Potential Biomarkers Research Articles

Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes.

Acanthamoeba causes a serious blinding keratopathy, Acanthamoeba keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of Acanthamoeba using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific Acanthamoeba keratitis cases.

Toxicity of Cancer Immunotherapies in Older Patients: Does Age Make a Difference?

The use of immunotherapy agents especially immune checkpoint inhibitors is growing, and toxicities known as immune-related adverse events affecting any organ system may develop as a consequence of the treatment. With an ageing population, a considerable number of patients who will receive these therapies will be older adults. However, older patients who have highly heterogenous clinical characteristics, age-related changes in the immune system, a higher prevalence of comorbidities and frailty have been poorly represented in clinical trials, leaving gaps in understanding the safety of immune checkpoint inhibitor agents in this subgroup. Therefore, the safety of immune checkpoint inhibitors is a primary point of consideration when treating older patients with cancer. The available evidence is conflicting, but it generally suggests that the incidence of immune-related adverse events is not necessarily higher in older patients, but it may have a different profile. It is important to also note that the management of immune-related adverse events can be a challenge in these patients, owing to the risks associated with the use of corticosteroids and a reduced physiological reserve. A comprehensive characterisation of immune ageing, potential biomarkers to predict immune-related adverse events, the use of measures for frailty, enrolling older patients with cancer to clinical trials and analysis of real-world data are necessary to improve the evidence-based decision making for immune checkpoint inhibitor treatment in a geriatric oncology population.

Suspect screening candidate exposure biomarkers of acetyl tributyl citrate and acetyl triethyl citrate after human oral administration

Acetyl tributyl citrate (ATBC) and acetyl triethyl citrate (ATEC) are widely used as plasticizers, but their metabolites as exposure biomarkers for biomonitoring, as well as approximate human metabolic pathways, are not well understood. This study addresses this knowledge gap by conducting suspect screening to propose specific metabolites in human urine as potential biomarkers of exposure and explore their kinetic profiles. Ten volunteers were administered deuterium labeled ATBC (ATBC-d3) and seven received ATEC or deuterium labeled ATEC (ATEC-d3), with urine samples collected over 48 h post-administration. Employing ultra-performance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (UPLC-qTOF/MS), six metabolites of ATBC were consistently detected, including (OH)3-ATBC-d3, ADBC-d3, OH-ADBC-d3, DBC, OH-DBC, and OH-DBA. For ATEC, four metabolites were identified: ADEC-d3, AMEC-d3, OH-ADEC-d3, and DEC. Based on their high detection frequency, relative response, and specificity to their parent compounds, ADBC-d3 and OH-ADBC-d3 were identified as promising candidate biomarkers for ATBC exposure, while ADEC-d3 emerged as a suitable biomarker for ATEC. Estimated urinary elimination half-lives ranged from 1.0 to 9.9 h for ATBC metabolites and 1.6 to 3.0 h for ATEC metabolites. One-compartment kinetic modeling provided preliminary insights into metabolite kinetics. The study suggests that ATBC may undergo more hydroxylation compared to ATEC, but further quantitative analysis is needed to confirm this observation. This research advances the understanding of ATBC and ATEC metabolism in humans, providing a foundation for future exposure assessments and toxicological studies. The identified biomarkers and preliminary metabolic profiles offer valuable starting points for biomonitoring and risk assessment of these alternative plasticizers.

Prognostic significance of tertiary lymphoid structures in gastric neuroendocrine carcinoma with association to delta-like ligand 3 and neuroendocrine expressions.

Gastric neuroendocrine carcinomas (NECs) are rare cancers with highly aggressive behavior. Although tertiary lymphoid structures (TLSs) are well-known prognostic factors in various cancers, their role in gastric NECs remain unexplored. Unique immunohistochemical subtypes of pulmonary NECs have been discovered, however, their feasibility in gastric NECs is unknown. The presence and maturation of TLSs (lymphoid aggregates, primary and secondary follicles) were assessed in 48 surgically resected gastric NECs and were compared with immunohistochemical subtypes, using a panel of ASCL1, NeuroD1, POU2F3, YAP1, and DLL3 with three neuroendocrine (NE) markers. Patients with secondary follicles had significantly better overall survival (OS) and recurrence-free survival (RFS; both, p = 0.004) than those without them. Based on the hierarchical clustering, gastric NECs were classified into all low/negative (31%), high-YAP1 (19%), high-DLL3/low-NE (29%), and high-NE (21%) expression groups. The high-DLL3/low-NE group was associated with absent TLSs (p = 0.026) and showed the worst OS (p = 0.026). Distant metastasis and a lack of secondary follicles were poor independent prognostic factors of OS and RFS. The assessment of TLSs is a feasible and potent biomarker for gastric NECs, thus enabling better prognosis and moreeffective immunotherapy. Furthermore, gastric NECs can be categorized as four immunohistochemically distinct groups, of which the high-DLL3/low-NE group has the worst OS with lack of TLSs.

