Small Peptides Research Articles

Increased Cellular Uptake of ApoE3- or c(RGD)-Modified Liposomes for Glioblastoma Therapy Depending on the Target Cells.

As effective treatment of glioblastoma is still an unmet need, targeted delivery systems for efficient treatment are of utmost interest. Therefore, in this paper, surface modifications with a small peptide c(RGD) or physiological protein (ApoE3) were investigated. Cellular uptake in murine endothelial cells (bEnd.3) and different glioma cells (human U-87 MG, rat F98) was tested to elucidate possible differences and to correlate the uptake to the receptor expression. Different liposomal formulations were measured at 1 and 3 h for three lipid incubation concentrations. We calculated the liposomal uptake saturation S and the saturation half-time t1/2. An up to 9.6-fold increased uptake for ApoE3-modified liposomes, primarily in tumor cells, was found. Contrarily, c(RGD) liposomes showed a stronger increase in uptake in endothelial cells (up to 40.5-fold). The uptake of modified liposomes revealed enormous differences in S and t1/2 when comparing different tumor cell lines. However, for ApoE3-modified liposomes, we proved comparable saturation values (~25,000) for F98 cells and U-87 MG cells despite a 6-fold lower expression of LRP1 in F98 cells and a 5-fold slower uptake rate. Our findings suggest that cellular uptake of surface-modified liposomes depends more on the target structure than the ligand type, with significant differences between cell types of different origins.

Physicochemical Characterization of the Oral Biotherapeutic Drug IMUNOR®.

IMUNOR is an oral biotherapeutic drug that had been developed, registered, and approved in 1997 in the Czech Republic and Slovakia. IMUNOR is a dialyzable leukocyte extract (DLE) prepared from swine leukocytes. It is characterized as a mixture of small peptides with molecular weights smaller than 12 kDa and a specific portion of nucleotides. The medical uses of IMUNOR include therapeutic applications within its registered range of indications, primarily for the treatment of immunodeficiencies, allergies, and certain acute or relapsing bacterial infections in adults and children. Despite the long-term clinical application of DLE, with strong evidence of positive therapeutic effects and no serious side effects, a detailed physicochemical specification of this mixture was lacking. We developed several methods for more in-depth physicochemical characterization of IMUNOR, including a spectrophotometric method for quantification of the total protein concentration and total DNA concentration in a mixture, several chromatographic methods for identification of individual components present in significant concentrations in IMUNOR, such as HPLC methods and the Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis method, and characterization of amino acid composition of this mixture. For the investigation of the variability among different batches of IMUNOR, five to nine representative batches from a standard manufacturing process on an industrial scale were utilized. Using the analytical methods, we verified and confirmed the batch-to-batch reproducibility of the biological product IMUNOR.

Nicotinamide benefited amino acid metabolism and rumen fermentation pattern to improve growth performance of growing lambs.

Nicotinamide (NAM) is easily degraded in the rumen, the rumen-protected NAM (RPN) supplementation might enable the use of NAM in ruminants. This study aimed to elucidate the effects of RPN supplementation on growth performance, rumen fermentation, antioxidant status and AA metabolism in growing lambs. A total of 128 healthy and similar lambs (21.3 ± 0.28 kg, 70 ± 6.3 days of age) were allotted to 1 of 4 groups. The treatments were 0, 0.5, 1 and 2 g/d RPN supplementation. The RPN products (50% bioavailability) were fed at 0700 h every day for 12 weeks. All lambs were fed the same pelleted total mixed rations to allow ad libitum consumption and had free access to water. The RPN tended to increase the average daily gain and feed efficiency. The tendencies of RPN × Day interaction were found for dry matter intake during the entire study (P = 0.078 and 0.073, respectively). The proportions of acetic acid, isobutyric acid and isovaleric acid were decreased, whereas the proportions of propionic acid and valeric acid were increased (P < 0.05). The ratio of acetic acid to propionic acid was decreased (P < 0.05). Moreover, the antioxidative status was enhanced and the glucose concentration was increased by RPN (P < 0.05). In addition, 17 amino acids (AAs) were detected in plasma, of which 11 AAs were increased by RPN (P < 0.05). Plasma metabolomics analysis identified 1395 compounds belonging to 15 classes, among which 7 peptides were significantly changed after RPN supplementation. Overall, the results suggested that RPN supplementation favoured the rumen fermentation pattern to propionic acid-type with benefited glucose metabolism, enhanced antioxidant capacity, and changed the AA and small peptide metabolism. This study provides a new perspective for studying the relationship between vitamin and AA metabolism.

