Expression Score Research Articles

Added value of FDG-PET for detection of progressive supranuclear palsy

BackgroundDiagnostic criteria for progressive supranuclear palsy (PSP) include midbrain atrophy in MRI and hypometabolism in [18F]fluorodeoxyglucose (FDG)-positron emission tomography (PET) as supportive features. Due to limited data regarding their relative...

Toll-Like Receptor 7-Expressed Macrophages Are Involved in the Pathogenesis of Esophageal Achalasia and Esophagogastric Junction Outflow Obstruction.

Esophageal achalasia is a typical esophageal motility disorder (EMD). Although viral infections have been hypothesized to play a role in the pathogenesis of esophageal achalasia, its etiology remains unclear. This study used esophageal muscle layer specimens collected during per-oral endoscopic myotomy (POEM) procedures to investigate the association between esophageal achalasia and esophagogastric junction outflow obstruction (EGJOO) and pattern recognition receptors. Patients with esophageal achalasia and EGJOO who underwent POEM were allocated to the EMD group. Biopsies of the inner circular muscle were conducted during the POEM procedure. The control group comprised individuals diagnosed with esophageal squamous cell carcinoma who underwent surgical resection. Expression of pattern recognition receptors, including Toll-like receptor (TLR) 7, was examined by polymerase chain reaction. Immunohistochemical staining was performed to determine TLR7 expression sites in the esophageal muscle layer, and the relationship between TLR7 mRNA expression and clinical score was investigated. Our analysis revealed a notable upregulation of TLR7 mRNA levels within the muscle layer of esophageal achalasia and EGJOO, in contrast to those of control specimens. In contrast, the correlation between TLR7 and clinical score was not significant. Immunohistochemical staining revealed increased numbers of TLR7-expressing macrophages between the muscle layers. TLR7-expressing macrophages are involved in the innate immune response underlying esophageal achalasia and EGJOO. This result will lead to the elucidation of new pathogenetic mechanisms and the development of novel therapeutic targets.

Prevalence of dry eye in people over 50 years old in Beichen district, Tianjin city: a cross-sectional population-based survey

BackgroundA cross-sectional population-based survey in the Beichen district of Tianjin was conducted to estimate the prevalence of dry eye disease (DED) among the population over 50 years old with Dry Eye Workshop (DEWS) II and Chinese expert consensus (CEC) criteria.MethodsA total of 5791 subjects over 50 years old were enrolled. Ocular surface disease index (OSDI) questionnaire, lipid layer thickness (LLT), partial blink ratio (PBR), fluorescein tear film breakup time (FBUT), Schirmer I test (SIT), fluorescein staining, meibomian gland dropout, meibomian gland expression scores (MES) and quantity scores (MQS) was assessed. Additionally, basic information, weight, disease history, living habits, anxiety, and depression condition were collected.ResultsAccording to the CEC, the prevalence of DED was 39.0%, whereas 44.0% based on DEWS II. The prevalence of DED increased with age and was substantially greater among women (41.1%, 95% CI, 39.5-42.6%) than males (35.1%, 95% CI, 33.1 -37.2%) (p < 0.001). Furthermore, the severity of DED was more severe in women (p = 0.006). The associated risk factors were age, female, depression, smoking, insomnia, and glaucoma. On the other hand, 53.6% of these populations were diagnosed as asymptomatic DED, and the morbidity was higher in males (p = 0.007).ConclusionsThe prevalence of DED in China was relatively high, which was associated with aging, female(sex), depression, smoking and sleep problems. Hence, it is crucial for clinicians and caregivers to be aware of the existence of asymptomatic DED within the susceptible population.

26 Applying single cell RNA sequencing of sarcomatoid renal cell carcinoma for the development of a novel transcriptomic biomarker to predict immunotherapy response