Diagnostic and screening potential of plasma exosome miR‑99b‑5p and its combination with other miRNAs for colorectal cancer.

Extracellular vesicles (EVs) secreted by tumor cells have been documented to hold viable biomarker potential. Therefore, the present study evaluated the potential clinical value of EV-microRNAs (miRNAs or miRs) in the plasma exosomes of patients with colorectal cancer (CRC) for the early diagnosis and screening of CRC. In total, 95 plasma samples were collected at The Third Affiliated Hospital of Guangzhou Medical University (Guangzhou, China) between 2017 and 2019. Specifically, 68 samples were from patients with CRC and 27 were from healthy control (HC) donors. High-throughput sequencing was used to detect the expression of miRNAs in the isolated plasma EVs, which was subsequently verified by reverse transcription-quantitative PCR. Receiver operating characteristic (ROC) curves were used to analyze the diagnostic potential of single and combined miRNAs for CRC. Bioinformatics analysis was employed to predict the target genes of candidate miRNAs. Compared with those in the HC group, the CRC group expressed higher levels of miR-99b-5p and miR-409-3p, especially during the early stages of CRC. Clinicopathological analysis confirmed the higher expression levels of miR-99b-5p during the early stages, as well as higher expression levels in the colon compared with those in the rectum. ROC curve analysis revealed that the area under the curve (AUC) of miR-99b-5p for the diagnosis of early CRC was 73.5% (P=0.007). The early diagnostic capability of miR-99b-5p combined with miR-409-3p for CRC was evaluated, and the AUC was found to be 74.1% (P=0.006). In addition, the AUC of the combination of miR-99b-5p, miR-409-3p and carcinoembryonic antigen was 81.2% (P<0.001), indicating that this three-parameter combination displayed higher diagnostic power compared with any single miRNA for early CRC screening. The results from the present study suggest that the expression of miR-99b-5p in plasma exosomes is significantly upregulated in CRC, which holds potential for the early diagnosis of this cancer type. Such potential can be enhanced further by combining it with other miRNAs. Therefore, the present study provides a comprehensive but preliminary insight for the viability of miR-99b-5p (alone or combined with other miRNAs) for CRC diagnosis, which requires further exploration in the future.

Urinary Complement C3 and Vitamin D-Binding Protein Predict Adverse Outcomes in Patients with Acute Kidney Injury after Cardiac Surgery.

Acute kidney injury (AKI) is associated with adverse outcomes, including death and dialysis. The goal of this study was to identify prognostic biomarkers of AKI that could be used across multiple phenotypes of AKI and across different species. Liquid chromatography/tandem mass spectrometry analysis of urine samples from three species (human, rat, and mouse) and four etiologies of AKI identified five potential biomarkers, of which two were validated, complement C3 and vitamin D-binding protein, in a cohort of 157 patients that developed AKI following cardiothoracic surgery. We studied the relationship between the biomarker's concentration in the urine and the development of a composite primary endpoint (stage 3 AKI within 10 days or death within 30 days). Of the 153 patients who developed AKI following cardiovascular surgery, 17 met the combined primary outcome. The median concentration of urine complement C3 adjusted to urine creatinine had the best predictive value and was significantly higher in the primary outcome group than in the controls. Similarly, the median concentration of vitamin D-binding protein was higher in the primary outcome group. The studies provide proof in principle that cross-species discovery analyses could be a valuable tool for identifying novel prognostic biomarkers in AKI. Urine complement C3 and vitamin D-binding protein could be promising early predictors of adverse outcomes in patients who develop AKI after cardiac surgery.

