Plasma Protein Research Articles

Causal effects of plasma proteome on intervertebral disc degeneration: a comprehensive mendelian randomization study.

Intervertebral disc degeneration (IVDD) considerably impacts global disability and quality of life. Although potential links between plasma proteins and IVDD exist, their causal correlation remains undefined. This study explored the causal links between plasma proteins and IVDD employing genome-wide association study data. For this observational study, summary statistics for plasma proteins were derived from an Icelandic population, paralleled with genome-wide data on IVDD obtained from the FinnGen consortium. Using two-sample Mendelian randomization, we assessed the causal relationship between 4,907 plasma proteins and IVDD. Standard sensitivity analyses encompassing heterogeneity, pleiotropy, and leave-one-out cross-validation tests confirmed the stability and robustness of the findings. Subsequently, through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein interaction analyses, we delved into the functional interrelation among identified plasma proteins. A causal association with IVDD was identified for 47 plasma proteins; myoneurin, intersectin 1, and eukaryotic translation initiation factor 4 gamma 3 maintained significant correlations post multiple correction tests (P < 1.02 × 10- 5), influencing IVDD development positively. GO/KEGG pathway analyses confirmed that multiple pathways may be involved in IVDD development. The study underscores the causal correlation between plasma protein levels and IVDD risk. These identified proteins could emerge as unique biomarkers for IVDD, contributing to its predictive measures. The findings further our understanding of IVDD pathomechanisms and prospective therapeutic targets.

Evaluation of Ethanolic Extract of Red Seaweed (Gracilariopsis lemaneiformis) on Growth and Haematological Parameters of Nile Tilapia (Oreochromis niloticus)

ABSTRACTSeaweed is multicellular marine macroalgae that enhances the immunity of aquatic organisms. The study was designed to assess the ethanolic extract (EtOH) extracted from red seaweed (Gracilariopsis lemaneiformis) on Nile tilapia (Oreochromis niloticus) to evaluate growth, immunity and haematological parameters. The EtOH was applied with fish feed in four treatments such as T1‐control (0% EtOH), T2 (5% w/v EtOH), T3 (10% w/v EtOH) and T4 (15% w/v EtOH) each with three replicates. The initial average weight of the fish was 17.53 ± 2.1 g. Results showed that the growth increased gradually with the percentage of red seaweed extract, whereas the mean weight gain was found significantly higher in T4 (51.5 ± 4.2) than in the control. The specific growth rate (%) and survival rate (%) were found higher in T4 at the lowest FCR compared to other treatments (p &lt; 0.05). The blood haemoglobin level of Nile tilapia was higher in T4 (11.5 g/dL) and lowest recorded in T1 (7.5 g/dL). However, the level of blood glucose interacted inversely with blood haemoglobin. The plasma protein level was also varied among the treatments (p &gt; 0.05). The blood parameters, refractive index (RI) and spleen somatic index (SSI) were significantly different among the treatments. The RI of blood plasma and SSI were found to be better in T4 treatment. The research indicated that red seaweed extracts significantly enhanced the growth and boosted the immunity level of Nile tilapia.

Recent Advances in Simulation Studies on the Protein Corona

When flowing through the blood stream, drug carriers such as nanoparticles encounter hundreds of plasma proteins, forming a protein layer on the nanoparticle surface, known as the “protein corona”. Since the protein corona influences the size, shape, and surface properties of nanoparticles, it can modulate their circulating lifetime, cytotoxicity, and targeting efficiency. Therefore, understanding the mechanism of protein corona formation at the atomic scale is crucial, which has become possible due to advances in computer power and simulation methodologies. This review covers the following topics: (1) the structure, dynamics, and composition of protein corona on nanoparticles; (2) the effects of protein concentration and ionic strength on protein corona formation; (3) the effects of particle size, morphology, and surface properties on corona formation; (4) the interactions among lipids, membranes, and nanoparticles with the protein corona. For each topic, mesoscale, coarse-grained, and all-atom molecular dynamics simulations since 2020 are discussed. These simulations not only successfully reproduce experimental observations but also provide physical insights into the protein corona formation. In particular, these simulation findings can be applied to manipulate the formation of a protein corona that can target specific cells, aiding in the rational design of nanomedicines for drug delivery applications.

Protein Biomarkers of Adverse Clinical Features and Events in Sarcomeric Hypertrophic Cardiomyopathy.

