Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer.

Microsatellite-stable colorectal cancer (MSS-CRC) is highly refractory to immunotherapy. Understanding tumor-intrinsic determinants of immunotherapy resistance is critical to improve MSS-CRC patient outcomes. Here, we demonstrate that high tumor expression of the core autophagy gene ATG16L1 is associated with poor clinical response to anti-PD-L1 therapy in KRAS-mutant tumors from IMblaze370 (NCT02788279), a large phase III clinical trial of atezolizumab (anti-PD-L1) in advanced metastatic MSS-CRC. Deletion of Atg16l1 in engineered murine colon cancer organoids inhibits tumor growth in primary (colon) and metastatic (liver and lung) niches in syngeneic female hosts, primarily due to increased sensitivity to IFN-γ-mediated immune pressure. ATG16L1 deficiency enhances programmed cell death of colon cancer organoids induced by IFN-γ and TNF, thus increasing their sensitivity to host immunity. In parallel, ATG16L1 deficiency reduces tumor stem-like populations in vivo independently of adaptive immune pressure. This work reveals autophagy as a clinically relevant mechanism of immune evasion and tumor fitness in MSS-CRC and provides a rationale for autophagy inhibition to boost immunotherapy responses in the clinic.

Modelling Based Approaches to Support Generic Drug Regulatory Submissions-Practical Considerations and Case Studies.

Model informed drug development (MiDD) is useful to predict in vivo exposure of drugs during various stages of the drug development process. This approach employs a variety of quantitative tools to assess the risks during the drug development process. One important tool in the MiDD tool kit is the Physiologically Based Pharmacokinetic Modelling (PBPK). This tool is extensively used to reduce the development cost and to accelerate the access of medicines to the patients. In this work, we provide an overview of PBPK modelling approaches in the generic drug development process, with a special emphasis on the bio-waiver applications. We describe herein approaches and common pitfalls while submitting model based justifications as a response to the regulatory deficiencies during the generic drug development process. With some in-house case studies, we have attempted to provide a clear path for PBPK model based justifications for bio-waivers. With this review, the gap between theoretical knowledge and practical application of modelling and simulation tools for generic drug product development could be potentially reduced.

Velocity tracking control best explains the modulation of saccade kinematics during eye-hand coordination.

Fast movements like saccadic eye movements that occur in the absence of sensory feedback are thought to be controlled by internal feedback. Such internal feedback provides an instantaneous estimate of the output, which serves as a proxy for sensory feedback, that can be used by the controller to correct deviations from the desired plan. In the predominant view, the desired plan/input is encoded in the form of a static displacement signal (endpoint model), believed to be encoded in the spatial map of the superior colliculus (SC). However, recent evidence has shown that SC neurons have a dynamic signal that correlates with saccade velocity, suggesting that information for velocity-based control is available for generating saccades. Motivated by this observation, we used a novel optimal control framework to test whether saccadic execution could be achieved by tracking a dynamic velocity signal at the input. We validated this velocity tracking model in a task where the peak saccade velocity was modulated by the speed of a concurrent hand movement independent of the saccade endpoint. A comparison showed that in this task, the velocity tracking model performed significantly better than the endpoint model. These results suggest that the saccadic system may have additional flexibility to incorporate a velocity-based internal feedback control when imposed by task goals or context.

Optimized Nonviral Gene Disruption in Primary Murine and Human Myeloid Cells.

Genetically engineered myeloid cells such as monocytes, macrophages, and dendritic cells have broad applications in basic and translational research. Their central roles in innate and adaptive immunity make them attractive as putative therapeutic cell products. However, efficient gene editing of primary myeloid cells presents unique challenges owing to their sensitivity to foreign nucleic acids and poor editing efficiencies using current methodologies (Hornung et al., Science 314:994-997, 2006; Coch et al., PLoS One 8:e71057, 2013; Bartok and Hartmann, Immunity 53:54-77, 2020; Hartmann, Adv Immunol 133:121-169, 2017; Bobadilla et al., Gene Ther 20:514-520, 2013; Schlee and Hartmann, Nat Rev Immunol 16:566-580, 2016; Leyva et al., BMC Biotechnol 11:13, 2011). This chapter describes nonviral CRISPR-mediated gene knockout in primary human and murine monocytes as well as monocyte-derived or bone marrow-derived macrophages and dendritic cells. Electroporation-mediated delivery of recombinant Cas9 complexed with synthetic guide RNAs can be applied for population-level disruption of single or multiple gene targets.

