Clinical Outcomes of Immune Checkpoint Inhibitors in Unique Cohorts Underrepresented in Clinical Trials.

Regulatory approval of immune checkpoint inhibitors (ICIs) was based on results of large, randomized clinical trials, resulting in limited outcomes data in patient cohorts typically underrepresented in such trials. The objective of this study was to evaluate the efficacy and safety of ICIs in these unique patient cohorts. This is a multicenter, retrospective analysis of real-world data at six academic and community clinics in the United States from 1 January 2011 to 1 April 2018. Patients were included if they had received at least one cycle of ICI treatment. Unique patient cohorts included age > 75 years, non-White race, positive smoking history, ECOG performance status (PS) ≥ 2, BMI ≥ 30 kg/m2, autoimmune diseases (AIDs), chronic viral infections (CVI), extensive prior lines of therapy (LOTs), or >three metastatic sites. Immune-related adverse events (irAEs), overall survival (OS), and time to treatment failure were evaluated in the entire cohort and in NSCLC patients treated with PD-(L)1 monotherapy. Outcomes and their association with unique patient cohorts were compared on univariate analysis and multivariate analysis to those without a particular characteristic in the entire NSCLC PD-(L)1 monotherapy cohorts. In total, 1453 patients were included: 56.5%-smokers, 30.4%-non-White, 22.8%-elderly, 20.8%-ECOG PS ≥ 2, 15.7%-history of AIDs, and 4.7%-history of CVI. The common ICIs were nivolumab (37.1%) and pembrolizumab (22.2%). Black patients, compared to White patients, experienced fewer irAEs (OR 0.54, p < 0.001). An ECOG PS of ≥2 (HR = 2.01, p < 0.001) and an increased number of previous LOTs were associated with poor OS (the median OS of 26.2 vs. 16.2 vs. 9.6 months for one vs. two vs. three prior LOTs, p < 0.001). The above results were confirmed in anti-PD-(L)1 monotherapy non-small cell lung cancer patients (n = 384). Overall, ICIs were safe and efficacious in these typically underrepresented patient cohorts. We noted ECOG PS ≥ 2 and an increased prior LOTs were associated with poor ICI efficacy, and Black patients, compared to White patients, experienced fewer irAEs.

De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features.

Selenophosphate synthetase (SEPHS) plays an essential role in selenium metabolism. Two mammalian SEPHS paralogues, SEPHS1 and SEPHS2, share high sequence identity and structural homology with SEPHS. Here, we report nine individuals from eight families with developmental delay, growth and feeding problems, hypotonia, and dysmorphic features, all with heterozygous missense variants in SEPHS1. Eight of these individuals had a recurrent variant at amino acid position 371 of SEPHS1 (p.Arg371Trp, p.Arg371Gln, and p.Arg371Gly); seven of these variants were known to be de novo. Structural modeling and biochemical assays were used to understand the effect of these variants on SEPHS1 function. We found that a variant at residue Trp352 results in local structural changes of the C-terminal region of SEPHS1 that decrease the overall thermal stability of the enzyme. In contrast, variants of a solvent-exposed residue Arg371 do not impact enzyme stability and folding but could modulate direct protein-protein interactions of SEPSH1 with cellular factors in promoting cell proliferation and development. In neuronal SH-SY5Y cells, we assessed the impact of SEPHS1 variants on cell proliferation and ROS production and investigated the mRNA expression levels of genes encoding stress-related selenoproteins. Our findings provided evidence that the identified SEPHS1 variants enhance cell proliferation by modulating ROS homeostasis. Our study supports the hypothesis that SEPHS1 plays a critical role during human development and provides a basis for further investigation into the molecular mechanisms employed by SEPHS1. Furthermore, our data suggest that variants in SEPHS1 are associated with a neurodevelopmental disorder.

Genotype-phenotype correlations in RHOBTB2-associated neurodevelopmental disorders.

PURPOSE: Missense variants clustering in the BTB domain region of RHOBTB2 cause a developmental and epileptic encephalopathy with early-onset seizures and severe intellectual disability. METHODS: By international collaboration, we assembled individuals with pathogenic RHOBTB2 variants and a variable spectrum of neurodevelopmental disorders. By western blotting, we investigated the consequences of missense variants in vitro. RESULTS: In accordance with previous observations, de novo heterozygous missense variants in the BTB domain region led to a severe developmental and epileptic encephalopathy in 16 individuals. Now, we also identified de novo missense variants in the GTPase domain in 6 individuals with apparently more variable neurodevelopmental phenotypes with or without epilepsy. In contrast to variants in the BTB domain region, variants in the GTPase domain do not impair proteasomal degradation of RHOBTB2 in vitro, indicating different functional consequences. Furthermore, we observed biallelic splice-site and truncating variants in 9 families with variable neurodevelopmental phenotypes, indicating that complete loss of RHOBTB2 is pathogenic as well. CONCLUSION: By identifying genotype-phenotype correlations regarding location and consequences of de novo missense variants in RHOBTB2 and by identifying biallelic truncating variants, we further delineate and expand the molecular and clinical spectrum of RHOBTB2-related phenotypes, including both autosomal dominant and recessive neurodevelopmental disorders.