Hypertrophic cardiomyopathy (HCM) is a heterogeneous condition that can lead to atrial fibrillation, heart failure, and sudden cardiac death in many individuals but mild clinical impact in others. The mechanisms underlying this phenotypic heterogeneity are not well defined. The aim of this study was to use plasma proteomic profiling to help illuminate biomarkers that reflect or inform the heterogeneity observed in HCM. The Olink antibody-based proteomic platform was used to measure plasma proteins in patients with genotype positive (sarcomeric) HCM participating in the HCM Registry. We assessed associations between plasma protein levels with clinical features, cardiac magnetic resonance imaging metrics, and the development of atrial fibrillation. We measured 275 proteins in 701 patients with sarcomeric HCM. There were associations between late gadolinium enhancement with proteins reflecting neurohormonal activation (NT-proBNP [N-terminal pro-B-type natriuretic peptide] and ACE2 [angiotensin-converting enzyme 2]). Metrics of left ventricular remodeling had novel associations with proteins involved in vascular development and homeostasis (vascular endothelial growth factor-D and TM [thrombomodulin]). Assessing clinical features, the European Society of Cardiology sudden cardiac death risk score was inversely associated with SCF (stem cell factor). Incident atrial fibrillation was associated with mediators of inflammation and fibrosis (MMP2 [matrix metalloproteinase 2] and SPON1 [spondin 1]). Proteomic profiling of sarcomeric HCM identified biomarkers associated with adverse imaging and clinical phenotypes. These circulating proteins are part of both established pathways, including neurohormonal activation and fibrosis, and less familiar pathways, including endothelial function and inflammatory proteins less well characterized in HCM. These findings highlight the value of plasma profiling to identify biomarkers of risk and to gain further insights into the pathophysiology of HCM.

Mendelian Randomization Estimates the Effects of Plasma and Cerebrospinal Fluid Proteins on Intelligence, Fluid Intelligence Score, and Cognitive Performance.

Observational studies have revealed associations between levels of plasma and cerebrospinal fluid (CSF) proteins and cognition-related traits. However, these associations may be influenced by confounding factors inherent in observational research. This study aims to identify plasma and CSF proteins associated with intelligence, fluid intelligence score, and cognitive performance through the application of Mendelian randomization (MR). Proteomic quantitative trait locus (pQTL) data for plasma and CSF proteins were sourced from existing genome-wide association study (GWAS). Intelligence, fluid intelligence score, and cognitive performance GWAS summary statistics provided comprehensive data for two-sample MR analysis. Extensive sensitivity analyses, including Steiger testing, reverse MR analysis, and Bayesian co-localization, were conducted to validate associations and identify shared genetic variants. Phenotype scanning explored potential pleiotropic effects. MR analysis identified several proteins in plasma and CSF significantly associated with intelligence, fluid intelligence scores, and cognitive performance. For intelligence, negatively associated proteins in plasma include endoplasmic reticulum aminopeptidase 2 (ERAP2) and secretogranin III (SCG3), while positively associated proteins are myeloperoxidase (MPO), signal regulatory protein alpha (SIRPA), regulator of microtubule dynamics 1 (RMDN1), and endoplasmic reticulum lectin 1 (ERLEC1). In CSF, C1-esterase inhibitor and carboxypeptidase E (CBPE) both exhibited positive associations with intelligence. For fluid intelligence scores, negatively associated proteins in plasma are copine 1 (CPNE1) and SCG3, while positively associated proteins are nudix hydrolase 12 (NUDT12) and RMDN1.In CSF, Macrophage Stimulating Protein (MSP) demonstrated a significant negative impact. For cognitive performance, negatively associated proteins in plasma include ERAP2, tyrosine kinase with immunoglobulin-like and EGF-like domains 1 (TIE1), and SCG3, while positively associated proteins are NUDT12, RMDN1, ERLEC1, and ectonucleotide pyrophosphatase/phosphodiesterase family member 5 (ENPP5). In CSF, C1-esterase inhibitor was positively associated, while MSP and soluble tyrosine kinase with immunoglobulin-like and EGF-like domains 1(sTie-1) showed a negative association. Bayesian co-localization analysis revealed significant genetic overlaps between SIRPA, RMDN1, and ERLEC1 in plasma with intelligence; NUDT12 and SCG3 in plasma with fluid intelligence scores; and TIE1, NUDT12, RMDN1, ERLEC1, and ENPP5 in plasma with cognitive performance. Additionally, significant co-localization was identified between C1-esterase inhibitor and CBPE in CSF with intelligence, as well as between C1-esterase inhibitor and sTie-1 in CSF with cognitive performance. Reverse causality analysis confirmed the causal direction from proteins to cognitive traits. This study identifies specific plasma and CSF proteins that significantly impact intelligence, fluid intelligence scores, and cognitive performance. These proteins could serve as biomarkers and targets for future research and therapeutic interventions aimed at sustaining cognitive abilities and reducing impairment risks.