In-silico binding affinity of a phage display library screened novel peptide against various FABPs.

In accordance to the American Heart Association (AHA), cardiovascular diseases (CVDs) are the leading cause of death around the globe, causing more than 19.1million deaths in 2020. Heart-type fatty acid binding protein (H-FABP) is required for the metabolism of fatty acids (FA) inside cardiomyocytes is reported as a biomarker for myocardial damage. As early as one hour after an Acute myocardial infarction (AMI), H-FABP can be used to detect myocardial ischemia. Thus, H-FABP based detection can reduce the burden on the emergency department. A peptide-based detection system can provide point-of-care diagnostics for CVDs. There is a lot of research being done on peptide-based detection, and it has a lot of potential to help with unmet medical diagnostic needs. A twelve (12) amino acid peptide has been discovered using Phage Display Library Screening. The affinity of peptide with H-FABP and other FABPs has been done using molecular docking and ADMET profile has been done. Molecular docking of small peptides against the target protein can play a crucial role in recognizing peptide binding sites and poses. The docking study was done using the HDOCK server and the visualization of the docked complex was done using Pymol and UCSF chimera. The molecular simulation study of three protein-peptide complexes were done which also validated the binding affinity of peptide with the proteins. The RMSD, RMSF and radius of gyration are also analyzed. The results indicate that H-FABP shows higher level of binding interaction with the peptide having bond length ranging from 2.3 to 3.4 Å. The screened peptide is suitable for H-FABP binding and can be used for prognosis purposes in the heart ischemic conditions.

The SCOOP-MIK2 immune pathway modulates Arabidopsis root growth and development by regulating PIN-FORMED abundance and auxin transport.

Plants synthesize hundreds of small secretory peptides, which are perceived by the receptor-like kinase (RLK) family at the cell surface. Various signaling peptide-RLK pairs ensure plant adaptation to distinct environmental conditions. Here, we report that SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) immune peptides modulate root growth and development by regulating PIN-FORMED (PIN)-regulated polar auxin transport in Arabidopsis. The SCOOP4 and SCOOP12 treatments impaired root gravitropic growth, auxin redistribution in response to gravistimulation, and PIN abundance in the PM. Furthermore, genetic and cell biological analyses revealed that these physiological and cellular effects of SCOOP4 and SCOOP12 peptides are mediated by the receptor MALE DISCOVERER1-INTERACTING RECEPTOR LIKE KINASE2 (MIK2) and the downstream mitogen-activated kinase MPK6. Biochemical evidence indicates that MPK6 directly phosphorylates the cytosolic loop of PIN proteins. Our work established a link between the immune signaling peptide SCOOPs and root growth pathways, providing insights into the molecular mechanisms underlying plant root adaptive growth in the defense response.

Bacillus subtilis-derived peptides disrupt quorum sensing and biofilm assembly in multidrug-resistant Staphylococcus aureus.

The formation of biofilms by multidrug-resistant bacterial pathogens, such as Staphylococcus aureus, increases these microorganisms' virulence and decreases the efficacy of common antibiotic regimens. Probiotics possess a variety of strain-specific strategies to reduce biofilm formation in competing organisms; however, the mechanisms and compounds responsible for these phenomena often go uncharacterized. In this study, we identified a mixture of small probiotic-derived peptides capable of Agr quorum sensing interference as one of the mechanisms driving antibiofilm activity against S. aureus. This collection of peptides also improved antibiotic killing and protected human gut epithelial cells from S. aureus-induced toxicity by stimulating an adaptive cytokine response. We conclude that purposeful strain screening and selection efforts can be used to identify unique probiotic strains that possess specially desired mechanisms of action. This information can be used to further improve our understanding of the ways in which probiotic and probiotic-derived compounds can be applied to prevent bacterial infections or improve bacterial sensitivity to antibiotics in clinical and agricultural settings.

