Bahar Sarikamis Johnson

Background: Microbiota-related metabolites and innate immune signaling molecules transported via plasma-derived extracellular vesicle (EV)-enriched fractions through the gut–brain axis may contribute to neuroinflammation and disease progression in Parkinson’s disease (PD). Therefore, this study aimed to investigate the levels of microbiota-associated molecules in plasma-derived EV-enriched fractions and their relationship with clinical parameters in patients with PD. Methods: This study included 38 patients with PD and 38 age-matched healthy spouses. Clinical evaluations, disease staging (Hoehn & Yahr, UPDRS), and cognitive/psychiatric tests (MMSE, BDI, BAI) were conducted. Uncorrected spot urinary indoxyl sulfate concentration and routine serum biochemical markers were analyzed. Plasma-derived EV-enriched fractions were isolated and analyzed for microbiota-related molecules (acetate, TLR2, TLR4, TLR5, LPS, and EGF) using ELISA and functional assays. Results: Clinical evaluations indicated mild-to-moderate disease severity in PD patients. Systemic analyses revealed elevated uncorrected spot urinary indoxyl sulfate alongside reduced serum folate, vitamin B12, and free T4, together with increased copper, iron, and zinc levels in PD. Acetate, LPS, TLR2, and TLR5 levels in the plasma-derived EV-enriched fractions were significantly upregulated. Exploratory correlation analyses (none significant after FDR correction) suggested that lower serum folate and TLR4 levels in the plasma-derived EV-enriched fractions were associated with higher motor symptom severity and treatment complications. ROC analyses showed that TLR2 levels in the plasma-derived EV-enriched fractions had the highest observed AUC among the evaluated markers for PD. Conclusions: In this exploratory cross-sectional study, patients with PD showed differences in microbiota-related molecules (acetate, LPS; urinary indoxyl sulfate as an uncorrected spot concentration) and host-associated innate immune markers (TLR2, TLR5) in plasma-derived EV-enriched fractions, and TLR2 had the highest observed AUC among the evaluated markers. These findings are compatible with, but do not demonstrate, a contribution of the gut microbiota to PD; vesicular association, microbial origin, and causality were not established. Whether dietary or other microbiota-targeted interventions could be beneficial remains an open question for future longitudinal and interventional studies.

Background/Objectives: Alzheimer’s disease (AD) is associated with impaired brain insulin signaling, oxidative stress, and neuroinflammation. This study investigated the effects of incensole acetate (IA) on sirtuin-associated insulin-signaling and cellular stress-response pathways using integrated computational and in vitro approaches. Methods: ADMET prediction, molecular docking, molecular dynamics simulations, and MM-PBSA analyses were performed for IA against SIRT1, SIRT3, and SIRT6 and compared with their corresponding reference ligands. An Aβ1–42-induced AD model was established in mesenchymal stem cell-derived neurons. The effects of IA on insulin-signaling components, sirtuins, Aβ, NF-κB, NRF2, and PPARα were evaluated using RT-qPCR, Western blotting, and immunofluorescence. Results: IA showed weaker docking affinities than the corresponding reference ligands for all three sirtuins, whereas trajectory-based analyses revealed target-dependent dynamic behavior. MM-PBSA-derived binding-energy estimates were −35.16 ± 3.32, −30.24 ± 3.63, and −38.26 ± 3.90 kcal/mol for IA with SIRT1, SIRT3, and SIRT6, respectively, with IA showing a more favorable relative energetic profile than 8L9 for SIRT6. In vitro, IA treatment was associated with reduced detectable Aβ levels and modulation of INSR, IRS, AKT, and AS160 expression. IA increased SIRT1 and SIRT6 expression, whereas SIRT3 protein levels were not significantly altered. IA also reduced NF-κB and increased NRF2 and PPARα expression. Conclusions: IA modulated insulin-signaling-related, sirtuin-associated, inflammatory, oxidative-stress, and metabolic markers in an Aβ1–42-induced cellular AD model. Computational analyses support potential IA–sirtuin interactions, particularly a favorable relative MM-PBSA energetic profile for SIRT6; however, direct sirtuin activation or causal sirtuin-mediated signaling was not established.

