A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline.

Here, we present a standardized, "off-the-shelf" proteomics pipeline working in a single 96-well plate to achieve deep coverage of cellular proteomes with high throughput and scalability. This integrated pipeline streamlines a fully automated sample preparation platform, a data-independent acquisition (DIA) coupled with high-field asymmetric waveform ion mobility spectrometer (FAIMS) interface, and an optimized library-free DIA database search strategy. Our systematic evaluation of FAIMS-DIA showing single compensation voltage (CV) at -35 V not only yields the deepest proteome coverage but also best correlates with DIA without FAIMS. Our in-depth comparison of direct-DIA database search engines shows that Spectronaut outperforms others, providing the highest quantifiable proteins. Next, we apply three common DIA strategies in characterizing human induced pluripotent stem cell (iPSC)-derived neurons and show single-shot mass spectrometry (MS) using single-CV (-35 V)-FAIMS-DIA results in >9,000 quantifiable proteins with <10% missing values, as well as superior reproducibility and accuracy compared with other existing DIA methods.

Variant biomarker discovery using mass spectrometry-based proteogenomics.

Genomic diversity plays critical roles in risk of disease pathogenesis and diagnosis. While genomic variants-including single nucleotide variants, frameshift variants, and mis-splicing isoforms-are commonly detected at the DNA or RNA level, their translated variant protein or polypeptide products are ultimately the functional units of the associated disease. These products are often released in biofluids and could be leveraged for clinical diagnosis and patient stratification. Recent emergence of integrated analysis of genomics with mass spectrometry-based proteomics for biomarker discovery, also known as proteogenomics, have significantly advanced the understanding disease risk variants, precise medicine, and biomarker discovery. In this review, we discuss variant proteins in the context of cancers and neurodegenerative diseases, outline current and emerging proteogenomic approaches for biomarker discovery, and provide a comprehensive proteogenomic strategy for detection of putative biomarker candidates in human biospecimens. This strategy can be implemented for proteogenomic studies in any field of enquiry. Our review timely addresses the need of biomarkers for aging related diseases.

Loss of PI3k activity of inositol polyphosphate multikinase impairs PDK1-mediated AKT activation, cell migration, and intestinal homeostasis.

Protein kinase B (AKT) is essential for cell survival, proliferation, and migration and has been associated with several diseases. Here, we demonstrate that inositol polyphosphate multikinase (IPMK's) lipid kinase property drives AKT activation via increasing membrane localization and activation of PDK1 (3-Phosphoinositide-dependent kinase 1), largely independent of class I PI3k (cPI3K). Deletion of IPMK impairs cell migration, which is partially associated with the abolition of PDK1-mediated ROCK1 disinhibition and subsequent myosin light chain (MLC) phosphorylation. IPMK is highly expressed in intestinal epithelial cells (IEC). Deleting IPMK in IEC reduced AKT phosphorylation and diminished the number of Paneth cells. Ablation of IPMK impaired IEC regeneration both basally and after chemotherapy-induced damage, suggesting a broad role for IPMK in activating AKT and intestinal tissue regeneration. In conclusion, the PI3k activity of IPMK is necessary for PDK1-mediated AKT activation and intestinal homeostasis.

A reference human induced pluripotent stem cell line for large-scale collaborative studies.

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.

The "Little MonSta" Deep-Sea Benthic, Precision Deployable, Multi-Sensor and Sampling Lander Array.

The "Little MonSta" benthic lander array consists of 8 ROV-deployable (remotely operated vehicle) instrumented lander platforms for monitoring physical and chemical oceanographic properties and particle sampling developed as part of the MMMonKey_Pro program (mapping, modeling, and monitoring key processes and controls in cold-water coral habitats in submarine canyons). The Little MonStas offer flexible solutions to meet the need to monitor marine benthic environments during a historically unprecedented time of climate-driven oceanic change, develop an understanding of meso-scale benthic processes (natural and man-made), and to calibrate geological environmental archives. Equipped with acoustic Doppler current profilers (ADCPs), sediment traps, nylon settlement plates and homing beacons, the compact and upgradable lander platforms can be deployed by ROVs to precise locations in extreme terrains to a water depth of 3000 m. The array allows cluster-monitoring in heterogeneous environments or simultaneous monitoring over wider areas. A proof-of-concept case study was presented from the cold-water coral habitable zone in the upper Porcupine Bank Canyon, where the Little MonStas collected 868.8 h of current speed, direction, temperature, and benthic particulate flux records, as well as 192 particle samples subsequently analyzed for particular organic carbon (POC), lithic sediment, live foraminifera, and microplastics. The potential to upgrade the Little MonStas with additional sensors and acoustic releases offers greater and more flexible operational capabilities.