Enhanced Biodegradation of Silk Fibroin Hydrogel for Preventing Postoperative Adhesion.

An absorbable adhesion barrier is a medical device that prevents postoperative adhesion and matches its biodegradation time with the regeneration period of its target tissues, which is important for antiadhesion effects. Physical hydrogels of Bombyx mori silk fibroin (SF) proteins are degradable in vivo. However, their biodegradation time is too long to exert antiadhesion effects. To shorten the biodegradation time of the SF hydrogels, we decreased the molecular weight (MW) of the SF proteins by alkaline treatment and prepared low-MW (LMW) SF hydrogels. The hydrogels contained less β-sheet crystalline and more amorphous structures than conventional, high-MW (HMW) SF hydrogels. Because of the potential loosened SF molecular structures in the hydrogel networks, the LMW SF hydrogels showed enhanced biodegradation (i.e., shorter in vitro enzymatic biodegradation time and faster in vivo biodegradation rate) as well as a lower affinity for plasma proteins and fibroblasts, which are involved in postoperative adhesion formation. An antiadhesion test using a rat abdominal adhesion model demonstrated that the LMW SF hydrogel applied to the abraded cecum was almost completely degraded within two weeks postimplantation, with a significantly lower adhesion severity score than that in the untreated model rat group. Conversely, the HMW SF hydrogel remained between the cecum and abdominal wall, with the same adhesion severity as that of the untreated model rat group. Therefore, we concluded that the antiadhesion effects of SF hydrogels were induced by enhanced biodegradation. The results of this study indicate the potential of LMW SF hydrogels as absorbable adhesion barriers.

Membrane-dependent reactions of blood coagulation: classical view and state-of-the-art concepts

The complex mechanism called hemostasis evolved in living organisms to prevent blood loss when a blood vessel is damaged. In this process, two closely interconnected systems are distinguished: platelet-vascular and plasmatic hemostasis. Plasmatic hemostasis is a system of proteolytic reactions, in which blood plasma proteins called coagulation factors are involved. A key feature of this system is the localization of enzymatic reactions on the surface of phospholipid membranes, which increases their rate by up to 5 orders of magnitude. This review describes the basic mechanisms of coagulation factors binding to phospholipid membranes, pathways for complex assembly and activation reactions, and discusses the role of membranes in this process, their composition and sources. The binding of coagulation factors to procoagulant membranes leads not only to the acceleration of coagulation reactions, but also to their selective localization in restricted areas and protection from being washed away by the flow. The efficiency of coagulation reactions is regulated by the composition of the outer layer of the membrane, primarily through a special mechanism of mitochondria-dependent necrotic platelet death.

Multimodal Data Integration to Predict Atrial Fibrillation

Abstract Background Many studies have utilized data sources such as clinical variables, polygenic risk scores, ECG, and plasma proteins to predict the risk of atrial fibrillation (AF). However, few studies have integrated all four sources from a single study to comprehensively assess AF prediction. Methods We included 8374 (Visit 3, 1993-1995) and 3,730 (Visit 5, 2011-2013) participants from the Atherosclerosis Risk in Communities Study to predict incident AF and prevalent (but covert) AF. We constructed a 1) clinical risk score using CHARGE-AF clinical variables, 2) polygenic risk score using pre-determined weights, 3) protein risk score using penalized and regularized logistic regression, and 4) ECG risk score from convolutional neural network. Risk prediction performance was measured using regularized logistic regression. Results After a median follow up of 15.1 years, 1910 AF events occurred since Visit 3 and 229 participants had prevalent AF at Visit 5. The AUC improved from 0.660 to 0.752 (95% CI, 0.741-0.763) and from 0.737 to 0.854 (95% CI, 0.828-0.880) after addition of polygenic risk score to the CHARGE-AF clinical variables for predicting incident and prevalent AF, respectively. Further addition of ECG and protein risk scores improved the AUC to 0.763 (95% CI, 0.753-0.772) and 0.875 (95% CI, 0.851-0.899) for predicting incident and prevalent AF, respectively. Conclusions A combination of clinical and polygenic risk scores was the most effective and parsimonious approach to predicting AF. Further addition of an ECG risk score or protein risk score provided only modest incremental improvement for predicting AF.