A Scalable Approach to Modeling on Accelerated Neuromorphic Hardware.

Neuromorphic systems open up opportunities to enlarge the explorative space for computational research. However, it is often challenging to unite efficiency and usability. This work presents the software aspects of this endeavor for the BrainScaleS-2 system, a hybrid accelerated neuromorphic hardware architecture based on physical modeling. We introduce key aspects of the BrainScaleS-2 Operating System: experiment workflow, API layering, software design, and platform operation. We present use cases to discuss and derive requirements for the software and showcase the implementation. The focus lies on novel system and software features such as multi-compartmental neurons, fast re-configuration for hardware-in-the-loop training, applications for the embedded processors, the non-spiking operation mode, interactive platform access, and sustainable hardware/software co-development. Finally, we discuss further developments in terms of hardware scale-up, system usability, and efficiency.

Semi-empirical quantum optics for mid-infrared molecular nanophotonics.

Nanoscale infrared (IR) resonators with sub-diffraction limited mode volumes and open geometries have emerged as new platforms for implementing cavity quantum electrodynamics at room temperature. The use of IR nanoantennas and tip nanoprobes to study strong light-matter coupling of molecular vibrations with the vacuum field can be exploited for IR quantum control with nanometer spatial and femtosecond temporal resolution. In order to advance the development of molecule-based quantum nanophotonics in the mid-IR, we propose a generally applicable semi-empirical methodology based on quantum optics to describe light-matter interaction in systems driven by mid-IR femtosecond laser pulses. The theory is shown to reproduce recent experiments on the acceleration of the vibrational relaxation rate in infrared nanostructures. It also provides physical insights on the implementation of coherent phase rotations of the near-field using broadband nanotips. We then apply the quantum framework to develop general tip-design rules for the experimental manipulation of vibrational strong coupling and Fano interference effects in open infrared resonators. We finally propose the possibility of transferring the natural anharmonicity of molecular vibrational levels to the resonator near-field in the weak coupling regime to implement intensity-dependent phase shifts of the coupled system response with strong pulses and develop a vibrational chirping model to understand the effect. The semi-empirical quantum theory is equivalent to first-principles techniques based on Maxwell's equations, but its lower computational cost suggests its use as a rapid design tool for the development of strongly coupled infrared nanophotonic hardware for applications ranging from quantum control of materials to quantum information processing.

The BrainScaleS-2 Accelerated Neuromorphic System With Hybrid Plasticity.

Since the beginning of information processing by electronic components, the nervous system has served as a metaphor for the organization of computational primitives. Brain-inspired computing today encompasses a class of approaches ranging from using novel nano-devices for computation to research into large-scale neuromorphic architectures, such as TrueNorth, SpiNNaker, BrainScaleS, Tianjic, and Loihi. While implementation details differ, spiking neural networks-sometimes referred to as the third generation of neural networks-are the common abstraction used to model computation with such systems. Here we describe the second generation of the BrainScaleS neuromorphic architecture, emphasizing applications enabled by this architecture. It combines a custom analog accelerator core supporting the accelerated physical emulation of bio-inspired spiking neural network primitives with a tightly coupled digital processor and a digital event-routing network.

Emulating Dendritic Computing Paradigms on Analog Neuromorphic Hardware.

BrainScaleS-2 is an accelerated and highly configurable neuromorphic system with physical models of neurons and synapses. Beyond networks of spiking point neurons, it allows for the implementation of user-defined neuron morphologies. Both passive propagation of electric signals between compartments as well as dendritic spikes and plateau potentials can be emulated. In this paper, three multi-compartment neuron morphologies are chosen to demonstrate passive propagation of postsynaptic potentials, spatio-temporal coincidence detection of synaptic inputs in a dendritic branch, and the replication of the BAC burst firing mechanism found in layer 5 pyramidal neurons of the neocortex.

CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation.

Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In Saccharomyces cerevisiae, γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub-assemblies, which associate helically to template MT growth. γTuRC assembly provides a key point of regulation for the MT cytoskeleton. Here, we combine crosslinking mass spectrometry, X-ray crystallography, and cryo-EM structures of both monomeric and dimeric γTuSCs, and open and closed helical γTuRC assemblies in complex with Spc110p to elucidate the mechanisms of γTuRC assembly. γTuRC assembly is substantially aided by the evolutionarily conserved CM1 motif in Spc110p spanning a pair of adjacent γTuSCs. By providing the highest resolution and most complete views of any γTuSC assembly, our structures allow phosphorylation sites to be mapped, surprisingly suggesting that they are mostly inhibitory. A comparison of our structures with the CM1 binding site in the human γTuRC structure at the interface between GCP2 and GCP6 allows for the interpretation of significant structural changes arising from CM1 helix binding to metazoan γTuRC.

Microtubule-associated proteins and motors required for ectopic microtubule array formation in Saccharomyces cerevisiae.

The mitotic spindle is resilient to perturbation due to the concerted, and sometimes redundant, action of motors and microtubule-associated proteins. Here, we utilize an inducible ectopic microtubule nucleation site in the nucleus of Saccharomyces cerevisiae to study three necessary steps in the formation of a bipolar array: the recruitment of the γ-tubulin complex, nucleation and elongation of microtubules (MTs), and the organization of MTs relative to each other. This novel tool, an Spc110 chimera, reveals previously unreported roles of the microtubule-associated proteins Stu2, Bim1, and Bik1, and the motors Vik1 and Kip3. We report that Stu2 and Bim1 are required for nucleation and that Bik1 and Kip3 promote nucleation at the ectopic site. Stu2, Bim1, and Kip3 join their homologs XMAP215, EB1 and kinesin-8 as promoters of microtubule nucleation, while Bik1 promotes MT nucleation indirectly via its role in SPB positioning. Furthermore, we find that the nucleation activity of Stu2 in vivo correlates with its polymerase activity in vitro. Finally, we provide the first evidence that Vik1, a subunit of Kar3/Vik1 kinesin-14, promotes microtubule minus end focusing at the ectopic site.

A Combined Experimental-Theoretical Study on Diels-Alder Reaction with Bio-Based Furfural: Towards Renewable Aromatics.

The synthesis of relevant renewable aromatics from bio-based furfural derivatives and cheap alkenes is carried out by using a Diels-Alder/aromatization sequence. The prediction and the control of the ortho/meta selectivity in the Diels-Alder step is an important issue to pave the way to a wide range of renewable aromatics, but it remains a challenging task. A combined experimental-theoretical approach reveals that, as a general trend, ortho and meta cycloadducts are the kinetic and thermodynamic products, respectively. The nature of substituents, both on the dienes and dienophiles, significantly impacts the feasibility of the reaction, through a modulation on the nucleo- and electrophilicity of the reagents, as well as the ortho/meta ratio. We show that the ortho/meta selectivity at the reaction equilibrium stems from a subtle interplay between charge interactions, favoring the ortho products, and steric interactions, favoring the meta isomers. This work also points towards a path to optimize the aromatization step.

De Novo Variants in the ATPase Module of MORC2 Cause a Neurodevelopmental Disorder with Growth Retardation and Variable Craniofacial Dysmorphism.

MORC2 encodes an ATPase that plays a role in chromatin remodeling, DNA repair, and transcriptional regulation. Heterozygous variants in MORC2 have been reported in individuals with autosomal-dominant Charcot-Marie-Tooth disease type 2Z and spinal muscular atrophy, and the onset of symptoms ranges from infancy to the second decade of life. Here, we present a cohort of 20 individuals referred for exome sequencing who harbor pathogenic variants in the ATPase module of MORC2. Individuals presented with a similar phenotype consisting of developmental delay, intellectual disability, growth retardation, microcephaly, and variable craniofacial dysmorphism. Weakness, hyporeflexia, and electrophysiologic abnormalities suggestive of neuropathy were frequently observed but were not the predominant feature. Five of 18 individuals for whom brain imaging was available had lesions reminiscent of those observed in Leigh syndrome, and five of six individuals who had dilated eye exams had retinal pigmentary abnormalities. Functional assays revealed that these MORC2 variants result in hyperactivation of epigenetic silencing by the HUSH complex, supporting their pathogenicity. The described set of morphological, growth, developmental, and neurological findings and medical concerns expands the spectrum of genetic disorders resulting from pathogenic variants in MORC2.

In Liquid Infrared Scattering Scanning Near-Field Optical Microscopy for Chemical and Biological Nanoimaging.