Context-specific early recruitment of small motor units in the shoulder muscle reflects a reach movement plan.

Understanding how motor plans are transformed into appropriate patterns of muscle activity is a central question in motor control. Although muscle activity during the delay period has not been reported using conventional electromyographic (EMG) approaches, we isolated motor unit activity using a high-density surface EMG signal from the anterior deltoid muscle to test whether heterogeneity in motor units could reveal early preparatory activity. Consistent with our previous work (Rungta SP, Basu D, Sendhilnathan N, Murthy A. J Neurophysiol 126: 451-463, 2021), we observed early selective recruitment of small amplitude size motor units during the delay period for hand movements similar to the observed early recruitment of small-amplitude motor units in neck muscles of nonhuman primates performing delayed saccade tasks. This early activity was spatially specific and increased with time and resembled an accumulation to threshold model that correlated with movement onset time. Such early recruitment of ramping motor units was observed at the single trial level as well. In contrast, no such recruitment of large amplitude size motor units, called nonrampers, was observed during the delay period. Instead, nonrampers became spatially specific and predicted movement onset time after the delay period. Interestingly, spatially specific delay period activity was only observed for hand movements but was absent for isometric force-driven cursor movements. Nonetheless, muscle activity was correlated with the time it took to initiate movements in both task conditions for nonrampers. Overall, our results reveal a novel heterogeneity in the EMG activity that allows the expression of early motor preparation via small amplitude size motor units that are differentially activated during movement initiation.NEW & NOTEWORTHY We studied the spatial and temporal aspects of response preparation in the anterior deltoid muscle using high-density surface EMG. Our results show that early spatially specific ramping activity that predicted reaction times could be accessed from muscle activity but was absent during isometric force-driven cursor movements. Such ramping activity could be quantified using an accumulator framework across trials, as well as within single trials, but was not observed in isometric reach tasks involving cursor movements.

Albumin-hitchhiking: Fostering the pharmacokinetics and anticancer therapeutics.

Nanotherapeutics demonstrate poor accumulation in the tumor microenvironment due to poor extravasation and penetration into the tumor. Therapeutics such as oligonucleotides, peptides and other biologicals suffer from low systemic half-life and rapid degradation. Albumin-hitchhiking has emerged as an effective strategy to enhance tumor-specific accumulation of various therapeutics. Hitchhiking on serum albumin (SA) have shown to improve biological half-life of various therapeutics including nanocarriers (NCs), biologics, oligonucleotides, vaccines, etc. In addition, passive and active accumulation of SA-riding therapeutics in the tumor, site-specific drug release, and SA-mediated endosomal escape have improved the potential of various anticancer modalities such as chemo-, immune-, vaccine, and gene therapies. In this review, we have discussed the advantages of employing SA-hitchhiking in anticancer therapies. In addition, vaccine strategies employing inherent lymph-nodes accumulating property of albumin have been discussed. We have presented a clinical overview of SA-hitchhiked formulations along with possible bottlenecks for improved clinical outcomes. We have also discussed the role of physiologically based pharmacokinetics (PBPK) modelling for efficient characterization of anti-cancer nanotherapeutics.

Neck muscle activity reflects neural patterns of sequential saccade planning in head-restrained primates.

