mimetic TPC2 agonist TPC2‐A1‐P is shown, restoring pathological hallmarks in a mouse model of MLIV. Graphical Abstract Mutations in proteins of the endolysosomal machinery such as lysosomal enzymes or lysosomal membrane proteins often result in severe neurodegenerative disease, including mucolipidosis type IV, Niemann–Pick type C1, or Batten disease.

Mitochondrial disease associated with the pathogenic m.3243A>G variant is a common, clinically heterogeneous, neurogenetic disorder. Using multiple linear regression and linear mixed modelling, we evaluated which commonly assayed tissue (blood N  = 231, urine N  = 235, skeletal muscle N  = 77) represents the m.3243A>G mutation load and mitochondrial DNA (mtDNA) copy number most strongly associated with disease burden and progression. m.3243A>G levels are correlated in blood, muscle and urine ( R 2  = 0.61–0.73). Blood heteroplasmy declines by ~2.3%/year; we have extended previously published methodology to adjust for age. In urine, males have higher mtDNA copy number and ~20% higher m.3243A>G mutation load; we present formulas to adjust for this. Blood is the most highly correlated mutation measure for disease burden and progression in m.3243A>G‐harbouring individuals; increasing age and heteroplasmy contribute ( R 2  = 0.27, P  < 0.001). In muscle, heteroplasmy, age and mtDNA copy number explain a higher proportion of variability in disease burden ( R 2  = 0.40, P  < 0.001), although activity level and disease severity are likely to affect copy number. Whilst our data indicate that age‐corrected blood m.3243A>G heteroplasmy is the most convenient and reliable measure for routine clinical assessment, additional factors such as mtDNA copy number may also influence disease severity. Synopsis The m.3243A>G pathogenic mtDNA variant is associated with a highly heterogeneous multisystem disorder and varying mutation levels across tissues. In this study, mutation levels were characterised in three commonly sampled tissues ‐ blood, urine, skeletal muscle ‐ and correlated with disease burden. Urine m.3243A>G heteroplasmy levels display more variability than blood levels and must be corrected for a ˜20% lower level in females. Blood m.3243A>G heteroplasmy levels must be corrected for a decline of ˜2.3% per year. Disease burden and progression are more strongly associated with blood m.3243A>G heteroplasmy levels than urine levels. 27% of the variance in disease burden can be attributed to blood m.3243A>G heteroplasmy and age. Age, m.3243A>G heteroplasmy level and mtDNA copy number in skeletal muscle explain 40% of the variance in disease burden. Graphical Abstract The m.3243A>G pathogenic mtDNA variant is associated with a highly heterogeneous multisystem disorder and varying mutation levels across tissues. In this study, mutation levels were characterised in three commonly sampled tissues ‐ blood, urine, skeletal muscle ‐ and correlated with disease burden.

Prevalence of type 2 diabetes (T2D) and obesity is increasing worldwide. Currently available therapies are not suited for all patients in the heterogeneous obese/T2D population, hence the need for novel treatments. Fibroblast growth factor 21 (FGF21) is considered a promising therapeutic agent for T2D/obesity. Native FGF21 has, however, poor pharmacokinetic properties, making gene therapy an attractive strategy to achieve sustained circulating levels of this protein. Here, adeno‐associated viral vectors (AAV) were used to genetically engineer liver, adipose tissue, or skeletal muscle to secrete FGF21. Treatment of animals under long‐term high‐fat diet feeding or of ob/ob mice resulted in marked reductions in body weight, adipose tissue hypertrophy and inflammation, hepatic steatosis, inflammation and fibrosis, and insulin resistance for > 1 year. This therapeutic effect was achieved in the absence of side effects despite continuously elevated serum FGF21. Furthermore, FGF21 overproduction in healthy animals fed a standard diet prevented the increase in weight and insulin resistance associated with aging. Our study underscores the potential of FGF21 gene therapy to treat obesity, insulin resistance, and T2D. Synopsis This study describes the use of adeno‐associated viral (AAV) vectors to achieve long‐term production of fibroblast growth factor 21 (FGF21) to treat obesity and insulin resistance. AAV‐FGF21 gene transfer to healthy animals also prevented age‐associated weight gain and insulin resistance. A one‐time administration of an AAV vector encoding FGF21 counteract obesity and insulin resistance for more than a year. The approach works in two different animal models of obesity, induced either by diet or genetic mutations. Administration of AAV‐FGF21 to healthy animals promotes healthy aging. AAV‐FGF21 pharmacological effects are demonstrated after genetic engineering of 3 different tissues (liver, adipose tissue and skeletal muscle). FGF21 gene therapy holds great translational potential in the fight against insulin resistance, T2D, obesity and related comorbidities. Graphical Abstract This study describes the use of adeno‐associated viral (AAV) vectors to achieve long‐term production of fibroblast growth factor 21 (FGF21) to treat obesity and insulin resistance. AAV‐FGF21 gene transfer to healthy animals also prevented age‐associated weight gain and insulin resistance.