Objective: Cancer-associated fibroblasts (CAFs) are critical components of the tumor microenvironment that greatly influence breast cancer progression. In this study, we used in silico analysis to determine the potential pathways and genes that could affect breast cancer progression associated with CAFs.Method: Data from breast cancer patients, collected through microarray and next-generation sequencing (NGS), were retrieved using the Gene Expression Omnibus (GEO) platform. The differentially expressed genes (DEGs) were determined and further analyzed through Gene Ontology (GO) and pathway analysis, and potential therapeutic targets were predicted via hub genes.Results: In CAFs, 940 genes were upregulated, and 561 genes were downregulated. These genes were significantly linked to pathways such as MAPK signaling, estrogen signaling, NF-kB signaling, IL-17 signaling, and TGF-ß signaling. These pathways suggest that CAFs are involved in the progression of breast cancer. The hub genes, namely ESR1, MET, IL1B, SMAD3, and FOS, were found to be enriched in key pathways and were associated with certain anti-tumor drugs that are either undergoing clinical trials or have been approved for clinical use.Conclusion: This findings suggest that critical genes such as ESR1, MET, IL1B, SMAD3, and FOS are predicted to contribute to CAF-mediated regulatory networks in breast cancer.

Background: Accurate preoperative prediction of lymph node metastasis (LNM) remains challenging in colon cancer. Ferroptosis, an iron-dependent regulated cell-death pathway, is implicated in tumor invasion and metastasis. Yet, the clinical value of routine iron-metabolism indices as indirect systemic indicators of ferroptosis-relevant biology remains underexplored. Methods: A multi-stage workflow was implemented. First, transformer-based literature mining (PubMedBERT, BioLinkBERT, BioBERT) prioritized ferroptosis-associated genes and metabolites. Second, transcriptomic validation was performed in TCGA-COAD and GSE39582 cohorts using differential expression analysis. Third, machine-learning models (logistic regression, random forest, XGBoost) were developed to predict pathologically confirmed LNM (n = 421) under three feature configurations: preoperative baseline, preoperative plus iron-metabolism markers, and a pathology-augmented model. LVI prediction was separately evaluated (n = 416) using ferroptosis-only, clinical-only, and combined sets. Results: Literature mining identified a core ferroptosis axis dominated by redox and iron-handling regulators. Transcriptomic analyses demonstrated robust tumor–normal separation and consistent perturbation of key ferroptosis genes (SLC7A11, GPX4, ACSL4, PTGS2). Preoperative models achieved moderate LNM discrimination (best AUC = 0.704), whereas a postoperative pathology-augmented explanatory benchmark achieved an AUC of 0.818. Out-of-fold risk stratification identified a low-risk subgroup with 26.7% nodal positivity, compared with 44.7% in the overall cohort. For LVI prediction, models based on iron-handling indices showed modest discrimination, and their addition to clinical variables produced model-dependent numerical changes in performance (maximum ΔAUC = +0.114). These routinely measured indices provided exploratory predictive information but should not be interpreted as direct measures of tumor ferroptosis. Conclusions: This integrative framework links ferroptosis-related biology with clinical machine learning and suggests that routine iron-handling indices may provide exploratory complementary information for LVI prediction and preoperative nodal-risk stratification, whereas postoperative pathology variables provide additional explanatory value but are not part of a deployable preoperative model.

Type A aortic dissections are pathologies with high mortality rates. Although ascending aortic aneurysms are typically planned for elective surgery, they are significant conditions in cardiovascular surgery due to their potential to cause type A aortic dissection. This study, which is the first to examine sirtuin 1 (SIRT1) in human ascending aortic tissues, aims to elucidate the relationship between ascending aortic pathologies and the SIRT1 protein. A case-control study was conducted using aortic tissues and demographic data from patients who underwent surgery for ascending aortic aneurysm and type A aortic dissection. Coronary artery bypass patients were selected as the control group. The groups were compared in terms of SIRT1 levels. The study included a total of 46 patients (16 in the aneurysm group, 14 in the dissection group, and 16 in the control group). The SIRT1 protein level was the highest in the ascending aortic aneurysm group (214, interquartile range [IQR] 79 - 270), followed by the dissection group (172, IQR 148 - 224), and the lowest in the control group (104, IQR 78 - 123) (P = 0.014). SIRT1 level was found to be low in patients with coronary artery disease (P = 0.001), peripheral artery disease (P = 0.008), and hypertension (P = 0.023). Type A aortic dissections are associated with elevated SIRT1 levels in the tissue. Systemic atherosclerotic diseases, such as coronary and peripheral artery diseases, are associated with decreased SIRT1 levels. There is also a relationship between hypertension and sirtuin1 levels.