Goal-directed behavior involves the transformation of neural movement plans into appropriate muscle activity patterns. Studies involving single saccades have shown that a rapid pathway links saccade planning in frontal eye fields (FEFs) to neck muscle activity. However, it is unknown if the rapid connection between FEF and neck muscle is also maintained during sequential saccade planning. Using neural recordings from FEF, and electromyographic (EMG) recordings from the dorsal neck muscles of head-restrained monkeys, we show that neural sequence planning signals are largely preserved in the neck EMG response. Like FEF movement neurons, we found that neck motor unit activity displayed an accumulation-to-threshold response before saccade onset. Responses of both neck motor units and FEF neurons displayed similar trends during saccade sequencing; multiple saccadic eye movements could be programmed in parallel, while processing bottlenecks, indexed by reduced accumulation rates, limited the extent of parallel programming. These results suggest that even without the need for overt head movements, neck muscle activity shows signatures of central gaze planning. We propose that multiple upcoming gaze plans are rapidly passed down from the FEF to the neck muscles to initiate recruitment for anticipated gaze movements. Similarities in neural and neck motor activity may enable synchronous yet controlled eye-head responses to sequential gaze shifts.NEW & NOTEWORTHY Gaze shifts, brought about by coordinated eye-head movements through the eye and neck muscle system, are a part of everyday behavior, yet the neuromuscular underpinnings of gaze sequences are unclear. Using a combination of behavioral analyses, neural recordings, and electromyographic recordings, we show that sequential saccade plans developing in neural oculomotor centers can be extracted from the neck muscle activity of head-restrained macaques. Neck motor units, thus provide a readout of central sequence planning signals.

Antigen-derived peptides engage the ER stress sensor IRE1α to curb dendritic cell cross-presentation.

Dendritic cells (DCs) promote adaptive immunity by cross-presenting antigen-based epitopes to CD8+ T cells. DCs process internalized protein antigens into peptides that enter the endoplasmic reticulum (ER), bind to major histocompatibility type I (MHC-I) protein complexes, and are transported to the cell surface for cross-presentation. DCs can exhibit activation of the ER stress sensor IRE1α without ER stress, but the underlying mechanism remains obscure. Here, we show that antigen-derived hydrophobic peptides can directly engage ER-resident IRE1α, masquerading as unfolded proteins. IRE1α activation depletes MHC-I heavy-chain mRNAs through regulated IRE1α-dependent decay (RIDD), curtailing antigen cross-presentation. In tumor-bearing mice, IRE1α disruption increased MHC-I expression on tumor-infiltrating DCs and enhanced recruitment and activation of CD8+ T cells. Moreover, IRE1α inhibition synergized with anti-PD-L1 antibody treatment to cause tumor regression. Our findings identify an unexpected cell-biological mechanism of antigen-driven IRE1α activation in DCs, revealing translational potential for cancer immunotherapy.

A Novel Approach to Justify Dissolution Differences in an Extended Release Drug Product using Physiologically Based Biopharmaceutics Modeling and Simulation.

Dr Reddy's Laboratories Ltd. developed generic version of XYZ extended release tablets (ER) and achieved bioequivalence as per criteria mentioned by USFDA in both fasting and fed conditions for higher strength formulation (1200 mg). However, on comparison of multimedia dissolution profiles in pH 4.5 acetate media, the f2 similarity value was <50. The lower strength formulation (600 mg) demonstrated faster dissolution profile. This was identified as strength-dependent sink condition difference and in vitro multiunit dissolution studies were used to justify sink differences between the higher and lower strengths. Additionally, a Physiologically Based Biopharmaceutics Model (PBBM) was developed using GastroPlusTM. The validity of this model was established using in-house human pharmacokinetic data. Further, this model was used to justify the insignificant in vivo impact of the faster dissolution profile for the lower strength formulation. This work provides a novel and less explored approach that can be used to obtain biowaiver for lower strength formulations when the standard biowaiver criteria cannot be met. This work also demonstrates the usefulness of PBBM to justify dissolution dissimilarity between dose proportional formulations and to evaluate its biopharmaceutics risk without the need for actual in vivo studies.

Structure-Based Design of Potent, Selective, and Orally Bioavailable VPS34 Kinase Inhibitors.