Gene therapy using recombinant adeno‐associated virus (rAAV) vectors to treat blinding retinal dystrophies has become clinical reality. Therapeutically impactful targeting of photoreceptors still relies on subretinal vector delivery, which detaches the retina and harbours substantial risks of collateral damage, often without achieving widespread photoreceptor transduction. Herein, we report the development of novel engineered rAAV vectors that enable efficient targeting of photoreceptors via less invasive intravitreal administration. A unique in vivo selection procedure was performed, where an AAV2‐based peptide‐display library was intravenously administered in mice, followed by isolation of vector DNA from target cells after only 24 h. This stringent selection yielded novel vectors, termed AAV2.GL and AAV2.NN, which mediate widespread and high‐level retinal transduction after intravitreal injection in mice, dogs and non‐human primates. Importantly, both vectors efficiently transduce photoreceptors in human retinal explant cultures. As proof‐of‐concept, intravitreal Cnga3 delivery using AAV2.GL lead to cone‐specific expression of Cnga3 protein and rescued photopic cone responses in the Cnga3 −/− mouse model of achromatopsia. These novel rAAV vectors expand the clinical applicability of gene therapy for blinding human retinal dystrophies. Synopsis Ocular gene therapy aims to improve or preserve vision in patients with inherited blinding disorders. The current technology still relies on subretinal administration of therapeutic vectors, which harbours risks of collateral damage and only treats a small portion of the affected retina. This study presents two novel engineered viral vectors capable of widespread targeting of retinal cells through a less invasive delivery route. Novel vectors AAV2.GL and AAV2.NN achieve widespread photoreceptor transduction in mouse, dog and non‐human primate after single intravitreal delivery. AAV2.GL and AAV2.NN have cone and rod photoreceptor tropism. AAV2.NN outperforms existing vectors in targeting rod photoreceptors in mice. Gene supplementation using AAV2.GL rescues cone function and CNGA3 protein expression in the Cnga3 −/− mouse model of achromatopsia. Graphical Abstract Ocular gene therapy aims to improve or preserve vision in patients with inherited blinding disorders. The current technology still relies on subretinal administration of therapeutic vectors, which harbours risks of collateral damage and only treats a small portion of the affected retina. This study presents two novel engineered viral vectors capable of widespread targeting of retinal cells through a less invasive delivery route.

Chimeric antigen receptor (CAR) T cell therapy, together with checkpoint inhibition, has been celebrated as a breakthrough technology due to the substantial benefit observed in clinical trials with patients suffering from relapsed or refractory B‐cell malignancies. In this review, we provide a comprehensive overview of the clinical trials performed so far worldwide and analyze parameters such as targeted antigen and indication, CAR molecular design, CAR T cell manufacturing, anti‐tumor activities, and related toxicities. More than 200 CAR T cell clinical trials have been initiated so far, most of which aim to treat lymphoma or leukemia patients using CD19‐specific CARs. An increasing number of studies address solid tumors as well. Notably, not all clinical trials conducted so far have shown promising results. Indeed, in a few patients CAR T cell therapy resulted in severe adverse events with fatal outcome. Of note, less than 10% of the ongoing CAR T cell clinical trials are performed in Europe. Taking lead from our analysis, we discuss the problems and general hurdles preventing efficient clinical development of CAR T cells as well as opportunities, with a special focus on the European stage. Graphical Abstract Authoritative, insightful overview of the problems and general hurdles preventing efficient clinical development of chimeric antigen receptor (CAR) T cell therapy for cancer as well as future opportunities.

