Expression Levels In Patients Research Articles

ACE2 and TMPRSS2 expression in patients before, during, and after SARS-CoV-2 infection.

During the SARS-CoV-2 pandemic angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) were constantly under the scientific spotlight, but most studies evaluated ACE2 and TMPRSS2 expression levels in patients infected by SARS-CoV-2. Thus, this study aimed to evaluate the expression levels of both proteins before, during, and after-infection. For that, nasopharyngeal samples from 26 patients were used to measure ACE2/TMPRSS2 ex-pression via qPCR. Symptomatic patients presented lower ACE2 expression levels before and after the infection than those in asymptomatic patients; however, these levels increased during SARS-CoV-2 infection. In addition, symptomatic patients presented higher expression levels of TMPRSS2 pre-infection, which decreased in the following periods. In summary, ACE2 and TMPRSS2 expression levels are potential risk factors for the development of symptomatic COVID-19, and the presence of SARS-CoV-2 potentially modulates those levels.

Abstract 1208: Plasma proteomics-based models for predicting therapeutic benefit and immune-related adverse events in non-small cell lung cancer patients treated with immunotherapy

Abstract Background: Immune checkpoint inhibitors (ICIs) have significantly improved outcomes for patients with metastatic non-small cell lung cancer (NSCLC). However, clinical management is challenging. The PD-L1 biomarker does not optimally guide the choice between ICI monotherapy and combination ICI-chemotherapy, and there are currently no biomarkers to predict immune-related adverse events (irAEs). Here, we describe a versatile platform based on plasma proteomics and machine learning for generating predictive tools to support treatment decisions. Methods: Pre-treatment plasma samples were collected from 616 NSCLC patients receiving ICI-based therapy (NCT04056247). Clinical benefit (CB) data and irAEs were recorded. Proteomic profiling of plasma samples was performed using the SomaScan® assay, covering ~7000 proteins per sample. Proteins associated with Clinical Benefit (progression-free survival at 12 months) were classified as resistance-associated proteins (RAPs). Proteins associated with grade ≥3 irAEs occurring within the first 100 days of treatment were classified as toxicity-associated proteins (TAPs). RAPs and TAPs were integrated into two separate machine learning-based models, yielding CB and irAE probabilities, respectively. The CB model used a CB probability threshold to assign patients a PROphet-positive or PROphet-negative result. Bioinformatic analysis was performed on RAPs and TAPs. Results: CB and irAE models displayed strong predictive performance with a high correlation between predicted probability and observed CB or irAE rate (CB model: R2=0.98; p-value<0.0001; irAE model: R2= 0.92; p-value <0.0001). In the CB model, patients classified as PROphet-positive achieved significantly longer overall survival (OS) than PROphet-negative patients, with a median OS of 25.9 vs. 10.8 months (hazard ratio, HR = 0.51; p-value<0.001). Furthermore, patients with PD-L1 ≥50% tumors and a PROphet-negative result had significantly longer OS with ICI-chemotherapy in comparison to ICI monotherapy (HR=0.23, p-value = 0.0003), suggesting that combination therapy is preferable for such patients despite high PD-L1 levels. Bioinformatic analysis showed that RAPs related to immune regulation, angiogenesis, chemo-resistance, and other potential resistance mechanisms displayed higher expression levels in patients who did not benefit from treatment. Neutrophil- and inflammation-related proteins were significantly enriched in patients who experienced irAEs. Conclusions: We describe two machine-learning based predictive tools that may be used separately or in combination to inform treatment decisions based on the patient’s likelihood to benefit from ICI therapy and to develop serious irAEs. Our findings also provide biological insights related to treatment resistance and immune-related toxicity. Citation Format: Michal Harel, Petros Christopoulos, Igor Puzanov, Jair Bar, Iris Kamer, Niels Reinmuth, Ina Koch, Mor Moskovitz, Adva Levy-Barda, Alona Zer, Michal Lotem, David Farrugia, Rivka Katzenelson, Gillian Price, Abed Agbarya, Helen Cheley, Adam Hassani, Mahmoud Abu-Amna, Tom Geldart, Anirban Chatterjee, Andreas Polychronis, Maya Gottfried, Yanyan Lou, Tatiana Harkovsky, Alison Brewster, Ido Wolf, Ella Tepper, Ben Yellin, Itamar Sela, Coren Lahav, Yehonatan Elon, Raya Leibowitz, Adam P. Dicker, Young Kwang Chae, Ryan J. Sullivan, David Carbone, David Gandara, Jarushka Naidoo. Plasma proteomics-based models for predicting therapeutic benefit and immune-related adverse events in non-small cell lung cancer patients treated with immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1208.