Recent studies emphasize the pivotal role of endoplasmic reticulum (ER) stress in Alzheimer’s disease (AD), highlighting the need for further investigation into this critical link. In response to ER stress, cells increase reactive oxygen species (ROS) production, leading to heightened oxidative stress. This interplay has sparked interest in antioxidant molecules such as squalene (SQ) as potential therapeutic agents. The primary objective of this study was to examine the impact of SQ on the unfolded protein response (UPR) pathway triggered by ER stress in an in vitro AD model. Herein, molecular docking analysis was performed to evaluate SQ interactions with target proteins, followed by in vitro assays. Human bone marrow-derived mesenchymal stem cells were differentiated into neuronal-like cells and characterized via immunostaining. The cells were then exposed to Aβ₁₋₄₂ toxicity to establish an in vitro AD model. To assess the effects of SQ treatment following Aβ_1–42 exposure, UPR-related proteins (BIP, p-PERK, PERK, eIF2α, p-eIF2α, ATF4, CHOP) were analysed by Western blotting; ROS levels were quantified to evaluate oxidative stress, and a TUNEL assay was performed to assess apoptosis. Our findings indicate that SQ alters protein expression within the UPR pathway in the AD experimental model. Notably, amyloid-β levels were significantly reduced in the SQ-treated group (p˂0.001). Furthermore, SQ reduced ROS levels. These results suggest that SQ holds potential as a therapeutic agent for mitigating amyloid-β toxicity. Graphical abstract Effects of Squalene (SQ) on UPR-related protein expression in neuronal cells. Results illustrate the expression levels of UPR-associated proteins (BIP, p-PERK, PERK, eIF2α, p-eIF2α, ATF4, CHOP) in neuronal cells with and without SQ treatment. SQ administration notably reduces p-PERK, p-eIF2α, ATF4, and CHOP levels, suggesting a regulatory effect on the UPR pathway. The downregulation of these proteins indicates that SQ may alleviate ER stress, potentially contributing to improved cellular homeostasis.

Understanding the mechanism behind Alzheimer’s disease is imperative due to the critical role of the autophagy pathway in protein homeostasis and neuronal survival. Autophagy pathway irregularities in neurons may increase exosome-mediated toxic protein transport, which can spread neurodegenerative diseases. Compelling evidence hints that acacetin (ACA) is a naturally occurring biocomponent exhibiting neuroprotective pharmacological properties. However, further molecular investigations are pressing to uncover the therapeutic potential of ACA. The present investigation endeavors to scrutinize the impact of ACA on the autophagy pathway and exosome release in an amyloid beta (Aβ) peptide-induced toxicity model. Herein, first, molecular modeling was performed between ACA and autophagy-related proteins. Afterward, the Aβ peptide-induced toxicity model cells were treated with ACA, and total and exosomal protein isolation was carried out and analyzed. Considering the findings, our molecular dynamics simulation of the ACA-protein complexes, spanning 100 ns, conclusively demonstrated stable protein–ligand interactions. Additionally, ACA was determined to regulate LC3II, Beclin-1, p62, and Lamp2a protein levels and reduce amyloid-β and Alix protein levels. In conclusion, our study highlights the significant in vitro neuroprotective effect of ACA against Aβ toxicity through autophagy. Moving forward, future studies may seek to elucidate the specific neuroprotective, therapeutic effects and mechanisms of ACA via autophagy in in vivo models. Addressing the identified limitations and capitalizing on the outlined future prospects are essential steps towards harnessing the therapeutic potential of ACA in combating neurodegenerative diseases, offering renewed hope for patients and caregivers alike.

Purpose: Achieving a pathological complete response (pCR) after neoadjuvant therapy in HER2-positive breast cancer patients is the most significant prognostic indicator, suggesting a low risk of recurrence and a survival advantage. This study aims to investigate clinicopathological parameters that can predict the response to neoadjuvant treatment in HER2 + breast cancers and to explore the roles of tumour-infiltrating lymphocytes (TILs), CD8 + T lymphocytes and PD-L1 expression. Methods: This single-centre retrospective study was conducted with 85 HER2-positive breast cancer patients who underwent surgery after receiving neoadjuvant therapy between January 2017 and January 2020. Paraffin blocks from these patients were selected for immunohistochemical studies. Results: A complete pathological response to neoadjuvant treatment was determined in 39 (45.9%) patients. High Ki-67 index (> 30%), moderate to high TIL infiltration, PD-L1 positivity and high CD8 cell count (≥ 25) were significantly associated with pCR in univariate analyses (p: 0.023, 0.025, 0.017 and 0.003, respectively). Multivariate regression analysis identified high Ki-67 index (> 30%) and CD8 cell infiltration as independent predictors for pCR in HER2-positive breast cancer. Conclusions: High Ki-67 index, and high CD8 cell count are strong predictors for pCR in HER2-positive breast cancer. Tumours with high Ki-67 index, high TILs and CD8 infiltration may represent a subgroup where standard therapies are adequate. Conversely, those with low TILs and CD8 infiltration may identify a subgroup where use of novel strategies, including those that increase CD8 infiltration could be applied.