Immunopathological markers and cell types linked to COVID-19 symptom manifestation

BackgroundNumerous studies have investigated the molecular properties that contribute to the symptoms of COVID-19, such as the virus’s genetic makeup, its replication mechanisms, and how it interacts with host cells. However, identifying the immunopathological properties, such as the immune system’s response, cytokine levels, and the presence of specific biomarkers, that are associated with the severity of the infection remains crucial for developing effective treatments and preventions.MethodsWe analyzed blood protein factor profiles from 420 individuals to identify features differentiating between test-negative healthy, asymptomatic, and symptomatic individuals using statistical comparison and the least absolute shrinkage and selection operator (i.e., LASSO) algorithm. Additionally, we examined single-cell RNA sequencing data from 141 individuals to identify specific cell types associated with the COVID-19 symptoms.ResultsHealthy individuals who tested negative had distinct blood protein factor levels compared to asymptomatic individuals. We identified two key protein factors, Serpin A10 and Complement C9, that differentiate between asymptomatic and symptomatic patients. Symptomatic patients showed lower levels of CD4+ T naïve, CD4+ T effector & memory, and CD8+ T naïve cells, along with higher levels of CD14+ classical monocytes compared to asymptomatic patients. Additionally, CD16+ non-classical monocytes, major producers of C1QA/B/C, appeared to contribute to the observed Complement C9 levels.ConclusionsThese findings advance our understanding of the immunopathological mechanisms underlying COVID-19 and may inform the development of targeted therapies and preventative measures. Future research should focus on further elucidating these mechanisms and exploring their potential clinical applications in managing COVID-19 severity.

Genomics-driven integrative analysis highlights immune-related plasma proteins for psychiatric disorders

BackgroundGenome-wide association studies (GWAS) have identified numerous variants associated with psychiatric disorders. However, it remains largely unknown on how GWAS risk variants contribute to psychiatric disorders. MethodsThrough integrating two largest, publicly available, independent protein quantitative trait loci datasets of plasma protein and nine large-scale GWAS summary statistics of psychiatric disorders, we first performed proteome-wide association study (PWAS) to identify psychiatric disorders-associated plasma proteins, followed by enrichment analysis to reveal the underlying biological processes and pathways. Then, we conducted Mendelian randomization (MR) and Bayesian colocalization (COLOC) analyses, with both discovery and parallel replication datasets, to further identify protein-disorder pairs with putatively causal relationships. We finally prioritized the potential drug targets using Drug Gene Interaction Database. ResultsPWAS totally identified 112 proteins, which were significantly enriched in biological processes relevant to immune regulation and response to stimulus including regulation of immune system process (adjusted P = 1.69 × 10−7) and response to external stimulus (adjusted P = 4.13 × 10−7), and viral infection related pathways, including COVID-19 (adjusted P = 2.94 × 10−2). MR and COLOC analysis further identified 26 potentially causal protein-disorder pairs in both discovery and replication analysis. Notably, eight protein-coding genes were immune-related, such as IRF3, CSK, and ACE, five among 16 druggable genes were reported to interact with drugs, including ACE, CSK, PSMB4, XPNPEP1, and MICB. ConclusionsOur findings highlighted the immunological hypothesis and identified potentially causal plasma proteins for psychiatric disorders, providing biological insights into the pathogenesis and benefit the development of preventive or therapeutic drugs for psychiatric disorders.

The Significance of Albumin Concentration and some of its Altered Forms in Iraqi Patients with Chronic Hepatitis B Virus