VPS34 is a class III phosphoinositide 3-kinase involved in endosomal trafficking and autophagosome formation. Inhibitors of VPS34 were believed to have value as anticancer agents, but genetic and pharmacological data suggest that sustained inhibition of VPS34 kinase activity may not be well tolerated. Here we disclose the identification of a novel series of dihydropyrazolopyrazinone compounds represented by compound 5 as potent, selective, and orally bioavailable VPS34 inhibitors through a structure-based design strategy. A water-interacting hydrogen bond acceptor within an appropriate distance to a hinge-binding element was found to afford significant VPS34 potency across chemical scaffolds. The selectivity of compound 5 over PIK family kinases arises from interactions between the hinge-binding element and the pseudo-gatekeeper residue Met682. As recent in vivo pharmacology data suggests that sustained inhibition of VPS34 kinase activity may not be tolerated, structure-activity relationships leading to VPS34 inhibition may be helpful for avoiding this target in other ATP-competitive kinase programs.

Neural mechanisms underlying the temporal control of sequential saccade planning in the frontal eye field.

Sequences of saccadic eye movements are instrumental in navigating our visual environment. While neural activity has been shown to ramp up to a threshold before single saccades, the neural underpinnings of multiple saccades is unknown. To understand the neural control of saccade sequences, we recorded from the frontal eye field (FEF) of macaque monkeys while they performed a sequential saccade task. We show that the concurrent planning of two saccade plans brings forth processing bottlenecks, specifically by decreasing the growth rate and increasing the threshold of saccade-related ramping activity. The rate disruption affected both saccade plans, and a computational model, wherein activity related to the two saccade plans mutually and asymmetrically inhibited each other, predicted the behavioral and neural results observed experimentally. Borrowing from models in psychology, our results demonstrate a capacity-sharing mechanism of processing bottlenecks, wherein multiple saccade plans in a sequence compete for the processing capacity by the perturbation of the saccade-related ramping activity. Finally, we show that, in contrast to movement-related neurons, visual activity in FEF neurons is not affected by the presence of multiple saccade targets, indicating that, for perceptually simple tasks, inhibition within movement-related neurons mainly instantiates capacity sharing. Taken together, we show how psychology-inspired models of capacity sharing can be mapped onto neural responses to understand the control of rapid saccade sequences.

Preparatory activity links the frontal eye field response with small amplitude motor unit recruitment of neck muscles during gaze planning.

A hallmark of intelligent behavior is that we can separate intention from action. To understand the mechanism that gates the flow of information between motor planning and execution, we compared the activity of frontal eye field neurons with motor unit activity from neck muscles in the presence of an intervening delay period in which spatial information regarding the target was available to plan a response. Although spatially specific delay period activity was present in the activity of frontal eye field neurons, it was absent in motor unit activity. Nonetheless, motor unit activity was correlated with the time it took to initiate saccades. Interestingly, we observed a heterogeneity of responses among motor units, such that only units with smaller amplitudes showed a clear modulation during the delay period. These small amplitude motor units also had higher spontaneous activity compared with the units which showed modulation only during the movement epoch. Taken together, our results suggest the activity of smaller motor units convey temporal information and explains how the delay period primes muscle activity leading to faster reaction times.NEW & NOTEWORTHY This study shows that the temporal aspects of a motor plan in the oculomotor circuitry can be accessed by peripheral neck muscles hundreds of milliseconds before the instruction to initiate a saccadic eye movement. The coupling between central and peripheral processes during the delay time is mediated by the recruitment pattern of motor units with smaller amplitude. These findings suggest that information processed in cortical areas could be read from periphery before execution.

Computational Mechanisms Mediating Inhibitory Control of Coordinated Eye-Hand Movements.