Abstract 5183: Retrospective analysis of CCNG1 expression in tumors, a novel biomarker in development for partnering with DRG-101, a tumor targeted retrovector encoding a CCNG1 inhibitor gene

Abstract Background: CCNG1, a non-canonical cyclin, is a novel biomarker in development for partnering with DRG-101 (DeltaRex-G), a tumor targeted retrovector encoding a CCNG1 inhibitor gene. Expanded access using DRG-101 is currently open for an intermediate-size population of advanced pancreatic cancer, sarcoma and carcinoma of breast (NCT04091295). Therefore, it is important to identify patients who might respond favorably to DRG-101 gene therapy. Previously, we reported that CCNG1 expression is enhanced in sarcoma tumors (Ann Oncol 34, 1980P, 2023). In this report, we have expanded the analysis to 137 patients with all cancer types and describe patients with known CCNG1 expression levels who have been treated with DRG-101. Methods: Archived formalin-fixed paraffin-embedded (FFPE) tumor specimens (n=137) from patients who were followed at the Sarcoma Oncology Research Center were collected, processed, and subjected to RNA sequencing. Briefly, RNA-seq libraries were sequenced to generate 50 million reads, aligned using Kallisto v0.42.4 to GENCODE v23 transcripts with default parameters. Only protein-coding, IGH/K/L- and TCR-related transcripts were retained for downstream processing, resulting in 20,062 protein-coding genes. Gene expression levels in patients of the reference cohorts are categorized as low/medium/high, defined by Low = < 17%; Medium-high = 50%-83%; Medium-low = 17%-49%; High = >83%. Results: Seventy women and sixty-seven men, ranging in age from 16 to 87 years, were studied. All tumors showed enhanced CCNG1 expression. Thirty (22%) tumors exhibited high CCNG1 expression, 53 (39%) showed medium-high CCNG1 expression, 48 (35%) displayed medium-low CCNG1 expression, and six (4%) had low CCNG1 expression. One hundred (73%) patients had metastatic disease, and 37 (27%) had localized disease. There was no correlation between CCNG1 expression and disease stage. As a result of these findings, the FDA-CBER authorized the use of DRG-101 in an Expanded Access program as platform therapy upon which one or more FDA approved cancer drugs/immunotherapies may be added. Historically, one patient with metastatic pancreatic cancer, one with early stage, HR+ HER2+ invasive breast cancer and one with early stage triple negative breast cancer are alive 15, 3 and 2.5 years in sustained remission with DRG-101 therapy, and had 24%, 23% and 74% CCNG1 tumor expression levels respectively. Five patients with advanced pancreatic cancer, sarcoma and breast cancer and known CCNG1 expression levels are currently being treated with DRG-101. Conclusions:(1) 100% of tumors tested showed enhanced CCNG1 expression at varying levels, and (2) the use of DRG-101 in combination with FDA approved cancer drugs/immunotherapies is on-going for an intermediate size population of advanced pancreatic cancer, sarcoma and carcinoma of breast. Citation Format: Nadezhda Omelchenko, Vaishali Kumar, Samantha Jeffrey, Grace Haroun, Don Brigham, William H. Isacoff, Sant Chawla. Retrospective analysis of CCNG1 expression in tumors, a novel biomarker in development for partnering with DRG-101, a tumor targeted retrovector encoding a CCNG1 inhibitor gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5183.

Prognostic Significance of the Cribriform Pattern in Prostate Cancer: Clinical Outcomes and Genomic Alterations.