Abstract Background Renal cell carcinoma with sarcomatoid features (sRCC) is a unique kidney cancer subtype associated with aggressive biology and poor clinical outcomes. Intriguingly, sRCC has recently exhibited preferential responsiveness to immune checkpoint blockade (ICB) therapies. Within the RCC population, however, there currently is a paucity of biomarkers predictive for ICB response, representing a critical unmet clinical need for optimal therapy selection. Therefore, we sought to derive a transcriptomic signature from sRCC samples encapsulating this paradoxical hyper-aggression and ICB-responsiveness to identify RCC patients most likely to benefit from ICB irrespective of sarcomatoid feature presence. Methods Nephrectomy specimens from patients with RCC were processed for single cell RNA sequencing (scRNAseq). Clustering was performed and annotated tumor cells were computationally isolated. Tumor cell counts were aggregated and differential expression between sRCC and non-sRCC cases was performed. Genes significantly upregulated in sRCC were next filtered against differential gene expression data of sRCC vs non-sRCC from three clinical RCC datasets (TCGA, CheckMate, &amp; Javelin101) to identify genes enriched in sRCC across scRNAseq and bulk RNA sequencing. The prognostic and predictive features of this gene signature were then assessed in cohorts of patients with RCC receiving ICB. Results In total, 73,123 unique cells from 18 RCC patients (10 sRCC; 8 clear cell RCC) were analyzed by scRNAseq, including 5,386 tumor cells. Differential gene expression of tumor clones revealed 20 genes significantly enriched in sRCC relative to ccRCC. Filtering against public differential gene expression data resulted in 10 genes included within the final Sarcomatoid Signature (SS). SS expression scores for clinical specimens were calculated by single-sample gene set enrichment analysis. SS scores were significantly enriched in sRCC patient tumors across TCGA KIRC, CheckMate, and IMmotion151 datasets (p&amp;lt;0.001 for all cohorts). Within TCGA KIRC, SS scores were significantly increased in patients with nuclear grade 4 (p&amp;lt;0.001) and metastatic (p&amp;lt;0.001) disease, while stratification by median SS score revealed worsened overall (HR=2.19, p&amp;lt;0.001) and disease-free (HR=2.08, p&amp;lt;0.001) survival among SS-high patients. Amongst the CheckMate cohort (including patient samples from the CheckMate-010 &amp; CheckMate-025 trials), SS-high patients experienced improved progression free survival (PFS) when treated with nivolumab relative to everolimus (HR=0.70, p=0.055), whereas no difference was seen between therapies in the SS-low patient population (HR=0.98, p=0.9). In the IMmotion151 trial, which was not utilized for gene filtering and signature refinement and thus represents an independent validation cohort, SS-high patients experienced reduced PFS duration (HR=1.39, p&amp;lt;0.001) irrespective of treatment arm. However, SS-high patients experienced improved objective response rates with the ICB-containing atezolizumab/bevacizumab regimen compared to sunitinib (p&amp;lt;0.001) and relative to SS-low patients receiving atezolizumab/bevacizumab (p=0.028) (Figure 1). Within the SS-high population, patients experienced prolonged PFS with atezolizumab/bevacizumab (HR=0.70, p=0.003) relative to sunitinib whereas no PFS difference between arms was seen in the SS-low population (HR=1.01, p&amp;gt;0.99). Conclusions This novel SS derived from scRNAseq demonstrates negative prognostic yet positive predictive value for ICB response. In a domain currently void of efficacious biomarkers, the SS, upon prospective validation, may assist in optimal therapy selection for patients with RCC.

Meibography signal intensity as a novel image biomarker for meibomian gland function: evidence from cross-sectional and longitudinal analyses.

Meibomian gland dysfunction (MGD), one of the most common ocular surface diseases, can induce dry eye and reduce patients' quality of life. Methodological limitations have resulted in contradictory interpretations of gland function. This study sought to investigate the correlation between meibography signal intensity (SI) and meibomian gland (MG) function and to validate an MGD classification strategy based on different levels of SI. A multicenter, cross-sectional analysis was conducted on 817 eyes from 361 patients with MGD and 52 healthy controls. Additionally, 78 eyes from 39 patients with MGD who had undergone LipiFlow treatment were recruited for longitudinal analyses. The SI value was obtained via meibography using an automated analyzer, and all participants underwent ocular surface examinations. A cross-sectional analysis was performed to determine SI distribution and its relationship to clinical characteristics via a generalized estimating equation model. Longitudinal analyses were conducted on the treatment cohort using a mixed-effects model to explore the outcome in different SI levels. Regression analysis revealed significant correlations between SI and lipid layer thickness (β=0.016), meibum expressibility (β=-0.676), meibum quality (β=-0.251), and fluorescein-stained tear-film break-up time (FBUT) (β=0.064) (all P values <0.001 for the above associations). Low-level SI MGD cases exhibited the most severe clinical signs, including the worst meibum expressibility (16% for level 3) and quality scores (19% for level 3), the shortest FBUT (3.82±0.13 s), and the thinnest lipid layer (65.68±2.58 nm), (all P values <0.05, respectively). Patients with medium SI showed the lowest ocular surface disease index (OSDI) value (26.64±1.06), the longest FBUT (4.56±0.08 s), and the thickest lipid layer (80.20±2.90 nm). After treatment, the high SI values reduced significantly at each follow-up point compared to baseline (all P values <0.05). The medium SI group demonstrated the greatest improvement in symptoms and signs, followed by the high SI group, and the low SI group. Automated measurements of SI can effectively reflect MG secretory activity. The proposed low, medium, and high SI classifications represent different functional subtypes of MGD.