Background: The liver synthesizes albumin, a pivotal protein with approximately 60-65% of total plasma proteins. During ischemic attacks linked to oxidative stress, reactive oxygen species, and acidosis, the properties of albumin undergo alterations. This leads to generation of ischemia-modified albumin, which is characterized by a diminished metal-binding capacity, particularly for transition metals like copper, nickel, and cobalt. Objectives: This study aimed to assess the significance of serum albumin and ischemia-modified albumin concentrations in Iraqi individuals with hepatitis B virus Methods: A case control study consisted of 50 patients with hepatitis B were recruited from Gastroenterology hospital in the Medical city/ Baghdad/ Iraq, during the period January to February in 2023, The patients group included males and females; whose ages ranged from 18 years to 77 years with a mean value 44 year. Meanwhile the study group consisted of 50 age- and sex-matched normal healthy individuals. Albumin concentration was determined in the serum samples, using a Biosystems kit, and ischemia modified albumin concentration were measured through the albumin cobalt binding test. The ischemia modified albumin/ [albumin] ratio and Ischemia modified albumin index were then calculated. Statistical Analysis: results were reported as a mean value ± standard deviation. The differences were considered highly significant if (p &lt; (0.001), and significant where (p = (0.002) and (p = (0.033) Results: lower serum albumin concentration was measured in the patients group, while the mean value of ischemia modified albumin concentration in the patients' group and healthy control were 0.466 ± 0.114 absorbance unit &amp; 0.395 ± 0.070 absorbance unit, respectively, with a statistically significant increase (P &lt; 0.001). The ischemia modified albumin ratio in the hepatitis B patients and control groups were 0.172 ± 0.073 and 0.117 ± 0.050, respectively, showing a significant increase as well (P &lt; 0.001). Additionally, the ischemia modified albumin index in the patients and the control groups were 0.491 ± 0.167 &amp; 0.390 ± 0.131, respectively, with a statically significant increase (p&lt;0.001) in the patients group. Conclusion: In the patients’ group with hepatitis B, serum albumin concentration is decreased, while the level of ischemia modified albumin, ischemia modified albumin ratio, and ischemia modified albumin index are increased. The elevation in ischemia modified albumin, ischemia modified albumin ratio, and ischemia modified albumin index were more prominent in younger patients and those with albumin concentration less than 4g/dl. Moreover, the prevalence of hepatitis B is higher in men compared to women.

Identification of extracellular matrix proteins in plasma as a potential biomarker for intervertebral disc degeneration.

Recently, there has been significant focus on extracellular matrix proteolysis due to its importance in the pathological progression of intervertebral disc degeneration (IVDD). The present study investigates the circulating levels of extracellular matrix proteins in the plasma of IVDD and determines their potential relevance as biomarkers in disc degeneration. Global proteomic analysis was performed in the plasma samples of 10 healthy volunteers (HV) and 10 diseased subjects (DS) after depletion of highly abundant proteins such as albumin and IgG. We identified 144 and 135 matrix-associated proteins in plasma samples from healthy volunteers (HV) and patients with disc degeneration (DS), respectively. Among these, 49 of the matrix-associated proteins were identical to the proteins found in intervertebral disc (IVD) tissues retrieved from the in-house library. Applying stringent parameters, we selected 28 proteins, with 26 present in DS and 21 in HV. 19 proteins were found common between the groups, two of which-aggrecan (ACAN) and fibulin 1 (FBLN1) - showed statistically significant differences. Specifically, ACAN was up-regulated and FBLN1 was down-regulated in the DS-plasma. In particular, DS-plasma exhibited specific expression of collagen type 2a1 (COL2A1), native to the nucleus pulposus. The distinct presence of collagen type 2a1 and the elevated expression of aggrecan in IVDD plasma may serve as the basis for the development of a potential biomarker for monitoring the progression of disc degeneration.

Identification of Plasma Protein Biomarkers for Predicting Lung Cancer.

Lung cancer remains a leading cause of cancer-related mortality worldwide, necessitating the development of effective early diagnostic strategies. Despite advancements in imaging and screening technologies, late-stage diagnoses remain common, limiting treatment options and reducing survival rates. Thus, there is a critical need for reliable, minimally invasive biomarkers to improve early detection and patient outcomes. Plasma protein biomarkers offer promising potential for early lung cancer detection and continuous disease monitoring. This study explored the potential of specific plasma protein markers as early indicators of lung cancer. Plasma samples were collected from normal healthy individuals and lung cancer patients, and protein purification and analysis were conducted using LC-MS/MS. A mixed-effect model was applied to select lung cancer-related protein markers based on label-free relative quantification values. We identified 29 proteins with potential for early lung cancer diagnosis, including complement proteins (CFB, C3, C8G, C1QA, C1R, C6), orosomucoid proteins (ORM1, ORM2), ceruloplasmin (CP), alpha-1-B glycoprotein (A1BG), and others. These proteins play diverse roles in immune response, inflammation, and cell signaling, suggesting their relevance in lung cancer pathophysiology. Our findings suggest the potential of plasma proteins as early diagnostic biomarkers for lung cancer. Further validation in larger cohorts is needed to confirm their clinical utility. Integrating these biomarkers into existing diagnostic modalities could enhance early detection accuracy, leading to improved patient outcomes.

