A Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Markers Using ProteographTM and Trapped Ion Mobility Mass Spectrometry.

There is a significant unmet need for clinical reflex tests that increase the specificity of prostate-specific antigen blood testing, the longstanding but imperfect tool for prostate cancer diagnosis. Towards this endpoint, we present the results from a discovery study that identifies new prostate-specific antigen reflex markers in a large-scale patient serum cohort using differentiating technologies for deep proteomic interrogation. We detect known prostate cancer blood markers as well as novel candidates. Through bioinformatic pathway enrichment and network analysis, we reveal associations of differentially abundant proteins with cytoskeletal, metabolic, and ribosomal activities, all of which have been previously associated with prostate cancer progression. Additionally, optimized machine learning classifier analysis reveals proteomic signatures capable of detecting the disease prior to biopsy, performing on par with an accepted clinical risk calculator benchmark.

Tracing coalition changes in knowledge in and engagement with childhood obesity prevention to improve intervention implementation.

BACKGROUND: While most coalition research focuses on studying the effects of peer relationship structure, this study examines the coevolution of coalition structure and behavior across three communities in the U.S. with the goal of identifying coalition dynamics that impact a childhood obesity prevention intervention.  METHODS: Over two years (2018-2020), three communities within the U.S. participated in a childhood obesity prevention intervention at different times. This intervention was guided by the Stakeholder-Driven Community Diffusion theory, which describes an empirically testable mechanism for promoting community change. Measures are part of the Stakeholder-driven Community Diffusion (SDCD) survey with demonstrated reliability, which include knowledge of and engagement with childhood obesity prevention and social networks. Data from three coalition-committees and their respective networks were used to build three different stochastic actor-oriented models. These models were used to examine the coevolution of coalition structure with coalition behavior (defined a priori as knowledge of and engagement with obesity prevention) among coalition-committee members and their nominated alters (Network A) and coalition-committee members only (Network B).  RESULTS: Overall, coalitions decrease in size and their structure becomes less dense over time. Both Network A and B show a consistent preference to form and sustain ties with those who have more ties. In Network B, there was a trend for those who have higher knowledge scores to increase their number of ties over time. The same trend appeared in Network A but varied based on their peers' knowledge in and engagement with childhood obesity prevention. Across models, engagement with childhood obesity prevention research was not a significant driver of changes in either coalition network structure or knowledge. CONCLUSIONS: The trends in coalition Network A and B's coevolution models may point to context-specific features (e.g., ties among stakeholders) that can be leveraged for better intervention implementation. To that end, examining tie density, average path length, network diameter, and the dynamics of each behavior outcome (i.e., knowledge in and engagement with childhood obesity prevention) may help tailor whole-of-community interventions. Future research should attend to additional behavioral variables (e.g., group efficacy) that can capture other aspects of coalition development and that influence implementation, and to testing the efficacy of network interventions after trends have been identified.

Expanded phenotype of AARS1-related white matter disease.

PURPOSE: Recent reports of individuals with cytoplasmic transfer RNA (tRNA) synthetase-related disorders have identified cases with phenotypic variability from the index presentations. We sought to assess phenotypic variability in individuals with AARS1-related disease. METHODS: A cross-sectional survey was performed on individuals with biallelic variants in AARS1. Clinical data, neuroimaging, and genetic testing results were reviewed. Alanyl tRNA synthetase (AlaRS) activity was measured in available fibroblasts. RESULTS: We identified 11 affected individuals. Two phenotypic presentations emerged, one with early infantile-onset disease resembling the index cases of AARS1-related epileptic encephalopathy with deficient myelination (n = 7). The second (n = 4) was a later-onset disorder, where disease onset occurred after the first year of life and was characterized on neuroimaging by a progressive posterior predominant leukoencephalopathy evolving to include the frontal white matter. AlaRS activity was significantly reduced in five affected individuals with both early infantile-onset and late-onset phenotypes. CONCLUSION: We suggest that variants in AARS1 result in a broader clinical spectrum than previously appreciated. The predominant form results in early infantile-onset disease with epileptic encephalopathy and deficient myelination. However, a subgroup of affected individuals manifests with late-onset disease and similarly rapid progressive clinical decline. Longitudinal imaging and clinical follow-up will be valuable in understanding factors affecting disease progression and outcome.

Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions.

Integrins are transmembrane receptors that, upon activation, bind extracellular ligands and link them to the actin filament (F-actin) cytoskeleton to mediate cell adhesion and migration. Cytoskeletal forces in migrating cells generated by polymerization- or contractility-driven "retrograde flow" of F-actin from the cell leading edge have been hypothesized to mediate integrin activation for ligand binding. This predicts that these forces should align and orient activated, ligand-bound integrins at the leading edge. Here, polarization-sensitive fluorescence microscopy of GFP-αVß3 integrins in fibroblasts shows that integrins are coaligned in a specific orientation within focal adhesions (FAs) in a manner dependent on binding immobilized ligand and a talin-mediated linkage to the F-actin cytoskeleton. These findings, together with Rosetta modeling, suggest that integrins in FA are coaligned and may be highly tilted by cytoskeletal forces. Thus, the F-actin cytoskeleton sculpts an anisotropic molecular scaffold in FAs, and this feature may underlie the ability of migrating cells to sense directional extracellular cues.

Binaural spatial adaptation as a mechanism for asymmetric trading of interaural time and level differences.

A classic paradigm used to quantify the perceptual weighting of binaural spatial cues requires a listener to adjust the value of one cue, while the complementary cue is held constant. Adjustments are made until the auditory percept appears centered in the head, and the values of both cues are recorded as a trading relation (TR), most commonly in µs interaural time difference per dB interaural level difference. Interestingly, existing literature has shown that TRs differ according to the cue being adjusted. The current study investigated whether cue-specific adaptation, which might arise due to the continuous, alternating presentation of signals during adjustment tasks, could account for this poorly understood phenomenon. Three experiments measured TRs via adjustment and via lateralization of single targets in virtual reality (VR). Targets were 500 Hz pure tones preceded by silence or by adapting trains that held one of the cues constant. VR removed visual anchors and provided an intuitive response technique during lateralization. The pattern of results suggests that adaptation can account for cue-dependent TRs. In addition, VR seems to be a viable tool for psychophysical tasks.

Reverberation enhances onset dominance in sound localization.

Temporal variation in sensitivity to sound-localization cues was measured in anechoic conditions and in simulated reverberation using the temporal weighting function (TWF) paradigm [Stecker and Hafter (2002). J. Acoust. Soc. Am. 112, 1046-1057]. Listeners judged the locations of Gabor click trains (4 kHz center frequency, 5-ms interclick interval) presented from an array of loudspeakers spanning 360° azimuth. Targets ranged ±56.25° across trials. Individual clicks within each train varied by an additional ±11.25° to allow TWF calculation by multiple regression. In separate conditions, sounds were presented directly or in the presence of simulated reverberation: 13 orders of lateral reflection were computed for a 10 m × 10 m room ( RT60≊300 ms) and mapped to the appropriate locations in the loudspeaker array. Results reveal a marked increase in perceptual weight applied to the initial click in reverberation, along with a reduction in the impact of late-arriving sound. In a second experiment, target stimuli were preceded by trains of "conditioner" sounds with or without reverberation. Effects were modest and limited to the first few clicks in a train, suggesting that impacts of reverberant pre-exposure on localization may be limited to the processing of information from early reflections.

Application of a new wall-less plate technology to complex multistep cell-based investigations using suspension cells.

Despite significant progresses, cell-based assays still have major limitations part to because of their plate format. Here, we present a wall-less plate technology based on unique liquid dynamics named DropArray that takes advantage of hydrophobic and hydrophilic surface properties. Liquid velocities within the DropArray plate were quantified through fluid dynamics simulation and complete retention of suspension cells experimentally demonstrated within the range of simulated shear stresses. Subsequently, we compared the DropArray technology with conventional microtiter plates in a cell-based protein-binding assay. Although the wall-less plate produced similar results with adherent cells, the advantage of the DropArray technology was absolutely clear when semiadherent or suspension cells were used in this multistep experimental procedure. The technology also was evaluated for the cell viability assay and generated similar results to conventional plate format while enabling significant reduction in toxic reagent use. Finally, we developed a DropArray cell-based assay to evaluate a bispecific antibody designed to engage cytotoxic T cells and trigger tumor cell killing. This assay enables for the first time the visualization and quantification of the specific killing events and represents a very powerful tool to further investigate functional aspects of the cancer immunotherapy.