Given the diverse clinical progression of prostate cancer (PC) and the evolving significance of histopathological factors in its management, this study aimed to explore the impact of cribriform pattern 4 (CP4) on clinical outcomes in PC patients and examine its molecular characteristics. This retrospective study analyzed data from The Cancer Genome Atlas (TCGA) database and included PC patients who underwent radical prostatectomy (RP) and had pathology slides available for the assessment of CP4. A multivariable competing risk regression analysis was used to assess the association between CP4 and progression-free survival (PFS) while adjusting for established PC prognostic factors. The frequency of genomic alterations was compared between patients with and without CP4 using the Fisher's exact test. Among the 394 patients analyzed, 129 (32.74%) had CP4. After a median follow-up of 40.50 months (IQR: 23.90, 65.60), the presence of CP4 was significantly associated with lower PFS (AHR, 1.84; 95% CI, 1.08 to 3.114; p = 0.023) after adjusting for covariates. Seven hub genes-KRT13, KRT5, KRT15, COL17A1, KRT14, KRT16, and TP63-had significantly lower mRNA expression levels in patients with CP4 compared to those without. PC patients with CP4 have distinct genomic alterations and are at a high risk of disease progression following RP. Therefore, these patients may benefit from additional post-RP treatments and should be the subject of a prospective randomized clinical trial.

Machine learning models based on quantitative dynamic contrast-enhanced MRI parameters assess the expression levels of CD3+, CD4+, and CD8+ tumor-infiltrating lymphocytes in advanced gastric carcinoma.

To explore the effectiveness of machine learning classifiers based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in predicting the expression levels of CD3+, CD4+, and CD8+ tumor-infiltrating lymphocytes (TILs) in patients with advanced gastric cancer (AGC). This study investigated 103 patients with confirmed AGC through DCE-MRI and immunohistochemical staining. Immunohistochemical staining was used to evaluate CD3+, CD4+, and CD8+ T-cell expression. Utilizing Omni Kinetics software, radiomics features (Ktrans, Kep, and Ve) were extracted and underwent selection via variance threshold, SelectKBest, and LASSO methods. Logistic regression (LR), support vector machine (SVM), random forest (RF), and eXtreme Gradient Boosting (XGBoost) are the four classifiers used to build four machine learning (ML) models, and their performance was evaluated using 10-fold cross-validation. The model's performance was evaluated and compared using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, positive predictive value, and negative predictive value. In terms of CD3+, CD4+, and CD8+ T lymphocyte prediction models, the random forest model outperformed the other classifier models in terms of CD4+ and CD8+ T cell prediction, with AUCs of 0.913 and 0.970 on the training set and 0.904 and 0.908 on the validation set, respectively. In terms of CD3+ T cell prediction, the logistic regression model fared the best, with AUCs on the training and validation sets of 0.872 and 0.817, respectively. Machine learning classifiers based on DCE-MRI have the potential to accurately predict CD3+, CD4+, and CD8+ tumor-infiltrating lymphocyte expression levels in patients with AGC.

Interferon Regulatory Factor 5 Gene Polymorphisms and mRNA Expression Levels Are Associated with Neuromyelitis Optica Spectrum Disorder.

Interferon regulatory factor 5 (IRF5) is a critical transcription factor in the toll-like receptor signaling pathway. It is associated with autoimmune disorders, such as rheumatoid arthritis, systemic lupus erythematosus, and inflammatory bowel disease. However, the relationship between the functional single nucleotide polymorphisms (SNPs) of IRF5 and its mRNA expression level in patients with neuromyelitis optica spectrum disorder remains unclear. The present study aimed to investigate the relationship between polymorphisms and mRNA expression levels of the IRF5 gene with the incidence of neuromyelitis optica spectrum disorder (NMOSD) in northern Chinese Han people. Two loci of the IRF5 gene (rs2004640 and rs2280714) of 164 patients with NMOSD and 269 healthy subjects were genotyped using the multiple SNaPshot technique. The frequencies of alleles, genotypes, and haplotypes were compared. Stratified analysis was performed according to age, sex, AQP4 status, onset age, and Expanded Disability Status Scale (EDSS) score. The IRF5 mRNA levels in peripheral blood mononuclear cells (PBMCs) of 64 NMOSD patients (32 patients in the acute stage and 32 patients in the remission stage) and 35 healthy subjects were detected by real-time PCR. The association of SNP polymorphisms with the mRNA expression level was determined by nonparametric tests. Allele and genotype frequency distributions of rs2004640 showed significant differences between both groups. Compared to healthy controls, the frequency of rs2004640 T allele markedly increased in patients (OR = 1.51, 95% CI = 1.09-2.08, P = 0.005). Minor allele T and GT genotype of rs2004640 that significantly increases the risk of NMOSD were discovered using genetic inheritance models (codominant, dominant, and overdominant) and haplotype analyses. Subsequent haplotype analyses revealed that the major haplotype "T-A" containing the risk alleles (the SNP sequence of the alleles was rs2004640 and rs2280714) had adverse effects on NMOSD. Based on the stratification analysis according to the EDSS score, the GT genotype frequency in the EDSS ≥ 4 group (38.2%) was markedly lower than that in the EDSS < 4 group (61.8%) (OR = 0.32, 95% CI = 0.15-0.68, P = 0.0054), with a significant difference. The IRF5 mRNA expression level was increased in NMOSD patients compared to that in normal subjects. IRF5 gene polymorphisms may be tightly associated with the genesis and progression of NMOSD in northern Chinese Han people. IRF5 mRNA expression was increased in patients with NMOSD and significantly increased in patients with acute phase. Perhaps IRF5 expression levels can be used as a predictor of disease activity in the future.