Significant progress has been made in understanding the computational and neural mechanisms that mediate eye and hand movements made in isolation. However, less is known about the mechanisms that control these movements when they are coordinated. Here, we outline our computational approaches using accumulation-to-threshold and race-to-threshold models to elucidate the mechanisms that initiate and inhibit these movements. We suggest that, depending on the behavioral context, the initiation and inhibition of coordinated eye-hand movements can operate in two modes-coupled and decoupled. The coupled mode operates when the task context requires a tight coupling between the effectors; a common command initiates both effectors, and a unitary inhibitory process is responsible for stopping them. Conversely, the decoupled mode operates when the task context demands weaker coupling between the effectors; separate commands initiate the eye and hand, and separate inhibitory processes are responsible for stopping them. We hypothesize that the higher-order control processes assess the behavioral context and choose the most appropriate mode. This computational mechanism can explain the heterogeneous results observed across many studies that have investigated the control of coordinated eye-hand movements and may also serve as a general framework to understand the control of complex multi-effector movements.

Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response.

Defective autophagy is strongly associated with chronic inflammation. Loss-of-function of the core autophagy gene Atg16l1 increases risk for Crohn's disease in part by enhancing innate immunity through myeloid cells such as macrophages. However, autophagy is also recognized as a mechanism for clearance of certain intracellular pathogens. These divergent observations prompted a re-evaluation of ATG16L1 in innate antimicrobial immunity. In this study, we found that loss of Atg16l1 in myeloid cells enhanced the killing of virulent Shigella flexneri (S.flexneri), a clinically relevant enteric bacterium that resides within the cytosol by escaping from membrane-bound compartments. Quantitative multiplexed proteomics of murine bone marrow-derived macrophages revealed that ATG16L1 deficiency significantly upregulated proteins involved in the glutathione-mediated antioxidant response to compensate for elevated oxidative stress, which simultaneously promoted S.flexneri killing. Consistent with this, myeloid-specific deletion of Atg16l1 in mice accelerated bacterial clearance in vitro and in vivo. Pharmacological induction of oxidative stress through suppression of cysteine import enhanced microbial clearance by macrophages. Conversely, antioxidant treatment of macrophages permitted S.flexneri proliferation. These findings demonstrate that control of oxidative stress by ATG16L1 and autophagy regulates antimicrobial immunity against intracellular pathogens.

Murine Monocyte and Macrophage Culture.

Myeloid progenitors in the bone marrow generate monocytes, macrophages, granulocytes and most dendritic cells. Even though these innate immune cells are part of the same lineage, each cell type plays a specific and critical role in tissue development, host defense and the generation of adaptive immunity. Protocols have been developed in the past to differentiate myeloid cell types from bone marrow cells, enabling functional investigation and furthering our understanding about their contribution to mammalian physiology. In this protocol, we describe a simple and rapid method to isolate monocytes from murine bone marrow, culture them for up to 5 days and lastly, differentiate them into bone marrow derived macrophages (Figure 1). Graphic abstract: Figure 1.Experimental outline depicting steps for murine monocyte and macrophage culture.

Neural correlates of goal-directed and non-goal-directed movements.

What are the cortical neural correlates that distinguish goal-directed and non-goal-directed movements? We investigated this question in the monkey frontal eye field (FEF), which is implicated in voluntary control of saccades. Here, we compared FEF activity associated with goal-directed (G) saccades and non-goal-directed (nG) saccades made by the monkey. Although the FEF neurons discharged before these nG saccades, there were three major differences in the neural activity: First, the variability in spike rate across trials decreased only for G saccades. Second, the local field potential beta-band power decreased during G saccades but did not change during nG saccades. Third, the time from saccade direction selection to the saccade onset was significantly longer for G saccades compared with nG saccades. Overall, our results reveal unexpected differences in neural signatures for G versus nG saccades in a brain area that has been implicated selectively in voluntary control. Taken together, these data add critical constraints to the way we think about saccade generation in the brain.

Spatiotemporal Coupling between Eye and Hand Trajectories during Curved Hand Movements.