Identification of Immune-Related Genes as Potential Biomarkers in Early Septic Shock

Plain Language SummarySeptic shock is a dangerous condition that happens when an infection spreads through the body and triggers a strong immune response, leading to the failure of multiple organs. Recognizing and treating septic shock quickly is crucial to prevent lasting damage to the body’s organs. However, doctors currently do not have highly effective tools to diagnose septic shock early. In this study, we looked at genetic information from patients with early septic shock. We used a large public database to find patterns in gene activity that could help identify the condition. By analyzing the genes, we could tell which types of immune cells were involved. We discovered that certain immune cells, like neutrophils, M0 macrophages (a kind of white blood cell that helps fight infections), and natural killer cells, were more active in patients with septic shock. We also found genes that are active during immune responses and disease progression. These genes were mostly involved in the body’s defense system, cell communication, and energy use. Among these genes, six stood out as being closely connected to M0 macrophages. These six genes could potentially serve as early warning signs for doctors to detect septic shock, as they were good at distinguishing between patients with and without the condition. In summary, the study identified six genes that might be useful for spotting septic shock early on. These findings could lead to better diagnostic tools, helping doctors to treat patients before their condition becomes critical.

Metabolomic analysis of the impact of red ginseng on equine physiology.

Red ginseng (RG), a traditional herbal remedy, has garnered attention owing to its diverse health benefits resulting from its complex composition. However, extensive research is needed to substantiate the efficacy of RG and understand the underlying mechanisms supporting these benefits. This study aimed to identify potential biomarkers and investigate the impact of RG on related metabolic pathways in horse plasma using liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. Ten horses were divided into control and RG groups, with the latter administered RG at a dose of 600 mg⋅kg-1⋅day-1 for 3 weeks. Subsequently, the plasma samples were collected and analyzed using LC-MS. Multivariate statistical analysis, volcano plots, and feature-based molecular networking were employed. The analysis identified 16 metabolites that substantially decreased and 21 metabolites that substantially increased following RG consumption. Among the identified metabolites were oleanolic acid, ursolic acid, and ginsenoside Rb1, which are known for their antioxidant and anti-inflammatory properties, as well as lipid species that influence sphingolipid and glycerophospholipid metabolism. Additionally, potential biomarkers, including major RG components, demonstrated distinct group clustering in principal component analysis and partial least squares-discriminant analysis, indicating their utility in assessing the physiological effects of RG consumption. This study contributes to a comprehensive understanding of the effects of RG on health.

The role of SIRT1 in autophagy and drug resistance: unveiling new targets and potential biomarkers in cancer therapy.

Cancer, the world's second leading cause of death after cardiovascular diseases, is characterized by hallmarks such as uncontrolled cell growth, metastasis, angiogenesis, hypoxia, and resistance to therapy. Autophagy, a cellular process that can both support and inhibit cancer progression, plays a critical role in cancer development and progression. This process involves the formation of autophagosomes that ultimately fuse with lysosomes to degrade cellular components. A key regulator of this process is Sirtuin 1 (SIRT1), which significantly influences autophagy. This review delves into the role of SIRT1 in modulating autophagy and its broader impacts on carcinogenesis. SIRT1 regulates crucial autophagy mediators, such as AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR), effectively promoting or suppressing autophagy. Beyond its direct effects on autophagy, SIRT1's regulatory actions extend to other cell death processes, including apoptosis and ferroptosis, thereby influencing tumor cell proliferation, metastasis, and chemotherapy responses. These insights underscore the complex interplay between SIRT1 and autophagy, with significant implications for cancer therapy. Targeting SIRT1 and its associated pathways presents a promising strategy to manipulate autophagy in cancer treatment. This review underscores the potential of SIRT1 as a therapeutic target, opening new avenues for enhancing cancer treatment efficacy.