Gene and cell therapy research recently reached a fundamental milestone toward the goal to deliver new medicines for orphan diseases. In 2016, the European Commission granted market approval to GlaxoSmithKline (GSK) for ex vivo hematopoietic stem cell (HSC) gene therapy for the treatment of adenosine deaminase (ADA)‐deficient severe combined immunodeficiency (SCID), a very rare congenital disorder of the immune system. The new medicine, named Strimvelis™, is an advanced therapy medicinal product (ATMP) (Salmikangas et al , 2015 ) originally developed by the San Raffaele Telethon Institute for Gene Therapy (SR‐Tiget), a joint venture between Telethon Foundation and San Raffaele Scientific Institute. This ATMP is the first ex vivo stem cell gene therapy to receive regulatory approval anywhere in the world. Strimvelis™ consists of a single infusion of autologous gene‐corrected HSC and is prepared from the patient's own bone marrow (BM) HSCs, which are genetically modified using a gamma‐retroviral vector to insert a functional copy of the ADA gene. Graphical Abstract An engaging account of the long road to approval of the first ever ex‐vivo stem cell gene therapy to receive regulatory approval, Strimvelis™, indicated for the treatment of ADA‐deficient severe combined immunodeficiency (SCID).

Retinitis pigmentosa, caused predominantly by mutations in photoreceptor genes, currently lacks comprehensive treatment. We discover that retinal microglia contribute non‐cell autonomously to rod photoreceptor degeneration by primary phagocytosis of living rods. Using rd10 mice, we found that the initiation of rod degeneration is accompanied by early infiltration of microglia, upregulation of phagocytic molecules in microglia, and presentation of “eat‐me” signals on mutated rods. On live‐cell imaging, infiltrating microglia interact dynamically with photoreceptors via motile processes and engage in rapid phagocytic engulfment of non‐apoptotic rods. Microglial contribution to rod demise is evidenced by morphological and functional amelioration of photoreceptor degeneration following genetic ablation of retinal microglia. Molecular inhibition of microglial phagocytosis using the vitronectin receptor antagonist cRGD also improved morphological and functional parameters of degeneration. Our findings highlight primary microglial phagocytosis as a contributing mechanism underlying cell death in retinitis pigmentosa and implicate microglia as a potential cellular target for therapy. Synopsis In Retinitis pigmentosa (RP), retinal microglia are shown to potentiate the rate of rod photoreceptor death via phagocytic and pro‐inflammatory mechanisms. This process may be common to multiple genetic etiologies of RP in mouse models and in human patients. Microglial phagocytosis of rod photoreceptors was initiated at the start of rod apoptosis with early infiltration of retinal microglia into the outer retina, upregulation of phagocytic molecules in microglia, and exposure of PS, an “eat‐me” signal, on rod photoreceptors. Microglial phagocytosis of rods included apoptotic cells but also cells that have not yet been committed to apoptosis and are negative for apoptotic markers, indicating microglial clearance of stressed but living rods. Infiltrating microglia demonstrated dynamic interactions with photoreceptors via motile processes that culminate in the overt phagocytosis of non‐apoptotic rods. The contribution of infiltrating microglia to rod demise was demonstrated by structural and functional rescue of photoreceptor degeneration. Microglia‐directed interventions may be of potential utility in prolonging the survival of photoreceptors and deferring irreversible vision loss associated with RP of different genetic etiologies. Graphical Abstract In Retinitis pigmentosa (RP), retinal microglia are shown to potentiate the rate of rod photoreceptor death via phagocytic and pro‐inflammatory mechanisms. This process may be common to multiple genetic etiologies of RP in mouse models and in human patients.