Mitohormesis during advanced stages of Duchenne muscular dystrophy reveals a redox-sensitive creatine pathway that can be enhanced by the mitochondrial-targeting peptide SBT-20

Mitochondrial creatine kinase (mtCK) regulates the “fast” export of phosphocreatine to support cytoplasmic phosphorylation of ADP to ATP which is more rapid than direct ATP export. Such “creatine-dependent” phosphate shuttling is attenuated in several muscles, including the heart, of the D2.mdx mouse model of Duchenne muscular dystrophy at only 4 weeks of age. However, the degree to which creatine-dependent and -independent systems of phosphate shuttling progressively worsen or potentially adapt in a hormetic manner throughout disease progression remains unknown. Here, we performed a series of proof-of-principle investigations designed to determine how phosphate shuttling pathways worsen or adapt in later disease stages in D2.mdx (12 months of age). We also determined whether changes in creatine-dependent phosphate shuttling are linked to alterations in mtCK thiol redox state. In permeabilized muscle fibres prepared from cardiac left ventricles, we found that 12-month-old male D2.mdx mice have reduced creatine-dependent pyruvate oxidation and elevated complex I-supported H2O2 emission (mH2O2). Surprisingly, creatine-independent ADP-stimulated respiration was increased and mH2O2 was lowered suggesting that impairments in the faster mtCK-mediated phosphocreatine export system resulted in compensation of the alternative slower pathway of ATP export. The apparent impairments in mtCK-dependent bioenergetics occurred independent of mtCK protein content but were related to greater thiol oxidation of mtCK and a more oxidized cellular environment (lower GSH:GSSG). Next, we performed a proof-of-principle study to determine whether creatine-dependent bioenergetics could be enhanced through chronic administration of the mitochondrial-targeting, ROS-lowering tetrapeptide, SBT-20. We found that 12 weeks of daily treatment with SBT-20 (from day 4–∼12 weeks of age) increased respiration and lowered mH2O2 only in the presence of creatine in D2.mdx mice without affecting calcium-induced mitochondrial permeability transition activity. In summary, creatine-dependent mitochondrial bioenergetics are attenuated in older D2.mdx mice in relation to mtCK thiol oxidation that seem to be countered by increased creatine-independent phosphate shuttling as a unique form of mitohormesis. Separate results demonstrate that creatine-dependent bioenergetics can also be enhanced with a ROS-lowering mitochondrial-targeting peptide. These results demonstrate a specific relationship between redox stress and mitochondrial hormetic reprogramming during dystrophin deficiency with proof-of-principle evidence that creatine-dependent bioenergetics could be modified with mitochondrial-targeting small peptide therapeutics.

Promoting ovalbumin amyloid fibrils formation by cold plasma treatment and improving its emulsifying properties

The potential of cold plasma (CP) treatment to promote the formation of amyloid fibrils (AFs) of ovalbumin (OVA) was evaluated relative to acidic heat fibrillation condition (pH = 2, 85 °C). Results indicated CP exhibited significant potential for promoting the formation of AFs of OVA, as evidenced by higher Thioflavin T (ThT) fluorescence intensity of AFs for CP-treated OVA (POVA) during the fibrillation process compared to AFs for native OVA under acidic heating conditions (NOVA). Long, curved and worm-like fibrils of CP-treated OVA with 2 min (POVA-2), which were thicker (3 nm in height) and longer (majority length ranging from 300 nm to 400 nm), were observed after 8 h of fibrillation, while irregular, short, worm-like fibrils of NOVA were detected. Unlike NOVA, which was only hydrolyzed into small peptides, the backbone of POVA-2 was cleaved into small peptide fragments, accompanied by the generation of dityrosine cross-linked aggregation/oligomer during fibrillation process, as evidenced by SDS-PAGE and dityrosine analysis. The result of hydrophobic, sulfhydryl and disulfide bonds, and dityrosine analysis showed hydrophobic interaction and dityrosine cross-links could be the main force driving the assembly and stacking of cross-β structures, leading to the formation of organized fibrillar structures for POVA-2, while only hydrophobic interaction was involved for NOVA. Additionally, analyses of emulsifying ability (EAI) and stability (ESI) of NOVA and POVA-2 displayed that both EAI and ESI of them were significantly improved, with POVA-2 exhibiting superior EAI compared to NOVA. Therefore, this study demonstrated CP is a promising technique to promote the generation of protein amyloid fibrils in a more efficient manner.