Progressive Amyloid-β Accumulation in the Brain leads to Altered Protein Expressions in the Liver and Kidneys of APP knock-in Mice

Impaired hepatic and renal function influence Alzheimer's disease (AD) progression; however, whether AD progression affects these important organ functions remains unclear. Here, we investigated the impact of AD progression, characterized by brain amyloid-beta (Aβ) accumulation, on liver and kidney function of AppNL-G-F/NL-G-F (APP-KI) mice using quantitative proteomics. SWATH-based quantitative proteomics revealed changes in mitochondrial, drug metabolism, and pharmacokinetic-related proteins in mouse liver and kidneys during the early (2-month-old) and intermediate (5-month-old) stages of Aβ accumulation. Notably, in 5-month-old APP-KI mouse liver, 25 phase I/II metabolizing enzymes (8 CYPs, 7 UGTs, 7 CESs, and 3 SLCs) and five transporters (2 ABCs and 3 SLCs) were significantly altered; specifically, Ugt1a9 and Slc33a1 protein abundances increased, whereas Ugt1a1 and Abcc3 protein abundances decreased. In the kidneys, 13 phase I/II metabolizing enzymes and 10 ABC-SLC transporters were altered, including Ugt1a6, Ugt1a7, Slc22a7, and Abcb1a. Additionally, plasma proteins, such as albumin and alpha-1-acid glycoprotein, which are critical for drug binding and distribution, were also altered. These results underscore the significant role of progressive brain Aβ accumulation in modifying hepatic and renal protein abundances, potentially influencing drug metabolism and disposition in AD. Our findings provide novel insights into the complex relationship between AD progression and organ dysfunction.

Adalimumab Treatment Effects on Inflammation and Adipose Tissue Mitochondrial Respiration in Hidradenitis Suppurativa.

Tumour necrosis factor (TNF)-α is a proinflammatory marker and has been shown to affect mitochondrial function in different tissues. We investigated the effect on adipose tissue (AT) inflammation and mitochondrial respiration in patients with hidradenitis suppurativa (HS) after 12 weeks of treatment with adalimumab, a TNF-α inhibitor. We sampled blood and an AT biopsy from 13 patients with HS and 10 control subjects after an overnight fast. The patients were retested after at least 12 weeks of treatment with adalimumab (40 mg/week). We measured macrophage content and mitochondrial respiration in the AT and interleukin (IL)-1β, IL-6, IL-10, high-sensitivity C-reactive protein (hsCRP), interferon-γ, TNF-α, adiponectin and leptin in plasma. Clinical scores and Dermatology Quality of Life Index (DLQI) were assessed. We found a higher anti-inflammatory macrophage content (CD206+) in the patient group compared with the control group, but no differences between before and after the intervention. No difference in mitochondrial respiration was observed. We observed higher plasma IL-6 and hsCRP concentrations in patients with HS compared to controls, with no differences before and after the intervention. The difference between controls and HS patients was abolished after the intervention. HS patients improved their DLQI after the intervention with no change in clinical scores. Treatment with adalimumab in patients with HS does not alter AT inflammation or mitochondrial respiratory capacity; however, we did see a higher content of anti-inflammatory macrophages in the patient group compared with the control group.

Plasma proteomic signatures of liver steatosis and fibrosis in people living with HIV: a cross-sectional study

Insights into the mechanisms driving metabolic dysfunction-associated steatotic liver disease (MASLD) in people living with HIV (PLHIV) remain limited. Plasma proteomics holds promise for biomarker discovery and the elucidation of biological mechanisms. We performed cross-sectional analyses on data from 1036 virally suppressed PLHIV using antiretroviral treatment (ART) from the Dutch multi-centre 2000HIV cohort. Participants underwent transient elastography to assess liver steatosis (controlled attenuation parameter (CAP)≥263dB/m) and -fibrosis (liver stiffness measurement (LSM)≥7.0kPa). Plasma protein concentrations (n=2367) (Olink® Explore Panel) were compared between PLHIV with vs. without liver steatosis and PLHIV with vs. without fibrosis. Enriched pathways (using GO, KEGG and Reactome libraries) and correlations with clinical characteristics wereassessed, and analyses were stratified by BMI category. In addition, concentrations of 242 proteins werecompared between individuals ("controls") with and without liver steatosis (ratio of methylene:methylene and water >5.6% on magnetic resonance spectroscopy) from a separate cohort (300-OB), all having a BMI >26kg/m2. Steatosis and fibrosis were associated with 67/2367 (2.2%) and 17/2367 (0.7%) differentially expressed proteins (DEP), respectively, enriched in mostly metabolic pathways. Immunoglobulin superfamily member 9 (IGSF9) was amongst the top DEP associated with both steatosis and fibrosis. Stratifying by BMI revealed 8/2367 DEP associated with steatosis in lean- and 12/2367 DEP in overweight/obese individuals, with two shared DEP (IGSF9 and GHR). Conversely, protein signatures of overweight/obese PLHIV (32/242 DEP) and overweight/obese HIV-uninfected individuals (32/242 DEP) exhibited substantial overlap with 16 shared DEP. Notably, DEP correlated with HIV characteristics in lean individuals but not in overweight/obese PLHIV. Lean and overweight/obese PLHIV exhibit distinct proteomic signatures associated with liver steatosis, with the former being more strongly correlated with HIV-specific factors and ART. In addition, we identified a protein, IGSF9, strongly related to liver fibrosis and steatosis across BMI categories. The 2000HIV study is funded by ViiV Healthcare.