Experimental measurements of the spectral absorption coefficient of pure fused silica optical fibers.

Knowledge of the spectral absorption coefficient of fused silica optical fibers is important in modeling heat transfer in the processes and applications in which these fibers are used. An experimental method used to measure the spectral absorption coefficient of optical fibers is presented. Radiative energy from a blackbody radiator set at different temperatures is directed through the optical fibers and into an FTIR spectrometer. Spectral instrument response functions are calculated for different fiber lengths. The ratios of the slopes of the instrument response functions for the different lengths of fibers are used to solve for the spectral absorption coefficient of the fibers. The spectral absorption coefficient of low OH pure fused silica optical fibers is measured between the wavelengths 1.5 and 2.5 µm.

Estimates of cochlear compression using distortion product otoacoustic emissions and growth of forward masking.

OBJECTIVE: The authors investigated the relationship between behavioral and physiologic estimates of cochlear compression. DESIGN: Cochlear compression was estimated in distortion product otoacoustic emission (DPOAE) fine structure minima and maxima near 4 kHz. The composite DPOAE response and separated generator and reflection components yielded three estimates in four young adults with normal hearing. DPOAE estimates were compared to behavioral compression estimates derived using a growth of forward masking (GOFM) paradigm. The DPOAE primary tone f2 and GOFM signal were identical and selected individually based on placement in a DPOAE fine structure minimum. RESULTS: Across participants, DPOAE compression estimates derived from the generator component were most similar to estimates derived from the GOFM paradigm and did not vary with DPOAE fine structure. CONCLUSIONS: These results suggest that the generator component may provide a quick, reliable estimate of cochlear compression in humans. This may prove useful in populations that cannot give behavioral responses.

Searching for the Scale-Able Weight Loss Intervention: Can One Size Fit All? Lessons to Be Learned from the EQUAL Trial.

Overweight and obesity affect 71.2% of adults in the United States, with cancer survivors not far behind at 70.3%. Subgroups such as those diagnosed with acute lymphoblastic leukemia (ALL) face even greater challenges. The Exercise and Quality Diet after Leukemia (EQUAL) trial sought to address weight management issues among ALL survivors by implementing a remotely delivered weight loss intervention, leveraging the previously proven Practice-based Opportunities for Weight Reduction (POWER) program. Despite a strong foundation and design, the EQUAL trial yielded null results. Key differences in study populations and intervention contexts between the EQUAL and POWER trials, such as the lack of primary care physician involvement in EQUAL, contributed to these outcomes. EQUAL's failure to meet its accrual target and poor adherence among participants highlighted challenges in engaging this unique population. Contrary to EQUAL's conclusions, evidence from other studies supports the efficacy of remote interventions for weight loss among cancer survivors. The lack of qualitative assessment among ALL survivors and key integration to inform intervention adaptations undermined EQUAL's impact. However, EQUAL's impressive retention rate offers valuable insights. Lessons from EQUAL underscore the need for well-fitted, remotely delivered interventions and the importance of thoughtfully adapted and tailored approaches to specific survivor populations. See related article by Fiedmann et al., p. 1158.

Intracellular Lactate Dynamics Reveal the Metabolic Diversity of Drosophila Glutamatergic Neurons.

Lactate, an intermediary between glycolysis and mitochondrial oxidative phosphorylation, reflects the metabolic state of neurons. Here, we utilized a genetically-encoded lactate FRET biosensor to uncover subpopulations of distinct metabolic states among Drosophila glutamatergic neurons. Neurons within specific subpopulations exhibited correlated lactate flux patterns that stemmed from inherent cellular properties rather than neuronal interconnectivity. Further, individual neurons exhibited consistent patterns of lactate flux over time such that stimulus-evoked changes in lactate were correlated with pre-treatment fluctuations. Leveraging these temporal autocorrelations, deep-learning models accurately predicted post-stimulus responses from pre-stimulus fluctuations. These findings point to the existence of distinct neuronal subpopulations, each characterized by unique lactate dynamics, and raise the possibility that neurons with correlated metabolic activities might synchronize across different neural circuits. Such synchronization, rooted in neuronal metabolic states, could influence information processing in the brain.