Cocaine-induced locomotor stimulation involves autophagic degradation of the dopamine transporter.

Cocaine exerts its stimulant effect by inhibiting dopamine reuptake leading to increased dopamine signaling. This action is thought to reflect binding of cocaine to the dopamine transporter (DAT) to inhibit its function. However, cocaine is a relatively weak inhibitor of DAT, and many DAT inhibitors do not share the behavioral actions of cocaine. We previously showed that toxic levels of cocaine induce autophagic neuronal cell death. Here, we show that subnanomolar concentrations of cocaine elicit neural autophagy in vitro and in vivo. Autophagy inhibitors reduce the locomotor stimulant effect of cocaine in mice. Cocaine-induced autophagy degrades transporters for dopamine but not serotonin in the nucleus accumbens. Autophagy inhibition impairs cocaine conditioned place preference in mice. Our findings indicate that autophagic degradation of DAT modulates behavioral actions of cocaine.

Influence of benthic currents on cold-water coral habitats: a combined benthic monitoring and 3D photogrammetric investigation.

Strong currents are a key component of benthic habitats by supplying food and nutrients to filter-feeding organisms such as cold-water corals. Although field measurements show that cold-water coral habitats exist in areas of elevated bottom currents, flume studies show that cold-water corals feed more effectively at lower flow speeds. This research aims to explore this disconnect in situ by utilising high spatial resolution ROV photogrammetric data coupled with high temporal resolution in situ acoustic doppler current profile measurements at seven study sites within the upper Porcupine Bank Canyon (uPBC), NE Atlantic. Object-based image analysis of photogrammetric data show that coral habitats vary considerably within the upper canyon. Although there is a regional hydrodynamic trend across the uPBC, this variation is likely driven locally by topographic steering. Although live coral tends not to face directly into the prevailing current direction, preferring lower local flows speeds, they can tolerate exposure to high-flow speeds of up to 114 cm s-1, the highest recorded in a Desmophyllum pertusum habitat. Not only do these high flow speeds supply food and nutrients, they may also help contribute to coral rubble production through physical erosion. These results can be incorporated into simulations of future deep-water habitat response to changing environmental conditions while extending the upper current speed threshold for cold-water corals.

IPMK Mediates Activation of ULK Signaling and Transcriptional Regulation of Autophagy Linked to Liver Inflammation and Regeneration.

Autophagy plays a broad role in health and disease. Here, we show that inositol polyphosphate multikinase (IPMK) is a prominent physiological determinant of autophagy and is critical for liver inflammation and regeneration. Deletion of IPMK diminishes autophagy in cell lines and mouse liver. Regulation of autophagy by IPMK does not require catalytic activity. Two signaling axes, IPMK-AMPK-Sirt-1 and IPMK-AMPK-ULK1, appear to mediate the influence of IPMK on autophagy. IPMK enhances autophagy-related transcription by stimulating AMPK-dependent Sirt-1 activation, which mediates the deacetylation of histone 4 lysine 16. Furthermore, direct binding of IPMK to ULK and AMPK forms a ternary complex that facilitates AMPK-dependent ULK phosphorylation. Deletion of IPMK in cell lines and intact mice virtually abolishes lipophagy, promotes liver damage as well as inflammation, and impairs hepatocyte regeneration. Thus, targeting IPMK may afford therapeutic benefits in disabilities that depend on autophagy and lipophagy-specifically, in liver inflammation and regeneration.