Lung cancer, predictive factor and ERCC1

Introduction: Excision repair cross-complementing group 1 (ERCC1) counteracts the cytotoxic effect of cisplatin through its role in DNA repair, and its expression level is a crucial factor for sensitivity to this drug. The objective of this study was to assess the impact of ERCC1 on tumor response and survival in patients with advanced non-small cell lung cancer (NSCLC) treated with a platinum-based regimen. Methods: Analysis of survival and tumor response based on the expression level of ERCC1 (detected by immunohistochemistry) in a cohort of NSCLC patients followed in a standard care setting. Results: Among the 77 cases of NSCLC included, ERCC1 expression was low in 64.9% of cases and high in 35.1% of cases. In the 52 patients treated with cisplatin, survival and tumor response were better in the low-expression group compared to the high-expression group: 14.35 months versus 9.49 months, p=0.022; Objective Response: 42.4% versus 0%, p=0.001. No significant difference was found based on protein expression level in patients treated with carboplatin. Conclusion: ERCC1 overexpression in patients treated with cisplatin predicts a poor tumor response and shorter survival.

METTL3-mediated m6A modification enhances ZDHHC16 expression in nonsmall- cell lung cancer patients, attenuating ferroptosis by suppressing CREB ubiquitination.

At present, the early diagnosis and treatment of non-small cell lung cancer (NSCLC) is still an urgent problem to be solved worldwide, including in China. The present work investigated the possible protective effect of ZDHHC16 in cell proliferation and metastasis of NSCLC and explored its possible mechanisms. ZDHHC16 expression level in patients with Non-Small-Cell Lung Cancer was up-regulation. ZDHHC16 gene is stabilized by m6A methylation. ZDHHC16 gene reduced ferroptosis of NSCLC by the rehabilitation of the mitochondrial structure. ZDHHC16 promoted CREB expression through the inhibition of CREB Ubiquitination. Confocalmicroscopy showed that ZDHHC16 reduced the CREB expression of NSCLC. ZDHHC16 up-regulation reduced CREB Ubiquitination, and down-regulation of ZDHHC16 promoted CREB Ubiquitination of NSCLC. CREB Agonists reduced the effects of ZDHHC16 on ferroptosis, not affecting the Warburg effect of NSCLC. CREB inhibitor reduced the effects of si-ZDHHC16 on ferroptosis, not affecting the Warburg effect of NSCLC. METTL3-mediated m6A modification increases ZDHHC16 stability. Our study revealed that the m6A-forming enzyme METTL3 upregulates ZDHHC16 expression in NSCLC patients, leading to the reduction of ferroptosis by inhibiting CREB ubiquitination.