Mitochondrial permeability transition dictates mitochondrial maturation upon switch in cellular identity of hematopoietic precursors.

The mitochondrial permeability transition pore (mPTP) is a supramolecular channel that regulates exchange of solutes across cristae membranes, with executive roles in mitochondrial function and cell death. The contribution of the mPTP to normal physiology remains debated, although evidence implicates the mPTP in mitochondrial inner membrane remodeling in differentiating progenitor cells. Here, we demonstrate that strict control over mPTP conductance shapes metabolic machinery as cells transit toward hematopoietic identity. Cells undergoing the endothelial-to-hematopoietic transition (EHT) tightly control chief regulatory elements of the mPTP. During EHT, maturing arterial endothelium restricts mPTP activity just prior to hematopoietic commitment. After transition in cellular identity, mPTP conductance is restored. In utero treatment with NIM811, a molecule that blocks sensitization of the mPTP to opening by Cyclophilin D (CypD), amplifies oxidative phosphorylation (OXPHOS) in hematopoietic precursors and increases hematopoiesis in the embryo. Additionally, differentiating pluripotent stem cells (PSCs) acquire greater organization of mitochondrial cristae and hematopoietic activity following knockdown of the CypD gene, Ppif. Conversely, knockdown of Opa1, a GTPase critical for proper cristae architecture, induces cristae irregularity and impairs hematopoiesis. These data elucidate a mechanism that regulates mitochondrial maturation in hematopoietic precursors and underscore a role for the mPTP in the acquisition of hematopoietic fate.

NDUFS4 regulates cristae remodeling in diabetic kidney disease.

The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generate diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that conditional male mice with genetic overexpression of Ndufs4 exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping protein STOML2 in linking NDUFS4 with improved cristae morphology. Together, we provide the evidence on the central role of NDUFS4 as a regulator of cristae remodeling and mitochondrial function in kidney podocytes. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.

Secondary deficiency of neuraminidase 1 contributes to CNS pathology in neurological mucopolysaccharidoses via hypersialylation of brain glycoproteins.

Mucopolysaccharidoses (MPS) are lysosomal storage diseases caused by defects in catabolism of glycosaminoglycans. MPS I, II, III and VII are associated with lysosomal accumulation of heparan sulphate and manifest with neurological deterioration. Most of these neurological MPS currently lack effective treatments. Here, we report that, compared to controls, neuraminidase 1 (NEU1) activity is drastically reduced in brain tissues of neurological MPS patients and in mouse models of MPS I, II, IIIA, IIIB and IIIC, but not of other neurological lysosomal disorders not presenting with heparan sulphate storage. We further show that accumulated heparan sulphate disrupts the lysosomal multienzyme complex of NEU1 with cathepsin A (CTSA), ß-galactosidase (GLB1) and glucosamine-6-sulfate sulfatase (GALNS) necessary to maintain enzyme activity, and that NEU1 deficiency is linked to partial deficiencies of GLB1 and GALNS in cortical tissues and iPSC-derived cortical neurons of neurological MPS patients. Increased sialylation of N-linked glycans in brain samples of human MPS III patients and MPS IIIC mice implicated insufficient processing of brain N-linked sialylated glycans, except for polysialic acid, which was reduced in the brains of MPS IIIC mice. Correction of NEU1 activity in MPS IIIC mice by lentiviral gene transfer ameliorated previously identified hallmarks of the disease, including memory impairment, behavioural traits, and reduced levels of the excitatory synapse markers VGLUT1 and PSD95. Overexpression of NEU1 also restored levels of VGLUT1-/PSD95-positive puncta in cortical neurons derived from iPSC of an MPS IIIA patient. Together, our data demonstrate that heparan sulphate-induced secondary NEU1 deficiency and aberrant sialylation of glycoproteins implicated in synaptogenesis, memory, and behaviour constitute a novel pathological pathway in neurological MPS spectrum crucially contributing to CNS pathology.

Exploratory Analysis of Social Networks Linked to the Provision of Beverages in Costa Rican Schools.