Enhancing the differential diagnosis of small pulmonary nodules: a comprehensive model integrating plasma methylation, protein biomarkers, and LDCT imaging features

BackgroundAccurate differentiation between malignant and benign pulmonary nodules, especially those measuring 5–10 mm in diameter, continues to pose a significant diagnostic challenge. This study introduces a novel, precise approach by integrating circulating cell-free DNA (cfDNA) methylation patterns, protein profiling, and computed tomography (CT) imaging features to enhance the classification of pulmonary nodules.MethodsBlood samples were collected from 419 participants diagnosed with pulmonary nodules ranging from 5 to 30 mm in size, before any disease-altering procedures such as treatment or surgical intervention. High-throughput bisulfite sequencing was used to conduct DNA methylation profiling, while protein profiling was performed utilizing the Olink proximity extension assay. The dataset was divided into a training set and an independent test set. The training set included 162 matched cases of benign and malignant nodules, balanced for sex and age. In contrast, the test set consisted of 46 benign and 49 malignant nodules. By effectively integrating both molecular (DNA methylation and protein profiling) and CT imaging parameters, a sophisticated deep learning-based classifier was developed to accurately distinguish between benign and malignant pulmonary nodules.ResultsOur results demonstrate that the integrated model is both accurate and robust in distinguishing between benign and malignant pulmonary nodules. It achieved an AUC score 0.925 (sensitivity = 83.7%, specificity = 82.6%) in classifying test set. The performance of the integrated model was significantly higher than that of individual methylation (AUC = 0.799, P = 0.004), protein (AUC = 0.846, P = 0.009), and imaging models (AUC = 0.866, P = 0.01). Importantly, the integrated model achieved a higher AUC of 0.951 (sensitivity = 83.9%, specificity = 89.7%) in 5–10 mm small nodules. These results collectively confirm the accuracy and robustness of our model in detecting malignant nodules from benign ones.ConclusionsOur study presents a promising noninvasive approach to distinguish the malignancy of pulmonary nodules using multiple molecular and imaging features, which has the potential to assist in clinical decision-making.Trial registration: This study was registered on ClinicalTrials.gov on 01/01/2020 (NCT05432128). https://classic.clinicaltrials.gov/ct2/show/NCT05432128.

Accelerating Fracture Healing in Delayed Uniting Fractures: A Clinical Study

Background: Delayed union fractures pose a significant clinical challenge, often requiring enhanced treatment modalities to accelerate healing and improve patient outcomes. Various techniques, including autologous bone grafting and biologic agents like platelet-rich plasma (PRP) and bone morphogenetic proteins (BMPs), have been employed to stimulate bone regeneration. However, the optimal approach remains debated. Objective: This study aimed to compare the efficacy of autologous bone grafting, biologic agents, and combined therapies in promoting fracture healing, reducing pain, improving functional outcomes, and enhancing patient satisfaction in delayed union fractures. Methods: A prospective study was conducted on 80 patients with delayed union fractures. Patients were randomly assigned to one of four groups: standard care (control), autologous bone grafting, biologic agents (PRP and BMPs), or a combination of bone grafting and biologic agents. Radiographic healing was assessed at 6, 12, and 24 weeks. Pain intensity was measured using the Visual Analog Scale (VAS), functional outcomes were assessed using the AAOS lower limb function scale, and patient satisfaction was evaluated using a Likert scale. Results: The combined therapy group exhibited significantly faster radiographic healing, with 80% of patients showing callus formation at 6 weeks and 95% achieving complete union at 24 weeks, compared to 35% in the control group. The combined group also reported the greatest reduction in VAS pain scores, with a mean decrease from 7.8 to 1.5 at 24 weeks (p&lt;0.001). Functional outcomes were significantly improved in the combined group, with a mean AAOS score of 100 at 24 weeks, compared to 70 in the control group (p&lt;0.001). Additionally, 90% of patients in the combined group reported high satisfaction, compared to 40% in the control group. Conclusion: The combination of autologous bone grafting and biologic agents, such as PRP and BMPs, significantly accelerates ..........