ANA-arthritis: clinical and biomarker characterization of a population for basket trials.

ANA-associated RMDs (ANA-RMDs-SLE, pSS, scleroderma, inflammatory myositis, mixed connective tissue disease (MCTD) and undifferentiated connective tissue disease) are a disease spectrum with overlapping clinical and immunological features. Musculoskeletal inflammation is common and impactful across ANA-RMDs. We evaluated musculoskeletal inflammation (ANA-arthritis) prevalence in a multi-disease ANA-RMD study, assessed its clinical impact across ANA-RMD diagnoses, proposed new basket groupings of patients and evaluated immunological profiles in legacy and new basket contexts. An observational study enrolled ANA-RMD patients. Demographic variables, comorbidities, therapies, disease activity instruments (BILAG, SLEDAI, ESSDAI, physician-VAS), patient-reported outcomes (SF36, FACIT-Fatigue, EQ5D, ICECAP-A, WPAI, patient-VAS) and biomarker profile (6 gene expression scores, flow cytometry, autoantibody profile) were analysed. Reclustering utilized Gaussian Mixture Modelling (GMM). Clinical and immune features of new and legacy clusters were compared. Inflammatory MSK symptoms were prevalent across ANA-RMDs, in 213/294 patients. In ANA-arthritis patients, most variables did not differ between diagnoses, excluding EQ5D-5L index and mobility domains (lower in MCTD/pSS, both p< 0.05). Fibromyalgia and osteoarthritis prevalence were similar across diagnoses. Therapy use differed significantly, biologic use being greatest in SLE (p< 0.05).GMM yielded two multi-disease clusters; High-MSK disease activity (n = 89) and Low-MSK disease activity (n = 124). High-MSK disease activity contained all patients with active joint swelling and had significantly higher prednisolone usage, PGA and Sm/RNP/SmRNP/Chromatin positivity, Tetherin-MFI and Interferon Score-A activity; with numerically lower fibromyalgia and osteoarthritis prevalence. We define ANA-Arthritis, a more clinically and immunologically homogeneous population than existing RMDs for trials, and a more prevalent population for therapies in the clinic.

Development of mutated β-catenin gene signature to identify CTNNB1 mutations from whole and spatial transcriptomic data in patients with HCC

Background & AimsPatients with β-catenin (encoded by CTNNB1)-mutated hepatocellular carcinoma (HCC) demonstrate heterogenous responses to first-line immune checkpoint inhibitors (ICIs). Precision-medicine based treatments for this subclass are currently in clinical development. Here, we report derivation of Mutated β-catenin Gene Signature (MBGS) to predict CTNNB1-mutational status in patients for future personalized medicine. MethodsCo-expression of mutant-Nrf2 and hMet ± mutant-β-catenin in murine livers in mice led to HCC development. Using bulk RNA-seq and intersectional transcriptomic analysis of various β-catenin-mutated and non-mutated HCC models, MBGS was derived. Integrated RNA/whole-exome-sequencing and spatial transcriptomic data from multiple HCC patient cohorts was assessed to address ability of MBGS to detect CTNNB1 mutation, tumor immune microenvironment and/or predict therapeutic responses. ResultsBulk RNA-seq comparing HCCs in mutant β-catenin-Nrf2, β-catenin-Met and β-catenin-Nrf2-Met to Nrf2-Met HCC model yielded 95 common upregulated genes. In TCGA-LIHC, differential gene expression analysis with FDR=0.05 and log2FC>1.5 on the 95 common genes comparing CTNNB1-mutated vs wild-type patients narrowed the gene panel to 13-genes MBGS. MBGS predicted CTNNB1-mutations in TCGA (n=374) and French (n=398) patient cohorts with ROC AUC of 0.90 and 0.94, respectively. Additionally, increased MBGS expression score was associated with lack of significant overall survival or progression-free survival effects in the atezolizumab-bevacizumab arm versus sorafenib arm in IMbrave150 cohort. MBGS performed comparable or superior to other CTNNB1-mutant classifiers. MBGS overlapped with Hoshida S3, Boyault G5/G6, and Chiang CTNNB1 subclass tumors in TCGA and in HCC spatial transcriptomic datasets visually depicting these tumors to be situated in an immune excluded tumor microenvironment. ConclusionsMBGS will aid in patient stratification to guide precision medicine therapeutics for CTNNB1-mutated HCC subclass as a companion diagnostic, as anti-β-catenin therapies become available.

Does Varying Platelet-Rich Fibrin Centri̇fugati̇on Protocols Enhance New Bone Formati̇on in Extracti̇on Site?