Imaging biological systems with simultaneous intrinsic chemical specificity and nanometer spatial resolution in their typical native liquid environment has remained a long-standing challenge. Here, we demonstrate a general approach of chemical nanoimaging in liquid based on infrared scattering scanning near-field optical microscopy (IR s-SNOM). It is enabled by combining AFM operation in a fluid cell with evanescent IR illumination via total internal reflection, which provides spatially confined excitation for minimized IR water absorption, reduced far-field background, and enhanced directional signal emission and sensitivity. We demonstrate in-liquid IR s-SNOM vibrational nanoimaging and conformational identification of catalase nanocrystals and spatio-spectral analysis of biomimetic peptoid sheets with monolayer sensitivity and chemical specificity at the few zeptomole level. This work establishes the principles of in-liquid and in situ IR s-SNOM spectroscopic chemical nanoimaging and its general applicability to biomolecular, cellular, catalytic, electrochemical, or other interfaces and nanosystems in liquids or solutions.

Vibrational exciton nanoimaging of phases and domains in porphyrin nanocrystals.

Much of the electronic transport, photophysical, or biological functions of molecular materials emerge from intermolecular interactions and associated nanoscale structure and morphology. However, competing phases, defects, and disorder give rise to confinement and many-body localization of the associated wavefunction, disturbing the performance of the material. Here, we employ vibrational excitons as a sensitive local probe of intermolecular coupling in hyperspectral infrared scattering scanning near-field optical microscopy (IR s-SNOM) with complementary small-angle X-ray scattering to map multiscale structure from molecular coupling to long-range order. In the model organic electronic material octaethyl porphyrin ruthenium(II) carbonyl (RuOEP), we observe the evolution of competing ordered and disordered phases, in nucleation, growth, and ripening of porphyrin nanocrystals. From measurement of vibrational exciton delocalization, we identify coexistence of ordered and disordered phases in RuOEP that extend down to the molecular scale. Even when reaching a high degree of macroscopic crystallinity, identify significant local disorder with correlation lengths of only a few nanometers. This minimally invasive approach of vibrational exciton nanospectroscopy and -imaging is generally applicable to provide the molecular-level insight into photoresponse and energy transport in organic photovoltaics, electronics, or proteins.

Direct Catalytic Conversion of Furfural to Furan-derived Amines in the Presence of Ru-based Catalyst.

The production of amine intermediates from biomass is capturing increasing attention. Herein, a simple and efficient preparation of l furan-derived amines was developed [e.g., 1-(furan-2-yl)-4-methylpentan-2-amine] with high yield (up to 95 %) from (E)-1-(furan-2-yl)-5-methylhex-1-en-3-one. The catalyst used was Ru/C, and it was recyclable up to the fourth cycle. To further realize cost-efficiency, a one-reactor tandem concept was attempted. To this aim direct reaction from furfural was investigated. A high yield (74 %) towards 1-(furan-2-yl)-4-methylpentan-2-amine could be achieved starting directly from furfural in the presence of methyl isobutyl ketone, NH3 , H2 , and Ru/C catalyst.

Accelerated Physical Emulation of Bayesian Inference in Spiking Neural Networks.

The massively parallel nature of biological information processing plays an important role due to its superiority in comparison to human-engineered computing devices. In particular, it may hold the key to overcoming the von Neumann bottleneck that limits contemporary computer architectures. Physical-model neuromorphic devices seek to replicate not only this inherent parallelism, but also aspects of its microscopic dynamics in analog circuits emulating neurons and synapses. However, these machines require network models that are not only adept at solving particular tasks, but that can also cope with the inherent imperfections of analog substrates. We present a spiking network model that performs Bayesian inference through sampling on the BrainScaleS neuromorphic platform, where we use it for generative and discriminative computations on visual data. By illustrating its functionality on this platform, we implicitly demonstrate its robustness to various substrate-specific distortive effects, as well as its accelerated capability for computation. These results showcase the advantages of brain-inspired physical computation and provide important building blocks for large-scale neuromorphic applications.

Purcell-Enhanced Spontaneous Emission of Molecular Vibrations.

Infrared (IR) spectroscopy of molecular vibrations provides insight into molecular structure, coupling, and dynamics. However, picosecond scale intermolecular and intramolecular many-body interactions, nonradiative relaxation, absorption, and thermalization typically dominate over IR spontaneous emission. We demonstrate how coupling to a resonant IR antenna can enhance spontaneous emission of molecular vibrations. Using time-domain nanoprobe spectroscopy we observe an up to 50% decrease in vibrational dephasing time T_{2,vib}, based on the coupling-induced population decay with T_{κ}≃550 fs and an associated Purcell factor of >10^{6}. This rate enhancement of the spontaneous emission of antenna-coupled molecular vibrations opens new avenues for IR coherent control, quantum information processing, and quantum chemistry.

