Deploying an artificial intelligence-based online search tool to increase patients' access to and understanding of solid tumor gastrointestinal clinical trials.

BACKGROUND: The number and complexity of clinical trials is growing, making finding and accessing trials increasingly challenging. A key barrier to increasing recruitment efficiency is patients' low awareness of trials as an option. They rarely hear about trials from oncologists, unless these are based at a research center, which introduces trial population biases. Even if patients decide to search for trial information on their own, it is difficult for laypeople to understand. Trial search tools exist, but have multiple shortcomings: complex navigation, limited search functionality, data too complex for non-specialists, and next steps unclear. METHODS: Access to trials via a novel trial search tool using technology, including artificial intelligence (AI), to restructure trial information and match patients to trials was the focus of this study. We focused on 6 gastrointestinal cancers for evaluating the search tool's AI model in which their trial information was restructured based on key eligibility differentiators identified. Research participants were recruited with the support of patient associations leveraging social media. They were asked to complete a survey evaluating an established tool and the novel tool to find trials relevant for them. They assessed aspects of the tools' usability on 5-level Likert scales. RESULTS: Survey respondents had a base level of awareness of trials, with patient associations and the internet as leading information sources. The novel tool made it easier to find trials, led to an improvement in ease of understanding information presented and provided more clarity on what the next steps towards enrollment would be. Overall, this led to higher patient satisfaction. CONCLUSIONS: Novel patient-focused tools can unlock trial access for all patients. Democratizing trial information will not only increase trial accrual, but also patient satisfaction while reducing disparities. This tool could also be of value for academic or community oncologists who face similar issues when navigating trials for patients.

The itinerary of autophagosomes: from peripheral formation to kiss-and-run fusion with lysosomes.

Macroautophagy, a constitutive process in higher eukaryotic cells, mediates degradation of many long-lived proteins and organelles. The actual events occurring during the process in the dynamic system of a living cell have never been thoroughly investigated. We aimed to develop a live-cell assay in which to follow the complete itinerary of an autophagosome. Our experiments show that autophagosomes are formed randomly in peripheral regions of the cell. They then move bidirectionally along microtubules, accumulating at the microtubule-organizing centre, in a similar way to lysosomes. Their centripetal movement is dependent on the motor protein dynein and is important for their fusion with lysosomes. Initially, autophagosomes dock on to lysosomes, independent of lysosomal acidification. Two kinds of fusion then occur: complete fusions, creating a hybrid organelle, or more often kiss-and-run fusions, i.e. transfer of some content while still maintaining two separate vesicles. Surprisingly, the autophagolysosomal compartment seems to be more long lived than expected. Our study documents many aspects of autophagosome behaviour, adding to our understanding of the mechanism and control of autophagy. Indeed, although the formation of autophagosomes is completely different from any other vesicular structures, their later itinerary appears to be very similar to those of other trafficking pathways.

Novel targets for Huntington's disease in an mTOR-independent autophagy pathway.

Autophagy is a major clearance route for intracellular aggregate-prone proteins causing diseases such as Huntington's disease. Autophagy induction with the mTOR inhibitor rapamycin accelerates clearance of these toxic substrates. As rapamycin has nontrivial side effects, we screened FDA-approved drugs to identify new autophagy-inducing pathways. We found that L-type Ca2+ channel antagonists, the K+ATP channel opener minoxidil, and the G(i) signaling activator clonidine induce autophagy. These drugs revealed a cyclical mTOR-independent pathway regulating autophagy, in which cAMP regulates IP3 levels, influencing calpain activity, which completes the cycle by cleaving and activating G(s)alpha, which regulates cAMP levels. This pathway has numerous potential points where autophagy can be induced, and we provide proof of principle for therapeutic relevance in Huntington's disease using mammalian cell, fly and zebrafish models. Our data also suggest that insults that elevate intracytosolic Ca2+ (like excitotoxicity) inhibit autophagy, thus retarding clearance of aggregate-prone proteins.

Lysosomal positioning coordinates cellular nutrient responses.

mTOR (mammalian target of rapamycin) signalling and macroautophagy (henceforth autophagy) regulate numerous pathological and physiological processes, including cellular responses to altered nutrient levels. However, the mechanisms regulating mTOR and autophagy remain incompletely understood. Lysosomes are dynamic intracellular organelles intimately involved both in the activation of mTOR complex 1 (mTORC1) signalling and in degrading autophagic substrates. Here we report that lysosomal positioning coordinates anabolic and catabolic responses with changes in nutrient availability by orchestrating early plasma-membrane signalling events, mTORC1 signalling and autophagy. Activation of mTORC1 by nutrients correlates with its presence on peripheral lysosomes that are physically close to the upstream signalling modules, whereas starvation causes perinuclear clustering of lysosomes, driven by changes in intracellular pH. Lysosomal positioning regulates mTORC1 signalling, which in turn influences autophagosome formation. Lysosome positioning also influences autophagosome-lysosome fusion rates, and thus controls autophagic flux by acting at both the initiation and termination stages of the process. Our findings provide a physiological role for the dynamic state of lysosomal positioning in cells as a coordinator of mTORC1 signalling with autophagic flux.