Finding a protocol that could prevent bone resorption and be implemented in clinical practice would be crucial in providing sufficient bone to replace missing teeth with implants. The study aimed to determine the effectiveness of different centrifugation platelet-rich fibrin (PRF) protocols in new bone formation and bone regenerative markers. This randomized clinical trial was conducted at Izmir Katip Çelebi Research Hospital, a population-based facility in Izmir. Study subjects were composed of patients who required extraction of anterior teeth. Exclusion criteria included periodontal disease, resorption of alveolar bone, defects, smoking, alcoholism, and systemic diseases. The independent variable was the PRF protocol. The subjects were randomly assigned to one of three groups: Leukocyte Platelet-Rich Fibrin (L-PRF), Advanced Platelet-Rich Fibrin (A-PRF) and control groups (healing naturally). The primary outcome of interest was the percentage of new bone formation, determined by analyzing the staining intensity in histomorphometric assessments of bone samples collected 8weeks after extraction. The secondary outcomes were regenerative effects measured by the immunohistochemical expression of markers such as osteocalcin, alkaline phosphatase, and proliferating cell nuclear antigen. Potential benefits were evaluated by clinical observations of pain, swelling, membrane visibility and healing. Age, sex and health conditions. Histologic comparative staining intensities and biomarkers expression between groups were evaluated by one way analysis of variance. A difference of P<.05 was considered statistically significant. The study included 57 subjects, with a mean age of 45years (±5.6); 29 were male (51%) and 28 female (49%). The control group had a mean new bone formation of 32.68% (±2.5), the A-PRF group 61.37% (±3.0), and the L-PRF group 70.74% (±3.5) (P<.001). The A-PRF group showed significantly higher osteocalcin expression than the control group (P=.013). Alkaline phosphatase and proliferating cell nuclear antigen expression scores for PRF groups were significantly higher than the control group's (P=.001). Both groups demonstrated significantly lower pain scores, reduced gingival swelling, better membrane visibility, and healing compared to the control group. PRF enhanced bone formation rates, with L-PRF showing the most significant effect.

Bioinformatic analysis of differentially expressed genes in lung cancer bone metastasis and their implications for disease progression in lung cancer patients.

Lung cancer is the most commonly diagnosed cancer and the leading cause of cancer-related death worldwide. Moreover, it is highly susceptible to distant metastasis, which is the main cause of pain in advanced lung cancer, and frequently occurs in the bone. This study aimed to identify the differentially expressed genes (DEGs) related to metastatic bone disease in lung cancer using bioinformatics methods and to analyze the risk factors influencing the incidence of secondary bone metastasis in lung cancer. Gene expression profiles from the GSE175601 and GSE10799 datasets in the Gene Expression Omnibus (GEO) database were analyzed to screen for the DEGs associated with lung cancer bone metastasis. The STRING database was used to construct a protein-protein interaction (PPI) network, and the MCODE plugin was used to identify the key genes. The expression of these important genes in lung tumor tissues and their correlation with prognosis were validated in The Cancer Genome Atlas (TCGA) database. An examination of clinical data from patients diagnosed with stage IV lung adenocarcinoma treated at the Anhui No. 2 Provincial People's Hospital was conducted. Immunohistochemistry was used to examine the expression of key genes in lung cancer tumor tissues. A binary logistic regression analysis was conducted to examine the interactions in the expression of critical genes associated with bone metastasis in lung carcinoma patients. In total, 59 DEGs were identified in the GSE175601 and GSE10799 datasets through Venn diagram construction. The PPI network analysis revealed two significant modules and eight candidate genes (LAPTM5, LCP2, CD53, ARHGAP25, C1QA, DES, MYH11, and VIM). According to TCGA database analysis, in carcinogenic tissues of the lung, the expression of these eight critical genes is downregulated. Further, only the lung cancer patients who had high expressions of ARHGAP25 had an improved progress-free interval (PFI) (P<0.05), disease-specific survival (DSS), and overall survival (OS). Of the 49 with stage IV lung adenocarcinoma patients included in the study, 27 (55.10%) developed bone metastasis. The immunohistochemical (IHC) results indicated that the expression score of ARHGAP25 was significantly lower in the group with bone metastasis (3.93±2.95) than the group without bone metastasis (6.64±3.62) (P=0.006). The proportion of patients with low ARHGAP25 expression was significantly higher in the group with bone metastasis (70.37%, 19/27) than the group without bone metastasis (31.82%, 7/22) (P=0.007). The binary logistic regression analysis identified serum alkaline phosphatase (ALP) and ARHGAP25 expression levels as independent risk factors for the occurrence of secondary bone metastatic disease in lung carcinoma patients. The key gene ARHGAP25 identified through bioinformatics for lung cancer bone metastasis was significantly downregulated. Its low expression constitutes an independent risk factor for secondary bone metastatic disease in patients with lung carcinoma.