Disruption of PHF21A causes syndromic intellectual disability with craniofacial anomalies, epilepsy, hypotonia, and neurobehavioral problems including autism.

Background: PHF21A has been associated with intellectual disability and craniofacial anomalies based on its deletion in the Potocki-Shaffer syndrome region at 11p11.2 and its disruption in three patients with balanced translocations. In addition, three patients with de novo truncating mutations in PHF21A were reported recently. Here, we analyze genomic data from seven unrelated individuals with mutations in PHF21A and provide detailed clinical descriptions, further expanding the phenotype associated with PHF21A haploinsufficiency. Methods: Diagnostic trio whole exome sequencing, Sanger sequencing, use of GeneMatcher, targeted gene panel sequencing, and MiSeq sequencing techniques were used to identify and confirm variants. RT-qPCR was used to measure the normal expression pattern of PHF21A in multiple human tissues including 13 different brain tissues. Protein-DNA modeling was performed to substantiate the pathogenicity of the missense mutation. Results: We have identified seven heterozygous coding mutations, among which six are de novo (not maternal in one). Mutations include four frameshifts, one nonsense mutation in two patients, and one heterozygous missense mutation in the AT Hook domain, predicted to be deleterious and likely to cause loss of PHF21A function. We also found a new C-terminal domain composed of an intrinsically disordered region. This domain is truncated in six patients and thus likely to play an important role in the function of PHF21A, suggesting that haploinsufficiency is the likely underlying mechanism in the phenotype of seven patients. Our results extend the phenotypic spectrum of PHF21A mutations by adding autism spectrum disorder, epilepsy, hypotonia, and neurobehavioral problems. Furthermore, PHF21A is highly expressed in the human fetal brain, which is consistent with the neurodevelopmental phenotype. Conclusion: Deleterious nonsense, frameshift, and missense mutations disrupting the AT Hook domain and/or an intrinsically disordered region in PHF21A were found to be associated with autism spectrum disorder, epilepsy, hypotonia, neurobehavioral problems, tapering fingers, clinodactyly, and syndactyly, in addition to intellectual disability and craniofacial anomalies. This suggests that PHF21A is involved in autism spectrum disorder and intellectual disability, and its haploinsufficiency causes a diverse neurological phenotype.

Demonstrating Advantages of Neuromorphic Computation: A Pilot Study.

Neuromorphic devices represent an attempt to mimic aspects of the brain's architecture and dynamics with the aim of replicating its hallmark functional capabilities in terms of computational power, robust learning and energy efficiency. We employ a single-chip prototype of the BrainScaleS 2 neuromorphic system to implement a proof-of-concept demonstration of reward-modulated spike-timing-dependent plasticity in a spiking network that learns to play a simplified version of the Pong video game by smooth pursuit. This system combines an electronic mixed-signal substrate for emulating neuron and synapse dynamics with an embedded digital processor for on-chip learning, which in this work also serves to simulate the virtual environment and learning agent. The analog emulation of neuronal membrane dynamics enables a 1000-fold acceleration with respect to biological real-time, with the entire chip operating on a power budget of 57 mW. Compared to an equivalent simulation using state-of-the-art software, the on-chip emulation is at least one order of magnitude faster and three orders of magnitude more energy-efficient. We demonstrate how on-chip learning can mitigate the effects of fixed-pattern noise, which is unavoidable in analog substrates, while making use of temporal variability for action exploration. Learning compensates imperfections of the physical substrate, as manifested in neuronal parameter variability, by adapting synaptic weights to match respective excitability of individual neurons.

ALG11-CDG syndrome: Expanding the phenotype.

ALG11-Congenital Disorder of Glycosylation (ALG11-CDG, also known as congenital disorder of glycosylation type Ip) is an inherited inborn error of metabolism due to abnormal protein and lipid glycosylation. We describe two unrelated patients with ALG11-CDG due to novel mutations, review the literature of previously described affected individuals, and further expand the clinical phenotype. Both affected individuals reported here had severe psychomotor disabilities and epilepsy. Their fibroblasts synthesized truncated precursor glycan structures, consistent with ALG11-CDG, while also showing hypoglycosylation of a novel biomarker, GP130. Surprisingly, one patient presented with normal transferrin glycosylation profile, a feature that has not been reported previously in patients with ALG11-CDG. Together, our data expand the clinical and mutational spectrum of ALG11-CDG.