Therapeutic role of miR-19a/b protection from influenza virus infection in patients with coronary heart disease

Patients with pre-existing medical conditions are at a heightened risk of contracting severe acute respiratory syndrome (SARS), SARS-CoV-2, and influenza viruses, which can result in more severe disease progression and increased mortality rates. Nevertheless, the molecular mechanism behind this phenomenon remained largely unidentified. Here, we found that microRNA-19a/b (miR-19a/b), which is a constituent of the miR-17-92 cluster, exhibits reduced expression levels in patients with coronary heart disease in comparison to healthy individuals. The downregulation of miR-19a/b has been observed to facilitate the replication of influenza A virus (IAV). miR-19a/b can effectively inhibit IAV replication by targeting and reducing the expression of SOCS1, as observed in cell-based and coronary heart disease mouse models. This mechanism leads to the alleviation of the inhibitory effect of SOCS1 on the interferon (IFN)/JAK/STAT signaling pathway. The results indicate that the IAV employs a unique approach to inhibit the host's type I IFN-mediated antiviral immune responses by decreasing miR-19a/b. These findings provide additional insights into the underlying mechanisms of susceptibility to flu in patients with coronary heart disease. miR-19a/b can be considered as a preventative/therapy strategy for patients with coronary heart disease against influenza virus infection.

HINT2 may be One Clinical Significance Target for Patient with Diabetes Mellitus and Reduced ROS-Induced Oxidative Stress and Ferroptosis by MCU.

The World Health Organization (WHO) predicted that patients with diabetes around the world will increase to 600 million by 2040, of which about 1/3 will develop diabetic nephropathy (DN). Therefore, the present study aimed to uncover therapeutic effect of HINT2 and determined its possible mechanisms. Patients with diabetes mellitus and normal volunteers were enrolled at our hospital. Male C57BL/6 mice were fed with a high fat diet and injected intraperitoneally with STZ for once (100 mg/kg body weight). Mouse podocytes (MPC5) cells were induced with 20 mmol/l D-glucose. Inhibition of HINT2 mRNA expression levels in patients with DN was observed, compared with normal group. The serum of HINT2 mRNA expression was negative in correlation with blood sugar, tubulo-interstitial damage, glomerular damage score or urine protein level in patients with DN. HINT2 expression in kidney tissue of mice with DN were downregulated. HINT2 presented reduced DN and inflammation and ROS-induced oxidative stress in model of DN. HINT2 promoted ferroptosis in model of DN by mitochondrial membrane potential. HINT2 suppressed MCU expression in model of DN. HINT2 protein combined with MCU protein increased MCU protein ubiquitination. HINT2 triggers mitochondrial Ca2+ influx to increase ROS production level by MCU. Taken together, these findings demonstrated that HINT2 reduced ROS-induced Oxidative stress and ferroptosis by MCU, suggesting that HINT2 may be a feasible strategy to treat DN.

M6A methylation of FKFB3 reduced pyroptosis of gastric cancer by NLRP3.

Gastric cancer is a kind of malignant tumor that seriously endangers human life and health. Its incidence rate and mortality rate are among the highest in the global malignant tumors. Therefore, this study explored the role of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) in the progression of gastric cancer and its underlying mechanism. Patients with gastric cancer were collected, and human GC cell lines (stomach gastric carcinoma 7901, stomach gastric carcinoma 823 , human gastric carcinoma cell line 803 and adenocarcinoma gastric stomach) were used in this study. We utilized glucose consumption, cell migration, and ELISA assay kits to investigate the function of GC. To understand its mechanism, we employed quantitative PCR (qPCR), western blot, and m6A methylated RNA immunoprecipitation assay. FKFB3 protein expression levels in patients with gastric cancer were increased. The induction of PFKFB3 mRNA expression levels in patients with gastric cancer or gastric cancer cell lines. Gastric cancer patients with high PFKFB3 expression had a lower survival rate. PFKFB3 high expression possessed the probability of pathological stage, lymph node metastasis or distant metastasis in patients with gastric cancer. PFKFB3 upregulation promoted cancer progression and Warburg effect progression of gastric cancer. PFKFB3 upregulation reduced pyroptosis and suppressed nucleotidebinding domain, leucinerich repeat containing protein 3-induced pyroptosis of gastric cancer. M6A-forming enzyme methyltransferase-like 3 increased PFKFB3 stability. Taken together, the M6A-forming enzyme methyltransferase-like 3 increased PFKFB3 stability and reduced pyroptosis in the model of gastric cancer through the Warburg effect. The PFKFB3 gene represents a potential therapeutic strategy for the treatment of gastric cancer.

LncRNA HOTAIR Inhibits miR-19a-3p to Alleviate Foam Cell Formation and Inflammatory Response in Atherosclerosis.