Ki-67 expression and its correlation with clinicopathological parameters in Iraqi breast cancer patients

Breast cancer is the most common cancer worldwide and the major cause of cancer-related death among women in both developed and developing countries. In Iraq, breast cancer accounted for 37.9% of all malignant cases in 2020 and 15.3% of cancer-related fatalities. Relevant biomarkers play an important role in predicting prognosis and deciding the most effective therapy for each patient to delay metastases and reduce mortality. Objective: This study aimed to assess the significance of Ki-67 expression as a prognostic biomarker in breast cancer patients as well as investigate the correlations between Ki-67 and their clinicopathological features. Methods: The case-control study comprised sixty newly diagnosed breast cancer patients and ten women with benign breast tumors who served as controls. We assessed the tissue expression level of Ki-67 protein using the immunohistochemistry technique. Results: Our results showed that the median immunohistochemical expression scores of Ki-67 in the newly diagnosed breast cancer group were higher than those of the control group; the difference was significant (p &lt; 0.001). The Ki-67 expression score in breast cancer cells increases with tumor size and grade. Ki-67 expression showed a substantial negative correlation with estrogen receptor expression and a significant positive correlation with HER2 expression.

Predicting the Prognosis and Immunotherapeutic Response of Triple-Negative Breast Cancer by Constructing a Prognostic Model Based on CD8+ T Cell-Related Immune Genes

ObjectiveTriple-negative breast cancer (TNBC) poses a significant challenge for treatment efficacy. CD8+ T cells, which are pivotal immune cells, can be effectively analyzed for differential gene expression across diverse cell populations owing to rapid advancements in sequencing technology. By leveraging these genes, our objective was to develop a prognostic model that accurately predicts the prognosis of patients with TNBC and their responsiveness to immunotherapy. MethodsSample information and clinical data of TNBC were sourced from The Cancer Genome Atlas and METABRIC databases. In the initial stage, we identified 67 differentially expressed genes associated with immune response in CD8+ T cells. Subsequently, we narrowed our focus to three key genes, namely CXCL13, GBP2, and GZMB, which were used to construct a prognostic model. The accuracy of the model was assessed using the validation set data and receiver operating characteristic (ROC) curves. Furthermore, we employed various methods, including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, immune infiltration, and correlation analyses with CD274 (PD-L1) to explore the model's predictive efficacy in immunotherapeutic responses. Additionally, we investigated the potential underlying biological pathways that contribute to divergent treatment responses. ResultsWe successfully developed a model capable of predicting the prognosis of patients with TNBC. The areas under the curve (AUC) values for the 1-, 3-, and 5-year survival predictions were 0.618, 0.652, and 0.826, respectively. Employing this risk model, we stratified the samples into high- and low-risk groups. Through KEGG enrichment analysis, we observed that the high-risk group predominantly exhibited enrichment in metabolism-related pathways such as drug and chlorophyll metabolism, whereas the low-risk group demonstrated significant enrichment in cytokine pathways. Furthermore, immune landscape analysis revealed noteworthy variations between (PD-L1) expression and risk scores, indicating that our model effectively predicted the response of patients to immune-based treatments. ConclusionOur study demonstrates the potential of CXCL13, GBP2, and GZMB as prognostic indicators of clinical outcomes and immunotherapy responses in patients with TNBC. These findings provide valuable insights and novel avenues for developing immunotherapeutic approaches targeting TNBC.

Comprehensively prognostic and immunological analyses of GLP-1 signaling-related genes in pan-cancer and validation in colorectal cancer.

Background: Glucagon-like peptide-1 (GLP-1) has crucial impact on glycemic control and weight loss physiologically. GLP-1 receptor agonists have been approved for treatment of diabetes and obesity. Emerging evidence suggests that GLP-1 receptor agonists exert anticancer effect in tumorigenesis and development. However, the role and mechanism of GLP-1 signaling-related genes in pan-cancer still need further study. Methods: We comprehensively investigated the aberrant expression and genetic alterations of GLP-1 signaling-related genes in 33 cancer types. Next, GLP-1 signaling score of each patient in The Cancer Genome Atlas were established by the single-sample gene set enrichment analysis. In addition, we explored the association of GLP-1 signaling score with prognostic significance and immune characteristics. Furthermore, qRT-PCR and immunohistochemistry staining were applied to verify the expression profiling of GLP-1 signaling-related genes in colorectal cancer (CRC) tissues. Wound-healing assays and migration assays were carried out to validate the role of GLP-1 receptor agonist in CRC cell lines. Results: The expression profiling of GLP-1 signaling-related genes is commonly altered in pan-cancer. The score was decreased in cancer tissues compared with normal tissues and the lower expression score was associated with worse survival in most of cancer types. Notably, GLP-1 signaling score was strongly correlated with immune cell infiltration, including T cells, neutrophils, dendritic cells and macrophages. In addition, GLP-1 signaling score exhibited close association with tumor mutation burden, microsatellite instability and immunotherapy response in patients with cancer. Moreover, we found that the expression of GLP-1 signaling-related genes ITPR1 and ADCY5 were significantly reduced in CRC tissues, and GLP-1 receptor agonist semaglutide impaired the migration capacity of CRC cells, indicating its protective role. Conclusion: This study provided a preliminary understanding of the GLP-1 signaling-related genes in pan-cancer, showing the prognosis significance and potential immunotherapeutic values in most cancer types, and verified the potential anticancer effect of GLP-1 receptor agonist in CRC.