Potential Biomarkers and Therapeutic Targets in Companion Animals

Potential Biomarkers and Therapeutic Targets in Companion Animals

Network Pharmacology Integrated With Quantum‐Polarized Ligand Docking and Molecular Simulation Revealed the Anti‐Diabetic Potential of Curcumin

AbstractDiabetes mellitus is a chronic metabolic disorder affecting millions of people worldwide and causes serious complications such as diabetic nephropathy. Curcumin, a natural polyphenol derived from turmeric, has demonstrated antidiabetic, anti‐inflammatory, and antioxidant properties. However, the molecular mechanisms underlying curcumin's anti‐diabetic effects remain incompletely understood. This study employed network pharmacology, molecular docking, and simulation techniques to explore the potential targets, and key pathways of curcumin in the treatment of diabetes. Using SwissTarget prediction and Superpred databases, we predicted the molecular targets for curcumin, while diabetes‐associated genes were obtained from DisGeNet. We identified 60 common targets for curcumin in diabetes. Protein‐protein interaction (PPI) analysis revealed three sub‐networks and ten hub genes with AKT1, TNF‐α, EGFR, and STAT3 identified as key hub genes that could serve as potential biomarkers. Gene enrichment analysis indicated that these genes primarily regulate insulin resistance and other metabolic pathways. Quantum‐polarized ligand docking (QPLD) showed that curcumin establishes multiple hydrogen and hydrophobic interactions with the essential amino acids of these hub targets. Molecular simulation results demonstrated stable dynamic behavior, a compact structure, and variations in residue flexibility. Binding free energy calculations using MM/GBSA and MM/PBSA methods validate curcumin's strong binding to the potential targets. Total binding free energy using MM/GBSA ranged from −21.35 to −30.94 kcal/mol while MM/PBSA calculations showed total binding free energy values between −19.80 and −26.66 kcal/mol. Altogether, this study provides valuable insights into the molecular targets of curcumin in diabetes and lays the foundation for future advancements in diabetes treatment.

α9β1 integrin & its ligands as new potential biomarkers in FMF.

Background & objectives Familial Mediterranean Fever (FMF) manifests as a hereditary condition characterized by repeated bouts of fever, abdominal, chest, and joint discomfort, and swelling. Colchicine is the most common form of treatment, but it does not eliminate the disease. The underlying causes of the inflammatory mechanism are still not fully known. Methods A total of 20 healthy controls, 16 individuals with FMF in the attack period, and 14 in the remission period participated in the study. ITGA9, ITGB1, OPN, TNC, VEGF, VCAM-1, TGM2, TSP-1, Emilin-1, and vWF levels were measured by ELISA by obtaining serum from blood samples of individuals. In addition, gene expressions of α9β1 (ITGA9, ITGB1) and its best known ligands (TNC, SPP1) were analyzed by quantitative real-time PCR (qPCR). Results The findings of this study showed that serum levels of α9β1 and its ligands were higher in individuals with FMF in the attack period than in the healthy controls and the FMF group in the remission period (P<0.05). The marker levels of the healthy group were also higher than those in the remission period (p<0.05). In addition, when the gene expressions were compared between the healthy controls and FMF group, no significant difference was found for ITGA9, ITGB1, TNC, and SPP1 genes. Interpretation & conclusions The function of α9β1 and its ligands in FMF disease was investigated for the first time in this study as per our knowledge. Serum levels of these biomarkers may help identify potential new targets for FMF disease diagnosis and treatment approaches.

Potential tumor-specific antigens and immune landscapes identification for mRNA vaccine in thyroid cancer.

Tumor mRNA vaccines have been identified as a promising technology for cancer therapy in multiple cancer types, while their efficacy in thyroid cancer (THCA) is unclear. Immunotyping is strongly associated with the immune microenvironment and immune status in cancer, thus it is important in vaccination and therapeutic response. This study is to identify potential valuable antigens and novel immune subtypes of THCA for immune landscape construction, thus screening patients suitable for mRNA vaccination. The clinical information and gene expression files of 568 THCA cases were obtained from the TCGA dataset. The DNA copy number variation and the somatic mutation of THCA were visualized by the cBioPortal database. TIMER was used to investigate the immune infiltrating correlation with candidate antigens. Consensus clustering analysis was conducted to cluster data using the ConsensusClusterPlus package. The immune landscapes of THCA patients were visualized using the Monocle package. The critical hub genes for THCA mRNA vaccines were identified by WGCNA package. To validate, the immunohistochemistry and real-time quantitative PCR (RT-qPCR) were performed to detect the expression level of potential antigen for mRNA vaccine in tissue and cell lines in THCA. Thymidine kinase 1 (TK1) was identified as a potential biomarker of mRNA vaccine against THCA. It was confirmed to be significantly upregulated in THCA tissues and cells lines. Moreover, three novel immune subtypes of THCA were obtained based on the expression consistency of immune-associated genes. The S2 subtype was characterized as an immunological "cold" phenotype with a high expression of immunogenic cell death modulators. S1 and S3 subtypes were immunological "hot" phenotypes with immune checkpoints upregulation. Further, the immune landscape of THCA patients was visualized and ten hub genes for mRNA vaccines were identified. TK1 was a tumor-specific antigen of mRNA vaccines. The patients belonging to the S2 subtype ("cold" tumor) were suitable for mRNA vaccine therapy in THCA. Notably, ten hub genes were conducted as potential biomarkers for identifying suitable patients for mRNA vaccination. These findings provided novel insights into mRNA vaccine development against THCA.