Region-selective and site-specific glycation of influenza proteins surrounding the viral envelope membrane

Analysis of protein modifications is critical for quality control of therapeutic biologics. However, the identification and quantification of naturally occurring glycation of membrane proteins by mass spectrometry remain technically challenging. We used highly sensitive LC MS/MS analyses combined with multiple enzyme digestions to determine low abundance early-stage lysine glycation products of influenza vaccines derived from embryonated chicken eggs and cultured cells. Straightforward sequencing was enhanced by MS/MS fragmentation of small peptides. As a result, we determined a widespread distribution of lysine modifications attributed by the region-selectivity and site-specificity of glycation toward influenza matrix 1, hemagglutinin and neuraminidase. Topological analysis provides insights into the site-specific lysine glycation, localizing in the distinct structural regions of proteins surrounding the viral envelope membrane. Our finding highlights the proteome-wide discovery of lysine glycation of influenza membrane proteins and potential effects on the structural assembly, stability, receptor binding and enzyme activity, demonstrating that the impacts of accumulated glycation on the quality of products can be directly monitored by mass spectrometry-based structural proteomics analyses.

Precursors consumption preferences and thiol release capacity of the wine yeasts Saccharomyces cerevisiae, Torulaspora delbrueckii, and Lachancea thermotolerans

The aromatic profile of wine determines its overall final quality, and among the volatile molecules that define it, varietal thiols are responsible for shaping the distinctive character of certain wine varieties. In grape must, these thiols are conjugated to amino acids or small peptides in a non-volatile form. During wine fermentation, yeasts play a principal role in expressing these aromatic compounds as they internalise and cleavage these precursors, releasing the corresponding free and aroma-impacting fraction. Here, we investigate the impact of three wine yeasts (Saccharomyces cerevisiae, Torulaspora delbrueckii and Lachancea thermotolerans) on thiol releasing in synthetic grape must fermentations supplemented with different cysteinylated (Cys-4MSP and Cys-3SH) and glutathionylated (GSH-4MSP and GSH-3SH) precursors. We demonstrate higher consumption levels of cysteinylated precursors, and consequently, higher amounts of thiols are released from them compared to glutathionylated ones. We also report a significant impact of yeast inoculated on the final thiols released. Meanwhile T. delkbrueckii exhibits a great 3SHA releasing capacity, L. thermotolerans stands out because of its high 3SH release. We also highlight the synergic effect of the co-inoculation strategy, especially relevant in the case of S. cerevisiae and L. thermotolerans mixed fermentation, that has an outstanding release of 4MSP thiol. Although our results stem from a specific experimental approach that differs from real winemaking situations, these findings reveal the potential of unravelling the specific role of different yeast species, thiol precursors and their interaction, to improve wine production processes in the context of wine aroma enhancement.

Electrochemical Quantification of Enkephalin Peptides Using Fast-Scan Cyclic Voltammetry.