Mutational analysis of Phanerochaete chrysosporium´s purine transporter.

We present here a mutational analysis of the purine transporter from Phanerochaete chrysosporium (PhZ), a member of the AzgA-like subfamily within the Nucleobase Ascorbate Transporters family. We identified key residues that determine its substrate specificity and transport efficiency. Thirteen PhZ mutants were generated and heterologously expressed in Aspergillus nidulans. The growth of mutant strains in the presence of purines and toxic analogues and the uptake rate of radiolabelled hypoxanthine were evaluated. Results revealed that ten mutants showed differences in transport compared to the wild-type PhZ: six mutants completely lost function, two exhibited decreased transport activity, and two showed increased hypoxanthine uptake. Subcellular localization and expression level analyses indicated that the differences in transport activity were not due to trafficking issues to the plasma membrane or protein stability. A three-dimensional model of PhZ, constructed with the artificial intelligence-based AlphaFold2 program, suggested that critical residues for transport are located in transmembrane segments and an internal helix. In the latter, the A418 residue was identified as playing a pivotal role in transport efficiency despite being far from the putative substrate binding site, as mutant A418V showed an increased initial uptake efficiency for the transporter´s physiological substrates. We also report that residue L124, which lies in the putative substrate binding site, plays a critical role in substrate transport, emerging as an additional determinant in the transport mechanism of this family of transporters. These findings underscore the importance of specific residues in AzgA-like transporters and enhance our understanding of the intricate mechanisms governing substrate specificity and transport efficiency within this family.

Proteomic analysis of APOEε4 carriers implicates lipid metabolism, complement and lymphocyte signaling in cognitive resilience

BackgroundApolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late onset Alzheimer’s disease (AD). This case-cohort study used targeted plasma biomarkers and large-scale proteomics to examine the biological mechanisms that allow some APOEε4 carriers to maintain normal cognitive functioning in older adulthood.MethodsAPOEε4 carriers and APOEε3 homozygotes enrolled in the Women’s Health Initiative Memory Study (WHIMS) from 1996 to 1999 were classified as resilient if they remained cognitively unimpaired beyond age 80, and as non-resilient if they developed cognitive impairment before or at age 80. AD pathology (Aß42/40) and neurodegeneration (NfL, tau) biomarkers, as well as 1007 proteins (Olink) were quantified in blood collected at study enrollment (on average 14 years prior) when participants were cognitively normal. We identified plasma proteins that distinguished between resilient and non-resilient APOEε4 carriers, examined whether these associations generalized to APOEε3 homozygotes, and replicated these findings in the UK Biobank.ResultsA total of 1610 participants were included (baseline age: 71.3 [3.8 SD] years; all White; 42% APOEε4 carriers). Compared to resilient APOEε4 carriers, non-resilient APOEε4 carriers had lower Aß42/40/tau ratio and greater NfL at baseline. Proteomic analyses identified four proteins differentially expressed between resilient and non-resilient APOEε4 carriers at an FDR-corrected P < 0.05. While one of the candidate proteins, a marker of neuronal injury (NfL), also distinguished resilient from non-resilient APOEε3 homozygotes, the other three proteins, known to be involved in lipid metabolism (ANGPTL4) and immune signaling (PTX3, NCR1), only predicted resilient vs. non-resilient status among APOEε4 carriers (protein*genotype interaction-P < 0.05). Three of these four proteins also predicted 14-year dementia risk among APOEε4 carriers in the UK Biobank validation sample (N = 9420). While the candidate proteins showed little to no association with targeted biomarkers of AD pathology, protein network and enrichment analyses suggested that natural killer (NK) cell and T lymphocyte signaling (via PKC-θ) distinguished resilient from non-resilient APOEε4 carriers.ConclusionsWe identified and replicated a plasma proteomic signature associated with cognitive resilience among APOEε4 carriers. These proteins implicate specific immune processes in the preservation of cognitive status despite elevated genetic risk for AD. Future studies in diverse cohorts will be needed to assess the generalizability of these results.