Immunohistochemistry staining of Eag1 and p16/Ki-67 can help improve the management of patients with cervical intraepithelial Neoplasia after cold knife conversion

BackgroundImmunohistochemistry (IHC) is widely used in the management of patients with cervical intraepithelial neoplasia (CIN) but still has many limitations in clinical practice. We analyzed the correlation of new biomarkers with the severity of CIN and follow-up outcomes in patients after conization to improve the management of patients with CIN.MethodsIHC staining of Eag1 and p16/Ki-67 was performed on cervical tissue sections from 234 patients with suspected CIN2/3. After a series of follow-ups, including human papillomavirus (HPV) test and thinprep cytologic test (TCT) for 1–2 years, the outcomes were collected. IHC scores of biomarkers and follow-up results were used to analyze the correlation and assess the diagnostic efficiency of biomarkers.ResultsThe IHC staining intensity of Eag1 and p16/Ki-67 was significantly different from that of the CIN1-3 groups (p < 0.05). Eag1 expression scores were significantly different in the distribution between the two follow-up groups (p < 0.001). ROC curves based on the correlations between the follow-up outcomes and the Eag1 scores and IS of p16/ki-67 showed that Eag1 had a greater AUC (0.767 vs. 0.666). Logistic regression analysis of the combination of biomarkers revealed a greater AUC value than any single biomarker.ConclusionsEag1 expression was significantly correlated with CIN grade and follow-up outcomes after conization. IHC staining of combinations of biomarkers of Eag1, p16 and Ki-67 may help us to improve the ability to identify risk groups with abnormal follow-up outcomes after treatment for CIN.

SEC61 translocon gamma subunit is correlated with glycolytic activity, epithelial mesenchymal transition and the immune suppressive phenotype of lung adenocarcinoma.

Lung adenocarcinoma (LUAD) remains a predominant cause of cancer-related mortality globally, underscoring the urgency for targeted therapeutic strategies. The specific role and impact of the SEC61 translocon gamma subunit (SEC61G) in LUAD progression and metastasis remain largely unexplored. In this study, we use a multifaceted approach, combining bioinformatics analysis with experimental validation, to elucidate the pivotal role of SEC61G and its associated molecular mechanisms in LUAD. Our integrated analyses reveal a significant positive correlation between SEC61G expression and the glycolytic activity of LUAD, as evidenced by increased fluorodeoxyglucose (FDG) uptake on positron emission tomography (PET)/CT scans. Further investigations show the potential influence of SEC61G on metabolic reprogramming, which contributes to the immunosuppressive tumor microenvironment (TME). Remarkably, we identify a negative association between SEC61G expression levels and the infiltration of critical immune cell populations within the TME, along with correlations with immune checkpoint gene expression and tumor heterogeneity scores in LUAD. Functional studies demonstrate that SEC61G knockdown markedly inhibits the migration of A549 and H2030 LUAD cells. This inhibitory effect is accompanied by a significant downregulation of key regulators of tumor progression, including hypoxia-inducible factor-1 alpha (HIF-1α), lactate dehydrogenase A, and genes involved in the epithelial-mesenchymal transition pathway. In conclusion, our comprehensive analyses position SEC61G as a potential prognostic biomarker intricately linked to glycolytic metabolism, the EMT pathway, and the establishment of an immune-suppressive phenotype in LUAD. These findings underscore the potential of SEC61G as a therapeutic target and predictive marker for immunotherapeutic responses in LUAD patients.