Metabolomic signature identifies HDL and apolipoproteins as potential biomarker for systemic sclerosis with interstitial lung disease

BackgroundHigh-density lipoproteins (HDL) affect endothelial functions such as the expression of endothelial cell adhesion molecules and exert anti-apoptotic/-thrombotic functionalities. Therefore, profound analysis of lipoproteins may unveil biomarkers for (micro-)vasculopathy in systemic sclerosis (SSc) and mortality determining disease manifestations like interstitial lung disease (SSc-ILD). Because nuclear magnetic resonance (NMR) spectroscopy provides a wide range of lipoprotein parameters beyond the capabilities of classical analyses it has been used herein to examine lipoprotein profiles in SSc. MethodsTo detect the metabolic and lipidomic profile serum samples from clinically well-characterized SSc patients (n = 100) and age-and sex-matched healthy controls (n = 40) were analyzed by 1H NMR spectroscopy using Bruker's in-vitro diagnostic research (IVDr) protocol. Statistical analyses were performed to validate significant findings and to search for associations between lipoproteins and clinical phenotypes. ResultsPatients with SSc-ILD and lung fibrosis displayed reduced HDL levels. Furthermore, a reduction in apolipoprotein A1 + A2 and its HDL fractions reflected a distinct lipoprotein profile for SSc-ILD patients. This association was independent of potential clinical confounders for dyslipidemia. Notably, in SSc-ILD HDL levels correlate with FVC (forced vital capacity), DLCO (diffusion capacity of the lungs for carbon monoxide), and the modified Rodnan-Skin-Score. ConclusionThese results suggest HDL and its lipoproteins may be considered as potential new biomarkers for SSc-ILD. Immune-mediated HDL effects on the endothelium facilitate microvasculopathy - one of the pathophysiological hallmarks in SSc. Therefore, a closer prospective evaluation of the capability of HDL-determination and its lipoproteins regarding a more individualized evaluation of SSc-ILD is warranted.

Hemodynamic profiles in idiopathic intracranial hypertension: Doppler ultrasonography as a diagnostic tool for pulsatile tinnitus

Purpose: This study aims to evaluate the role of ophthalmic Doppler ultrasonography (USG) in differentiating IIH patients with and without bilateral PT by analyzing hemodynamic changes in the orbital vessels. Materials and Methods: A prospective, single-center, case-control study was conducted at Harran University from November 2023 to June 2024. The study included 20 IIH patients. Participants underwent clinical assessments, ophthalmic evaluations, brain imaging, lumbar puncture, and transorbital sonography. IIH patients were categorized into PT (n=8) and non-PT (n=12) groups. Doppler USG measured end-diastolic velocity (EDV), peak systolic velocity (PSV), time-averaged velocity (TAV), resistive index (RI), pulsatility index (PI), and systolic to the diastolic ratio (S/D) of the central retinal artery. Results: Significant differences were observed in left eye EDV and TAV, with lower values in the PT group. Although not statistically significant, right-eye EDV and TAV also trended lower in the PT group. Additionally, both eyes' PSV values showed a trend toward statistical significance, being lower in the PT group. ROC curve analysis identified optimal thresholds for left eye EDV (5.35; sensitivity 75%, specificity 83.33%) and TAV (9; sensitivity 50%, specificity 91.67%). Conclusion: Orbital Doppler USG reveals distinct hemodynamic profiles in IIH patients with PT, suggesting EDV and TAV as potential biomarkers. Larger cohort studies are needed to validate and clarify IIH-PT mechanisms.