Background: Atherosclerosis, a chronic inflammatory disease, poses a significant risk for cardiovascular disorders. Meanwhile, emerging evidence suggests that long noncoding RNAs (lncRNAs) play pivotal roles in diverse cardiovascular conditions. Nonetheless, the functional implications of lncRNAs in atherosclerosis remain largely unexplored. Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to assess lncRNA HOTAIR and miR-19a-3p expression levels in patients with atherosclerosis and macrophage-derived foam cells. The release of inflammatory factors was evaluated using enzyme-linked immunosorbent assay (ELISA), while lipid uptake by foam cells was assessed through Oil Red O staining. Additionally, the targeting relationship between lncRNA HOTAIR and miR-19a-3p was validated via a Luciferase reporter assay. Results: LncRNA HOTAIR exhibited downregulation in the plasma of atherosclerosis patients and was found to be inhibited by ox-LDL in human macrophage-derived foam cells. Overexpression of HOTAIR effectively reduced lipid uptake and suppressed the inflammatory response by downregulating the expression of TNF-α and IL-6 during foam cell formation. Mechanistically, HOTAIR mitigated foam cell formation by repressing the expression of miR-19a-3p. Conclusions: In conclusion, our findings, in conjunction with previous studies, elucidate the role of HOTAIR in atherosclerosis. Specifically, we demonstrate that HOTAIR plays a role in alleviating foam cell formation and suppressing the inflammatory response by inhibiting miR-19a-3p in the context of atherosclerosis. Our results suggest the involvement of the TNF-α/miR-19a/HBP1/MIF pathway in mediating these effects. These findings contribute to a better understanding of atherosclerosis's molecular mechanisms and highlight the potential therapeutic implications of targeting HOTAIR and its associated pathways.

RNF20 Reduces Cell Proliferation and Warburg Effect by Promoting NLRP3 Ubiquitination in Liver Cancer.

The present study explored that the effects and its possible mechanisms of ring finger protein 20 (RNF20) in Postoperative survival rate of liver cancer in clinical. All the serum samples were collected from our hospital. Quantitative polymerase chain reaction (PCR) and microarray analysis, and RNA pull down assay were used in this study. We found that the serum RNF20 mRNA expression level in patients with liver cancer were down-regulated. Postoperative survival rate of RNF20 high expression was higher than that of RNF20 low expression. Then, over-expression of RNF20 diminished liver cancer cell proliferation and metastasis. RNF20 reduced Warburg effect of liver cancer. RNF20 expression regulated NOD-like receptor protein 3 (NLRP3) expression and increased NLRP3 Ubiquitination. NLRP3 participated in the effects of RNF20 on cell proliferation, and not affected on Warburg effect of liver cancer. Our study demonstrated that the serum RNF20 expression level was down-regulated in liver cancer, and promoted postoperative survival rate. RNF20 can reduce cancer progression of liver cancer by NLRP3 signal pathway, suggesting that it may prove to be a potential therapeutic target for postoperative survival rate of liver cancer.

Impact of single nucleotide polymorphisms of immune checkpoint CTLA-4 (SNP rs231775 and rs5742909) in susceptibility to Hashimoto's thyroiditis patients

Background: Hashimoto thyroiditis is an autoimmune disorder causing thyroid cell destruction. This research aimed to evaluate CTLA-4 expression levels in patients with Hashimoto's thyroiditis, biochemical parameters. As well as understand the risk and protective effects of two CTLA-4 SNPs polymorphisms (rs231775 and rs5742909) in Iraqi patients. Methods: A case control study was conducted on 50 HT patients (5 men and 45 females) were assembled from Baghdad teaching hospital, Baghdad, Iraq. The relative Gene expression method was used to measure the gene expression of CTLA-4 using qRT-PCR. The single nucleotide polymorphisms of (318C/T (rs231775) and +49A/G (rs5742909) were sequenced for data analysis. Results: There was significant increase of serum CTLA-4 levels, similarity fold change of CTLA-4 was significant upregulated in HT patients compared to controls. The allele and genotypes frequencies according to HWB equilibrium showed significant differences in HT patients 318C/T (rs231775) AA genotypes, while no significant differences in the AG, GG genotypes, respectively compared to controls (p&lt;0.05), There were also no significant differences in the CTLA-4 SNP +49A/G (rs5742909), (CC, CT, TT) genotype, respectively. (p&gt;0.05). Both studied SNPs recoded higher upregulation of soluble and fold change of the immune check point (CTLA-4), respectively. Conclusion: The study reveals that CTLA-4 gene SNPs rs231775 and rs5742909 significantly influence soluble and the expression of CTLA-4 levels in HT patients, potentially causing Hashimoto disease and HT incidence and development.