Plasma membrane contributes to the formation of pre-autophagosomal structures.

Autophagy is a catabolic process in which lysosomes degrade intracytoplasmic contents transported in double-membraned autophagosomes. Autophagosomes are formed by the elongation and fusion of phagophores, which derive from pre-autophagosomal structures. The membrane origins of autophagosomes are unclear and may involve multiple sources, including the endoplasmic reticulum and mitochondria. Here we show in mammalian cells that the heavy chain of clathrin interacts with Atg16L1 and is involved in the formation of Atg16L1-positive early autophagosome precursors. Atg16L1 associated with clathrin-coated structures, and inhibition of clathrin-mediated internalization decreased the formation of both Atg16L1-positive precursors and mature autophagosomes. We tested and demonstrated that the plasma membrane contributes directly to the formation of early Atg16L1-positive autophagosome precursors. This may be particularly important during periods of increased autophagosome formation, because the plasma membrane may serve as a large membrane reservoir that allows cells periods of autophagosome synthesis at levels many-fold higher than under basal conditions, without compromising other processes.

1-O-Hexadecyl-2-O-methyl-3-O-(2'-acetamido-2'-deoxy-beta-D-glucopyranosyl)-sn-glycerol (Gln) induces cell death with more autophagosomes which is autophagy-independent.

Autophagic cell death has recently received a great deal of attention. However, a dependence of this type of cell death on the actual process of autophagy has only rarely been proven. Indeed, it is important to differentiate between cell death with an accumulation of autophagosomes and cell death actually caused by excessive or inhibited autophagy. The aim of this study was to elucidate the mechanism of action involved in the cytotoxicity of 1-O-hexadecyl-2-O-methyl-3-O-(2'-acetamido-2'-deoxy-beta-D-glucopyranosyl)-sn-glycerol (Gln) and specifically the involvement of autophagy in the effects observed. Our results show that Gln induces cell death associated with large increases in autophagolysosome number and size. However the cell death is independent of autophagy and caspase activation. Instead, Gln leads to lysosomal membrane permeabilization with a resulting leakage of hydrolases into the cytosol, which are then directly involved in cell death. The increased number of autophagolysosomes, however, is just a side effect of the neutralization of the lysosomal pH by Gln.

A block of autophagy in lysosomal storage disorders.

Most lysosomal storage disorders (LSDs) are caused by deficiencies of lysosomal hydrolases. While LSDs were among the first inherited diseases for which the underlying biochemical defects were identified, the mechanisms from enzyme deficiency to cell death are poorly understood. Here we show that lysosomal storage impairs autophagic delivery of bulk cytosolic contents to lysosomes. By studying the mouse models of two LSDs associated with severe neurodegeneration, multiple sulfatase deficiency (MSD) and mucopolysaccharidosis type IIIA (MPSIIIA), we observed an accumulation of autophagosomes resulting from defective autophagosome-lysosome fusion. An impairment of the autophagic pathway was demonstrated by the inefficient degradation of exogenous aggregate-prone proteins (i.e. expanded huntingtin and mutated alpha-synuclein) in cells from LSD mice. This impairment resulted in massive accumulation of polyubiquitinated proteins and of dysfunctional mitochondria which are the putative mediators of cell death. These data identify LSDs as 'autophagy disorders' and suggest the presence of common mechanisms in the pathogenesis of these and other neurodegenerative diseases.

Aggregate-prone proteins are cleared from the cytosol by autophagy: therapeutic implications.

Intracellular protein misfolding/aggregation are features of many late-onset neurodegenerative diseases, called proteinopathies. These include Alzheimer's disease, Parkinson's disease, tauopathies, and polyglutamine expansion diseases [e.g., Huntington's disease; and various spinocerebellar ataxias (SCAs), like SCA3]. There are no effective strategies to slow or prevent the neurodegeneration resulting from these diseases in humans. The mutations causing many proteinopathies (e.g., polyglutamine diseases and tauopathies) confer novel toxic functions on the specific protein, and disease severity frequently correlates with the expression levels of the protein. Thus, the factors regulating the synthesis and clearance of these aggregate-prone proteins are putative therapeutic targets. The proteasome and autophagy-lysosomal pathways are the major routes for mutant huntingtin fragment clearance. While the narrow proteasome barrel precludes entry of oligomers/aggregates of mutant huntingtin (or other aggregate-prone intracellular proteins), such substrates can be degraded by macroautophagy (which we will call autophagy). We showed that the autophagy inducer rapamycin reduced the levels of soluble and aggregated huntingtin and attenuated its toxicity in cells, and in transgenic Drosophila and mouse models. We extended the range of intracellular proteinopathy substrates that are cleared by autophagy to a wide range of other targets, including proteins mutated in certain SCAs, forms of alpha-synuclein mutated in familial forms of Parkinson's disease, and tau mutants that cause frontotemporal dementia/tauopathy. In this chapter, we consider the therapeutic potential of autophagy upregulation for various proteinopathies, and describe how this strategy may act both by removing the primary toxin (the misfolded/aggregate-prone protein) and by reducing susceptibility to apoptotic insults.