Biomarker Profiles in Serum and CSF for Early Diagnosis of Selected Neurodegenerative Diseases

Biomarker research and justification for neurodegenerative illnesses have seen enormous efforts over the last ten years. Bio-fluid-based biomarkers have been believed to provide a better and easier approach to detecting biomarkers for diagnosing nervous system pathologies. Objectives: To evaluate the diagnostic potential of certain biomarkers in serum and cerebrospinal fluid to diagnose Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease at an initial stage. Methods: 280 participants were taken and distributed into four groups, comprising, 70 patients with early-stage Alzheimer’s disease, 70 with early-stage Parkinson’s disease, 70 with early-stage Huntington’s disease, and 70 age-matched healthy controls. Blood and cerebrospinal fluid samples were drawn and medical history was taken from the patients. Serum and cerebrospinal fluid levels of amyloid-beta (Aβ42), total tau (t-tau), phosphorylated tau (p-tau), alpha-synuclein, huntingtin protein, and neuro-filament light chain were evaluated using enzyme-linked immunosorbent assays. Results: Alzheimer’s disease patients showed reduced serum Aβ42 (80.4 ± 15.6 pg/mL) and elevated t-tau (140.5 ± 18.2 pg/mL). Parkinson’s disease patients had raised serum alpha-synuclein (12.5 ± 2.3 ng/mL) and neuro-filament light chain. Huntington’s disease patients showed significant increases in serum huntingtin protein (8.2 ± 2.0 ng/mL). These profiles indicate efficacy in early diagnosis. Conclusions: It was concluded that Aβ42 and tau effectively detect Alzheimer’s disease, while Parkinson’s disease patients can be effectively diagnosed with Serum and cerebrospinal fluid levels of the neuro-filament light chain. Similarly, huntingtin protein and neuro-filament light chain are sensitive enough to detect Huntington’s disease at its early stages.

Plasma extracellular vesicle: a novel biomarker for neurodegenerative disease diagnosis

Extracellular vesicles (EVs) are membrane-bound structures that carry proteins, lipids, RNA, and DNA, playing key roles in cell communication and material transport. Recent research highlights their potential as disease biomarkers due to their stability in bodily fluids. This study explores using tau and TDP-43 proteins in plasma EVs as diagnostic biomarkers for frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Analyzing plasma EVs from clinical cohorts, the study found that the 3R/4R tau ratio and TDP-43 levels effectively differentiate between diagnostic groups with high accuracy. Notably, plasma EV biomarkers demonstrate higher diagnostic accuracy and stability compared to direct plasma testing, providing new insights and approaches for future research and clinical practice. Further research is needed to validate these biomarkers in diverse populations and to establish standardized protocols. Future studies should continue to explore the potential of EV biomarkers in a broader range of neurodegenerative diseases and delve deeper into the mechanisms of EV secretion and sorting to enhance their diagnostic utility.

Bioinformatics Tools Assist in The Screening of Potential Porcine-Specific Peptide Biomarkers of Gelatin and Collagen For Halal Authentication

Gelatin and collagen are two animal-derived ingredients that are widely used in various industries. Both have distinctive physico-chemical characteristic that made them ingredients of interest for many industrial players to be applied as there are vast arrays of usage in the food, cosmetic and biomedical fields. However, the origin of gelatin and collagen poses ethical and religious concerns, especially for Muslims and Jews who have restrictions on food consumption. Porcine by-products are of concern for religious and health reasons, and there is a demand for precise and reliable detection techniques. The limitation of DNA detection is due to extreme environment in food processing which results in low extractability of DNA. Therefore, peptide-based detection using mass spectrometry is required. However, identify the suitable marker is like searching needle in haystacks. Hence, combination of bioinformatics and mass spectrometry is proposed. This study aims to identify the specific peptide biomarkers by employing bioinformatics technique which can be applied to identify gelatin and collagen sources with the aid of mass spectrometry. In these approach, combination of Petunia Trans-Proteomic Pipeline (TPP, version 5.2.0) and sequence alignment ClustalW were applied to facilitate the MS data (LC-QTOF-MS) and peptide identification. As a result, 69 fasta file of protein sequence from both UniProtKB and NCBInr have been collected, 81 collagen peptides sequence and 118 gelatine peptides has been attainable that have the potential to distinguish different species. In conclusion, in silico protein sequence approaches helps to enable rapid screening of proteotypic peptides that can serve as species biomarkers proficiently.