Optimizing immunofluorescence with high-dynamic-range imaging to enhance PD-L1 expression evaluation for 3D pathology assessment from NSCLC tumor tissue

Assessing programmed death ligand 1 (PD-L1) expression through immunohistochemistry (IHC) is the golden standard in predicting immunotherapy response of non-small cell lung cancer (NSCLC). However, observation of heterogeneous PD-L1 distribution in tumor space is a challenge using IHC only. Meanwhile, immunofluorescence (IF) could support both planar and three-dimensional (3D) histological analyses by combining tissue optical clearing with confocal microscopy. We optimized clinical tissue preparation for the IF assay focusing on staining, imaging, and post-processing to achieve quality identical to traditional IHC assay. To overcome limited dynamic range of the fluorescence microscope’s detection system, we incorporated a high dynamic range (HDR) algorithm to restore the post imaging IF expression pattern and further 3D IF images. Following HDR processing, a noticeable improvement in the accuracy of diagnosis (85.7%) was achieved using IF images by pathologists. Moreover, 3D IF images revealed a 25% change in tumor proportion score for PD-L1 expression at various depths within tumors. We have established an optimal and reproducible process for PD-L1 IF images in NSCLC, yielding high quality data comparable to traditional IHC assays. The ability to discern accurate spatial PD-L1 distribution through 3D pathology analysis could provide more precise evaluation and prediction for immunotherapy targeting advanced NSCLC.

Dissecting the shared genetic architecture between anti-Müllerian hormone and age at menopause based on genome-wide association study

BackgroundWhile the phenotypic association between anti-Müllerian hormone (AMH) and age at menopause has been widely studied, the role of AMH in predicting the age at menopause is currently controversial, and the genetic architecture or causal relationships underlying these two traits is not well understood. AimWe aimed to explore the shared genetic architecture between AMH and age at menopause, to identify shared pleiotropic loci and genes, and to investigate causal association and potential causal mediators. Study DesignUsing summary statistics from publicly available genome-wide association studies on AMH (N=7,049) and age at menopause (N=201,323) in Europeans, we investigated the global genetic architecture between AMH and age at menopause through linkage disequilibrium score regression. We employed pleiotropic analysis under composite null hypothesis (PLACO), Functional Mapping and Annotation of Genetic Associations (FUMA), Multimarker analysis of GenoMic annotation (MAGMA), and colocalization analysis to identify loci and genes with pleiotropic effects. Tissue enrichment analysis based on GTEx data was conducted using the Linkage Disequilibrium Score for the specific expression of genes analysis (LDSC-SEG). Functional genes that were shared were additionally identified through summary data-based Mendelian randomization (SMR). The relationship between AMH and age at menopause was examined through two-sample Mendelian randomization (MR), and potential mediators were further explored using colocalization and metabolite-mediated analysis. ResultsA positive genetic association (correlation coefficient = 0.88, P = 1.33 × 10-5) was observed between AMH and age at menopause. By using PLACO and FUMA, 42 significant pleiotropic loci were identified that were associated with AMH and age at menopause, and ten of these (rs10734411, rs61913600, rs2277339, rs75770066, rs28416520, rs9796, rs11668344, rs403727, rs6011452, and rs62237617) had colocalized loci. Additionally, 245 significant pleiotropic genes were identified by MAGMA. Genetic associations between AMH and age at menopause were markedly concentrated in various tissues including whole blood, brain, heart, liver, muscle, pancreas, and kidneys. Further, SMR analysis revealed nine genes that may have a causative effect on both AMH and age at menopause. A potential causal effect of age at menopause on AMH was suggested by two-sample MR analysis, with very-low-density lipoprotein identified as a potential mediator. ConclusionsOur study revealed a shared genetic architecture between AMH and age at menopause, providing a basis for experimental investigations and individual therapies to enhance reproductive outcomes. Furthermore, our findings emphasized that relying solely on AMH is not sufficient for accurately predicting the age at menopause, and a combination of other factors needs to be considered. Exploring new therapeutics aimed at delaying at the onset of menopause holds promise, particularly when targeting shared genes based on their shared genetic architecture.

Interpretation of Epidermal Growth Factor Receptor Status in Microscopic Tumor-Free Surgical Margins and Lymph Nodes in Patients with Oral Squamous Cell Carcinoma: An Analysis of 125 Margins.