Endogenous opioid neuropeptides serve as important chemical signaling molecules in both the central and peripheral nervous systems, but there are few analytical tools for directly monitoring these molecules in situ. The opioid peptides share the amino acid motif, Tyr-Gly-Gly-Phe-, at the N-terminus. Met-enkephalin is a small opioid peptide comprised of only five amino acids with methionine (Met) incorporated at the C-terminus. Tyrosine (Tyr) and Met are electroactive, and their distinct electrochemical signatures can be utilized for quantitative molecular monitoring. This work encompasses a thorough voltammetric characterization of Tyr and Met redox chemistry as individual amino acids and when incorporated into small peptide fragments containing the shared Tyr-Gly-Gly-Phe- motif. NMR spectroscopy was used to determine the structure and conformation at near-physiological conditions. Voltammetric data demonstrate how the peak oxidation potential and the rate of electron transfer are dependent on the local chemical environment. Both the proximity of the electroactive residue to the C- or N-terminus and the hydrophobicity of the additional nonelectroactive amino acids profoundly affect sensitivity. Finally, the work uses the electrochemical signal for individual amino acids in a "training set", with a combination of principal component analysis and least-squares regression to accurately predict the voltammetric signal for short peptides comprising different combinations of those amino acids. Overall, this study demonstrates how fast-scan cyclic voltammetry can be utilized to discriminate between peptides with small differences in the chemical structure, thus establishing a framework for reliable quantification of small peptides in a complex signal, broadly speaking.

Placenta Extracellular Vesicles: Messengers Connecting Maternal and Fetal Systems.

The placenta operates during gestation as the primary communication organ between the mother and fetus. It is essential for gas, nutrient exchange, and fetal waste transfer. The placenta also produces a wide range of hormones and other factors that influence maternal physiology, including survival and activity of the corpus luteum of the ovary, but the means whereby the placenta shapes fetal development remain less clear, although the fetal brain is thought to be dependent upon the placenta for factors that play roles in its early differentiation and growth, giving rise to the term "placenta-brain axis". Placental hormones transit via the maternal and fetal vasculature, but smaller placental molecules require protection from fetal and maternal metabolism. Such biomolecules include small RNA, mRNA, peptides, lipids, and catecholamines that include serotonin and dopamine. These compounds presumably shuttle to maternal and fetal systems via protective extracellular vesicles (EVs). Placental EVs (pEVs) and their components, in particular miRNA (miRs), are known to play important roles in regulating maternal systems, such as immune, cardiovascular, and reproductive functions. A scant amount is known about how pEVs affect fetal cells and tissues. The composition of pEVs can be influenced by gestational diseases. This review will provide critical insight into the roles of pEVs as the intermediary link between maternal and fetal systems, the impact of maternal pathologies on pEV cargo contents, and how an understanding of biomolecular changes within pEVs in health and disease might be utilized to design early diagnostic and mitigation strategies to prevent gestational diseases and later offspring disorders.

Water‐Dispersible BODIPY Multifunctionalized Silicon Oxide Nanoparticles for Glutathione Sensing

AbstractGlutathione (GSH), a thiol containing small peptide, plays pivotal roles in maintaining cellular redox balance, metabolism, detoxification, and scavenging of free radicals. Aberrant GSH levels in cells and tissues are associated with various disorders, underscoring the importance of accurate GSH detection for clinical diagnosis and therapy monitoring. Several molecular probes have been designed as fluorescent‐based GSH sensors. However, their water insolubility and the need of using organic cosolvents hinder their applicability on biological samples. Alternatively, nanomaterials have proven to be highly promising for boosting the precision of treatments and enhancing the accuracy of diagnosing diseases, thanks to their compatibility with biological environments and improved cell uptake. Here, the synthesis and characterization of a boron‐dipyrromethene (BODIPY)‐based probe (PB) are reported, incorporating a fluorescent BODIPY core, chlorine substituents for reaction with GSH, and a linking moiety for conjugation to the surface of silicon oxide nanoparticles (SONPs). Functionalized SONPs with PB are also characterized at the nanoscale using high‐resolution transmission electron microscopy (HR‐TEM), dynamic light scattering (DLS), Zeta potential, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), UV–Vis absorption, and fluorescence spectroscopies, confirming the surface functionalization and water‐dispersibility of functionalized SONPs with PB. GSH sensing is evaluated in aqueous solution, conjugated to SONPs, and in living cells, showing promising potential for ratiometric GSH detection.