Unraveling Neurodevelopmental Disorders: Signalling Pathways as Potential Targets for Therapeutic Intervention in Autism Spectrum Disorder

Introduction: Autism Spectrum Disorder (ASD) presents a multifaceted challenge with limited therapeutic options and a need for early biomarkers. Understanding disrupted signalling pathways offers promise for intervention and assessment. Methods: Literature review spanning genetic, pre-clinical, and patient studies elucidating pathways implicated in ASD pathogenesis, including melatonin, mTOR, Retinoic acid, Hedgehog, Notch and Wnt signalling. Results: Core components of key signalling pathways, such as melatonin, mTOR, Retinoic acid, Hedgehog, Notch and Wnt, are dysregulated in ASD. These pathways regulate crucial aspects of the nervous system, including immune function, neuronal growth, neurotransmission, and metabolism. Discussion: Manipulating these pathways could potentially modify ASD traits by influencing brain development and immune homeostasis. Targeting specific nodes within these pathways may offer novel therapeutic approaches for ASD management. Additionally, identifying biomarkers associated with pathway dysregulation could enable earlier diagnosis and monitoring of disease progression. Conclusion: Understanding the intricate interplay of signalling pathways in ASD pathogenesis provides insights into potential therapeutic targets and biomarkers. Further research into the manipulation of these pathways and their impact on ASD traits is warranted to advance personalized treatment strategies and improve outcomes for individuals with ASD.

Autophagy-associated biomarkers ULK2, UVRAG, and miRNAs miR-21, miR-126, and miR-374: Prognostic significance in glioma patients.

As the pioneering study from Pakistan, our research distinctly focuses on validating the roles of autophagy-associated genes and MicroRNAs (miRs) in the unique context of our population for glioma prognosis. The study delves into the nuanced interplay of autophagy within a miR-modulated environment, prompting an exploration of its potential impact on glioma development and survival. Employing real-time PCR (qPCR), we meticulously assessed the expression profiles of autophagy genes and miRs in glioma tissues, complemented by immunohistochemistry on Formalin-fixed paraffin-embedded tissues from the same patients. Our comprehensive statistical analyses, including the data normality hypothesis Shapiro-Wilk test, the Mann-Whitney U-test, Spearman correlation test, and Kaplan-Meier survival analysis, were tailored to unravel the intricate associations specific to low- and high-grade glioma within our population. Clinicopathological analysis revealed a predominance of male patients (66%) with a median age of 35 years. Glioblastoma (32%) and Astrocytoma (36%) were the most prevalent histopathological subtypes. Molecular analysis showed significant correlations between prognostic markers (Ki-67, IDH-1, p53) and clinicopathological factors, including age, histological type, radiotherapy, and chemotherapy. In high-grade glioma, increased expression of AKT and miR-21, coupled with reduced ULK2 and LC3 expression was distinctly observed. While correlation analysis identified a strong positive correlation between ULK2 and UVRAG, PTEN, miR-7, and miR-100 in low-grade glioma, unveiling distinctive molecular signatures unique to our study. Furthermore, a moderate positive correlation emerged between ULK2 and mTOR, miR-7, miR-30, miR-100, miR-204, and miR-374, also between miR-21 and miR-126. Similarly, a positive correlation appeared between ULK2 and AKT, LC3, PI3K, PTEN, ULK1, VPS34, mTOR, Beclin1, UVRAG, miR-7 and miR-374. AKT positively correlated with LC3, PI3K, PTEN, ULK1, VPS34, mTOR, Beclin1, UVRAG, miR-7, miR-30, miR-204, miR-374, miR-126 and miR-21 weakly correlated with AKT and miR-30 in high-grade glioma, providing further insights into the autophagy pathway within our population. The enrichment analysis for miR-21, miR-126, and miR-374 showed MAPK pathway as a common pathway along with Ras, PI3K, and mTOR pathway. The low ULK2, UVRAG, and miR-374 expression group exhibited significantly poor overall survival in glioma, while miR-21 over-expression indicated a poor prognosis in glioma patients, validating it in our population. This study provides comprehensive insights into the molecular landscape of gliomas, highlighting the dysregulation of autophagy genes ULK2, and UVRAG and the associated miR-21, miR-126 and miR-374 as potential prognostic biomarkers and emphasizing their unique significance in shaping survival outcomes in gliomas within the specific context of the Pakistani population.