Eye and hand movements are often made in isolation but for reaching movements they are usually coupled. Despite this, evidence for spatial coupling between the eye and hand effector is mixed and have usually been restricted to straight-line movements, while real-world hand movements have complex trajectories. Here, using a novel obstacle avoidance task where an obstacle appeared in an infrequent number of trials, we establish a stronger link between the saccade and hand trajectory during more naturalistic curved hand trajectories. We illustrate that the hand trajectory was coupled to the end-point of the saccade which was executed just prior to the hand movement onset. Interestingly, while the saccade end-point was related to whether the hand trajectory followed a straight or a curved path, the y-component of saccade end-point was related to whether the hand took a path passing from over or below the obstacle. Further, we observed a relationship between saccade locations and hand sub-movements where the number and timing of saccades and number of hand velocity peaks were related. These results illustrate a robust spatiotemporal and kinematic coupling between saccades and complex hand movement trajectories suggesting a shared kinematic representation underlying eye-hand movements.

Perceptual Priming Can Increase or Decrease With Aging.

A decline in declarative or explicit memory has been extensively characterized in cognitive aging and is a hallmark of cognitive impairments. However, whether and how implicit perceptual memory varies with aging or cognitive impairment is unclear. Here, we compared implicit perceptual memory and explicit memory measures in three groups of participants: (1) 59 healthy young volunteers (20-30 years); (2) 269 healthy old volunteers (50-90 years) and (3) 21 patients with mild cognitive impairment, i.e., MCI (50-90 years). To measure explicit memory, participants were tested on standard recognition and recall tasks. To measure implicit perceptual memory, we used a classic perceptual priming paradigm. Participants had to report the shape of a visual search pop-out target whose color or position was varied randomly across trials. Perceptual priming was measured as the speedup in response time for targets that repeated in color or position. Our main findings are as follows: (1) Explicit memory was weaker in old compared to young participants, and in MCI patients compared to age- and education-matched controls; (2) Surprisingly, perceptual priming did not always decline with age: color priming was smaller in older participants but position priming was larger; (3) Position priming was less frequent in the MCI group compared to matched controls; (4) Perceptual priming and explicit memory were uncorrelated across participants. Thus, perceptual priming can increase or decrease with age or cognitive impairment, but these changes do not covary with explicit memory.

Targeting Autophagy to Treat Cancer: Challenges and Opportunities.

Autophagy is a catabolic process that targets its cargo for lysosomal degradation. In addition to its function in maintaining tissue homeostasis, autophagy is recognized to play a context-dependent role in cancer. Autophagy may inhibit tumor initiation under specific contexts; however, a growing body of evidence supports a pro-tumorigenic role of this pathway in established disease. In this setting, autophagy drives treatment resistance, metabolic changes, and immunosuppression both in a tumor-intrinsic and extrinsic manner. This observation has prompted renewed interest in targeting autophagy for cancer therapy. Novel genetic models have proven especially insightful, revealing unique and overlapping roles of individual autophagy-related genes in tumor progression. Despite identification of pharmacologically actionable nodes in the pathway, fundamental challenges still exist for successful therapeutic inhibition of autophagy. Here we summarize the current understanding of autophagy as a driver of resistance against targeted and immuno-therapies and highlight knowledge gaps that, if addressed, may provide meaningful advances in the treatment of cancer.

Neutrophil serine protease 4 is required for mast cell-dependent vascular leakage.

Vascular leakage, or edema, is a serious complication of acute allergic reactions. Vascular leakage is triggered by the release of histamine and serotonin from granules within tissue-resident mast cells. Here, we show that expression of Neutrophil Serine Protease 4 (NSP4) during the early stages of mast cell development regulates mast cell-mediated vascular leakage. In myeloid precursors, the granulocyte-macrophage progenitors (GMPs), loss of NSP4 results in the decrease of cellular levels of histamine, serotonin and heparin/heparan sulfate. Mast cells that are derived from NSP4-deficient GMPs have abnormal secretory granule morphology and a sustained reduction in histamine and serotonin levels. Consequently, in passive cutaneous anaphylaxis and acute arthritis models, mast cell-mediated vascular leakage in the skin and joints is substantially reduced in NSP4-deficient mice. Our findings reveal that NSP4 is required for the proper storage of vasoactive amines in mast cell granules, which impacts mast cell-dependent vascular leakage in mouse models of immune complex-mediated diseases.