Solutions to Overcome Competitive Displacement of Oligonucleotides from Nucleic Acid-Based Electrochemical Sensors in Biofluids

Nucleic acid-based electrochemical sensors (NBEs) can support continuous and highly selective molecular monitoring in biological fluids, both in vitro and in vivo, via affinity-based interactions. Such interactions afford a sensing versatility that is not supported by strategies that depend on target-specific reactivity. Thus, NBEs have significantly expanded the scope of molecules that can be monitored continuously in biological systems. Although sufficiently robust for continuous, multihour sensing of small molecules, peptides, and proteins in biological fluids both in vitro and in vivo, NBEs decay over periods longer than 12 hours of continuous operation if unprotected. Previous work has sought to deeply understand the mechanisms underlaying NBE sensor decay in biofluids, as a framework to later develop solutions that eliminate such degradation pathways. Here I present a biofluid mimetic that can be leveraged to specifically study competitive displacement of oligonucleotides from NBEs, a critical degradation pathway, and varying solutions to circumvent this degradation pathway.

Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides.

Biological language modeling has significantly advanced the prediction of membrane penetration for small molecule drugs and natural peptides. However, accurately predicting membrane diffusion for peptides with pharmacologically relevant modifications remains a substantial challenge. Here, we introduce PeptideCLM, a peptide-focused chemical language model capable of encoding peptides with chemical modifications, unnatural or non-canonical amino acids, and cyclizations. We assess this model by predicting membrane diffusion of cyclic peptides, demonstrating greater predictive power than existing chemical language models. Our model is versatile, able to be extended beyond membrane diffusion predictions to other target values. Its advantages include the ability to model macromolecules using chemical string notation, a largely unexplored domain, and a simple, flexible architecture that allows for adaptation to any peptide or other macromolecule dataset.

Preservation of retinal structure and function in two mouse models of inherited retinal degeneration by ONL1204, an inhibitor of the Fas receptor

Due to the large number of genes and mutations that result in inherited retinal degenerations (IRD), there has been a paucity of therapeutic options for these patients. There is a large unmet need for therapeutic approaches targeting shared pathophysiologic pathways in a mutation-independent manner. The Fas receptor is a major activator and regulator of retinal cell death and inflammation in a variety of ocular diseases. We previously reported the activation of Fas-mediated photoreceptor (PR) cell death in two different IRD mouse models, rd10 and P23H, and demonstrated the protective effect of genetic Fas inhibition. The purpose of this study was to examine the effects of pharmacologic inhibition of Fas in these two models by intravitreal injection with a small peptide inhibitor of the Fas receptor, ONL1204. A single intravitreal injection of ONL1204 was given to one eye of rd10 mice at P14. Two intravitreal injections of ONL1204 were given to the P23H mice, once at P14 and again at 2-months of age. The fellow eyes were injected with vehicle alone. Fas activation, rate of PR cell death, retinal function, and the activation of immune cells in the retina were evaluated. In both rd10 and P23H mice, ONL1204 treatment resulted in decreased number of TUNEL (+) PRs, decreased caspase 8 activity, enhanced photoreceptor cell counts, and improved visual function compared with vehicle treated fellow eyes. Treatment with ONL1204 also reduced immune cell activation in the retinas of both rd10 and P23H mice. The protective effect of pharmacologic inhibition of Fas by ONL1204 in two distinct mouse models of retinal degeneration suggests that targeting this common pathophysiologic mechanism of cell death and inflammation represents a potential therapeutic approach to preserve the retina in patients with IRD, regardless of the genetic underpinning.

Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity.

Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.