Squamous cell carcinomas are the most common type of oral cancer contributing for around 90%. The overall survival is below 50% for these patients. There is a requirement for a non-invasive marker to predict the prognosis. The epidermal growth factor (EGF) and their receptors (EGFR, ErbB-1) are not only documented to play a critical and an influential role in cell growth and differentiation in normal/healthy tissues, but may also plays an important role in malignant disease progression and tumorigenesis. This study was done to find the significance of EGF receptor expression on microscopic free tumour margins and lymph nodal margins to predict the survival of the patient in a 2-year follow-up. A prospective cohort study of 25 patients was performed in biopsy proven oral squamous cell carcinoma patients who reported to our department from July 2017 to June 2019. The data were collected from their histopathological report, they were- pTNM staging, surgical margins (superior and inferior, anterior, posterior), nodal status and scoring of EGFR expression on wax blocks was done. Total of 125 wax blocks were analysed for the study. Follow-up of 2years were recorded in the study to evaluate the survival of the patients. The expression of EGFR on microscopic tumour-free surgical margins and lymph nodes was p value 0.023 which was statistically significant. The level of significance between EGFR and status of patients after 2-year follow-up was having p value 0.031. Out of 25 patients, 5 patients were dead at a 2-year follow-up. Out of these 5 patients who were dead, 3 patients had a local recurrence and 2 patients had distant metastasis. This cohort study concludes that EGFR is an important prognostic marker and must be analysed in all microscopic tumour-free margins and lymph nodes in advanced oral squamous cell carcinomas to predict the local recurrences affecting the survival of the patients and the need for addition of anti-EGFR agents in adjuvant treatment. Since the sample size is small, large scale studied must be done to validate the need for adding anti-EGFR agents in adjuvant treatment to improve the survival of patients.

The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer.

Tumor hypoxia reduces radiotherapy efficacy. In this study, we explored whether some of the clinical effects of hypoxia could be due to interaction with the tumor microbiome. Hypoxic gene expression scores associated with certain microbes and elicited an adaptive transcriptional response in others that could contribute to poor clinical outcomes.

Management of Glaucoma-Related Dry Eye Disease with Intense Pulsed Light: A Randomized Control Study.

The objective of this study was to assess the effectiveness of intense pulsed light (IPL) therapy in individuals diagnosed with glaucoma and dry eye disease (DED). This randomized control study recruited 22 individuals diagnosed with glaucoma, ranging in age from 33 to 82 years. These participants were undergoing treatment with hypotensive eyedrops and had clinical indications and subjective complaints associated with dry eye. Each patient underwent three sessions of IPL therapy in one eye, while the contralateral eye served as the control eye (CT). The following parameters were assessed at three time points: baseline, week-2, and week-4. These parameters include non-invasive breakup time (NITBUT), tear meniscus height (TMH), conjunctivocorneal epithelial staining score (CS), tear film lipid layer (TFLL), meibomian gland expressibility score (MGEx), Schirmer I test, ocular bulbar redness score (OBRS), and ocular surface disease index (OSDI). Intraocular pressure (IOP), best-corrected visual acuity (BCVA), and corneal endothelial cell count (ECC) were assessed for safety. The clinical trial was registered on 25/12/2023 at ClinicalTrials.gov website (NCT06158984). Comparing baseline and 4-week measurements revealed that the IPL group found significant improvements in NITBUT (IPL: 8.74±2.60 sec. vs CT: 5.76±1.75 sec. p<0.01), TMH (IPL: 0.23±0.05mm vs CT: 0.19±0.06mm, p=0.011), C.S. (IPL: 1.14±0.56 vs CT: 1.95±1.17, p=0.005), TFLL (IPL: 2.91±2.91 vs CT:3.36±0.58, p=0.047), MGEx score (IPL: 1.14±0.35 vs CT: 1.45±0.51, p=0.020) and OSDI scores (IPL: 31.77±15.59 vs 50.59±21.55, p=0.002) significantly improved. Conversely, other parameters showed no significant improvements (p>0.05). The progression of ocular surface disease in individuals using topical anti-glaucoma medication may worsen if the condition is not addressed. Nevertheless, IPL therapy has the potential to result in significant improvements in both objective and subjective measures of dry eye. Best-corrected visual acuity, endothelial cell count, and intraocular pressure were determined to be within the permitted limits. No adverse events were reported during the course of the study.

Comparing Different Methods That Measure Bilingual Children’s Language Environment: A Closer Look at Audio Recordings and Questionnaires

The quantity of language input is a relevant predictor of children’s language development and is frequently used as a variable in child bilingualism research. Studies use various methods to measure bilingual language input quantity, but it is currently unknown what the optimal method is. We investigated the bilingual language input estimates of 31 Turkish–Dutch and 21 Polish–Dutch 3- to 5-year-old bilingual children, obtained via the questionnaire for Quantifying Bilingual Experience (Q-BEx) and day-long audio recordings made with Language Environment Analysis (LENA), and proposed a combined method that could overcome several shortcomings of the individual methods. The three methods are compared to each other in their correlation strength with receptive and expressive vocabulary scores. Each individual method correlated significantly with vocabulary scores, regardless of modality or language. Contrary to our hypothesis, the combined method did not correlate stronger with vocabulary outcomes than the Q-BEx and LENA individually did. The latter two did not differ significantly from each other in their correlational strength with vocabulary outcomes. These findings show that both the Q-BEx, LENA, and combined method can be deemed reliable to measure bilingual language input quantity. Future studies can make more informed decisions about their methodology in children’s bilingualism research.