Sugar-sweetened beverages (SSBs) are implicated in weight gain and adverse cardiometabolic heath. Social networks of stakeholders involved in providing potable water and sugar-sweetened beverages (SSBs) in high schools in Costa Rica were studied using social analysis network. In public and private schools, the interactions between the stakeholders in charge of providing beverages are fragmented and their role in preventing the availability of SSBs is weak. School canteen owners ultimately decide what beverages are available at school, which may cause students to choose beverages that increase the risk of overweight/obesity. It is therefore urgently necessary to improve the capacity for two-way interactions between the stakeholders to enhance their roles in the provision of beverages. Hence, it is essential to reinforce the stakeholders' leadership, and set up innovative ways to exert it in order to develop a shared vision of the types of drinks that should be available in the school environment.

Relational sanctification, communal coping, and depression among African American couples.

Despite the common use of religious buffers, African Americans are disproportionately affected by depressive symptoms. Communal coping may serve as one factor in helping religious African American couples alleviate the symptoms of depression. This study examines the association between relational sanctification and depressive symptoms as mediated by the communal coping of 467 African American married and cohabiting couples. Data from the sampled couples were analyzed using a common fate model, and analyses revealed higher scores on the measure of sanctification were associated with more communal coping; more communal coping was associated with fewer depressive symptoms among women and men, and communal coping acted as a mediator between relational sanctification and depressive symptoms in both partners. Findings from this study underscore the importance of considering how the religiosity and cooperative action of African American couples relate to depressive symptoms.

Implementing a stakeholder-driven community diffusion-informed intervention to create healthier, more equitable systems: a community case study in Greenville County, South Carolina.

This case study describes the application of a theory-informed, stakeholder-driven intervention with a group of 19 multi-sector stakeholders from an existing coalition to promote whole-of-community change that supports childhood obesity prevention. The intervention applied community-based system dynamics to design and implement activities that promoted insights into the systems driving childhood obesity prevalence and helped participants prioritize actions to influence those systems. This led to three new priority areas for the coalition: addressing food insecurity; building power among historically marginalized voices within the community; and supporting advocacy efforts to promote community-wide change beyond the coalition's previous focus on organizational-level policy, systems and environment change. The intervention spurred the application of community-based system dynamics to other health issues and in partner organizations, which demonstrates paradigm shifts about how to address complex public health issues in the community.

Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis.

Maintaining protein homeostasis is essential for cellular health. During times of proteotoxic stress, cells deploy unique defense mechanisms to achieve resolution. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response (MCSR), a unique stress response activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPR ER ), suggesting the presence of a Mitochondria to ER Stress Response (MERSR). During MERSR, the IRE1 branch of UPR ER is inhibited, introducing a previously unknown regulatory component of MCSR. Moreover, proteostasis is enhanced through the upregulation of the PERK-eIF2a signaling pathway, increasing phosphorylation of eIF2a and improving the ER's capacity to manage greater proteostasis load. MERSR activation in both poly-glutamine (poly-Q) and amyloid-beta (Aß) C. elegans disease models also led to improvement in both aggregate burden and overall disease outcome. These findings shed light on the coordination between the mitochondria and the ER in maintaining cellular proteostasis and provides further evidence for the importance of intercompartmental signaling.

Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility.

Single-cell whole-genome sequencing (scWGS) enables the assessment of genome-level molecular differences between individual cells with particular relevance to genetically diverse systems like solid tumors. The application of scWGS was limited due to a dearth of accessible platforms capable of producing high-throughput profiles. We present a technique that leverages nucleosome disruption methodologies with the widely adopted 10× Genomics ATAC-seq workflow to produce scWGS profiles for high-throughput copy-number analysis without new equipment or custom reagents. We further demonstrate the use of commercially available indexed transposase complexes from ScaleBio for sample multiplexing, reducing the per-sample preparation costs. Finally, we demonstrate that sequential indexed tagmentation with an intervening nucleosome disruption step allows for the generation of both ATAC and WGS data from the same cell, producing comparable data to the unimodal assays. By exclusively utilizing accessible commercial reagents, we anticipate that these scWGS and scWGS+ATAC methods can be broadly adopted by the research community.

NDUFS4 Regulates Cristae Remodeling in Diabetic Kidney Disease.

The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generated diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model to investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that these conditional mice exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping proteins in linking NDUFS4 with improved cristae morphology. Taken together, we discover the central role of NDUFS4 as a powerful regulator of cristae remodeling, respiratory supercomplexes assembly, and mitochondrial ultrastructure in vitro and in vivo. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.