The Mitochondrial-Derived Peptide MOTS-c May Refine Mortality and Cardiovascular Risk Prediction in Chronic Hemodialysis Patients: A Multicenter Cohort Study

Introduction: Uremic patients exhibit remarkably increased rates of mortality and cardiovascular (CV) events, but risk prediction in this setting remains difficult. Systemic mitochondrial dysfunction is pervasive in end-stage kidney disease and may contribute to CV complications. We tested the clinical significance of circulating MOTS-c, a small mitochondrial-derived peptide, as a biomarker for improving mortality and CV risk prediction in hemodialysis (HD) patients. Methods: We conducted a prospective, observational, multicenter study on 94 prevalent HD patients. The study endpoint was a composite of all-cause mortality and non-fatal CV events. The diagnostic and prognostic capacities of predictive models based on cohort-related risk factors were tested before and after the inclusion of MOTS-c. Results: MOTS-c levels were higher in HD patients than in controls (p < 0.001) and even more elevated (p = 0.01) in the 53 individuals experiencing the combined endpoint during follow-up (median duration: 26.5 months). MOTS-c was independently associated with the endpoint at either multivariate logistic (OR 1.020; 95% CI: 1.011–1.109; p = 0.03) or Cox regression analyses (HR 1.004; 95% CI: 1.000–1.025; p = 0.05) and the addition of this biomarker to prognostic models including the other cohort-related risk predictors (age, left ventricular mass, evidence of diastolic dysfunction, diabetes, pulse pressure) significantly improved the calibration, risk variability explanation, discrimination (receiver operating characteristic area under the curve from 0.727 to 0.743; C-index from 0.658 to 0.700), and particularly, the overall reclassification capacity (NRI 15.87%; p = 0.01). Conclusions: In HD patients, the mitochondrial-derived peptide MOTS-c may impart significant information to refine CV risk prediction, beyond cohort-related risk factors. Future investigations are needed to generalize these findings in larger and more heterogeneous cohorts.

A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells.

Vertebrate calcitonin-producing cells (C-cells) are neuroendocrine cells that secrete the small peptide hormone calcitonin in response to elevated blood calcium levels. Whereas mouse C-cells reside within the thyroid gland and derive from pharyngeal endoderm, avian C-cells are located within ultimobranchial glands and have been reported to derive from the neural crest. We use a comparative cell lineage tracing approach in a range of vertebrate model systems to resolve the ancestral embryonic origin of vertebrate C-cells. We find, contrary to previous studies, that chick C-cells derive from pharyngeal endoderm, with neural crest-derived cells instead contributing to connective tissue intimately associated with C-cells in the ultimobranchial gland. This endodermal origin of C-cells is conserved in a ray-finned bony fish (zebrafish) and a cartilaginous fish (the little skate, Leucoraja erinacea). Furthermore, we discover putative C-cell homologs within the endodermally-derived pharyngeal epithelium of the ascidian Ciona intestinalis and the amphioxus Branchiostoma lanceolatum, two invertebrate chordates that lack neural crest cells. Our findings point to a conserved endodermal origin of C-cells across vertebrates and to a pre-vertebrate origin of this cell type along the chordate stem.

A Euclidean transformer for fast and stable machine learned force fields

Recent years have seen vast progress in the development of machine learned force fields (MLFFs) based on ab-initio reference calculations. Despite achieving low test errors, the reliability of MLFFs in molecular dynamics (MD) simulations is facing growing scrutiny due to concerns about instability over extended simulation timescales. Our findings suggest a potential connection between robustness to cumulative inaccuracies and the use of equivariant representations in MLFFs, but the computational cost associated with these representations can limit this advantage in practice. To address this, we propose a transformer architecture called SO3krates that combines sparse equivariant representations (Euclidean variables) with a self-attention mechanism that separates invariant and equivariant information, eliminating the need for expensive tensor products. SO3krates achieves a unique combination of accuracy, stability, and speed that enables insightful analysis of quantum properties of matter on extended time and system size scales. To showcase this capability, we generate stable MD trajectories for flexible peptides and supra-molecular structures with hundreds of atoms. Furthermore, we investigate the PES topology for medium-sized chainlike molecules (e.g., small peptides) by exploring thousands of minima. Remarkably, SO3krates demonstrates the ability to strike a balance between the conflicting demands of stability and the emergence of new minimum-energy conformations beyond the training data, which is crucial for realistic exploration tasks in the field of biochemistry.