PD-L1 expression guidance on sintilimab versus pembrolizumab with or without platinum-doublet chemotherapy in untreated patients with advanced non-small cell lung cancer (CTONG1901): A phase 2, randomized, controlled trial

No direct comparison has been performed between different programmed cell death-1 (PD-1) inhibitors for first-line treatment in patients with advanced non-small cell lung cancer (NSCLC). The feasibility of using PD-L1-expression-guided immunotherapy remains unknown. In this open-label, phase 2 study (NCT04252365), patients with advanced NSCLC without EGFR or ALK alterations were randomized (1:1) to receive sintilimab or pembrolizumab monotherapy (PD-L1 expression ≥ 50%), or sintilimab or pembrolizumab plus platinum-based chemotherapy (PD-L1 expression < 50%). The sample size was calculated by optimal two-stage design. The primary endpoint was the objective response rate (ORR). The study included 71 patients (sintilimab arms, n = 35; pembrolizumab arms, n = 36) and met its primary endpoint, with a confirmed ORR of 51.4% (18/35) in the sintilimab arms. The confirmed ORR (95% confidence interval) was 46.2% (19.2%, 74.9%) and 42.9% (17.7%, 71.1%) for patients treated with sintilimab and pembrolizumab monotherapy; and 54.5% (32.2%, 75.6%) and 45.4% (24.4%, 67.8%) for those treated with sintilimab- and pembrolizumab-based combination therapies. The median progression-free survival was 6.9 versus 8.1 months for all sintilimab-treated versus all pembrolizumab-treated patients, respectively, in which it was 7.6 versus 11.0 months in monotherapy and 7.4 versus 7.1 months in combination therapies. The median overall survival was 14.9 versus 21.3 months for all sintilimab-treated versus all pembrolizumab-treated patients, respectively, in which it was 14.9 versus 22.6 months in monotherapy and 14.7 versus 17.3 months in combination therapies. Treatment-related adverse events were consistent with safety outcomes of monotherapy and combination therapy in previous phase III studies. However, the incidence of rash was higher with sintilimab than pembrolizumab monotherapy. This is the first prospective phase 2 study to directly compare two anti-PD-1 antibodies as first-line treatment in advanced NSCLC. Sintilimab was efficacious and well-tolerated irrespective of PD-L1 expression level in patients with advanced NSCLC and had similar efficacy and safety to pembrolizumab.

Role of Pink1-mediated mitophagy in adenomyosis.

Recent studies indicate that endometrial hypoxia plays a critical role in adenomyosis (AM) development. Mitochondria are extremely sensitive to hypoxic damage, which can result in both morphological and functional impairment. Mitophagy is a crucial mechanism for preserving mitochondrial quality by selectively removing damaged mitochondria, thus ensuring the proper functioning of the entire mitochondrial network. In response to hypoxia, PINK1 is activated as a regulator of mitophagy, but its role in AM requires further study. To explore the potential mechanism of mitophagy mediated by PINK1 in the pathogenesis of AM. The study compared PINK1, Parkin, OPTIN, P62, and NDP52 protein expression levels in patients with or without AM using clinical specimens and an AM mouse model. Pathological changes were compared using HE staining. Immunofluorescence and western blot were used to detect protein expression levels. Endometrial stromal cells (ESC) were isolated and examined for mitophagy, protein expression level, and cell invasion ability. Both the endometrial tissue from patients with AM and AM ESC displayed an upregulation of protein levels for PINK1, Parkin, OPTIN, P62, and NDP52 when compared with the control group. Then, HE staining confirmed the successful establishment of the AM mouse model. Moreover, the ultrastructural analysis using transmission electron microscopy revealed that AM mice's endometrial glandular epithelial and stromal cells had exhibited swollen, deformed, and reduced mitochondria along with an increase in the number of lysosomes and mitochondrial autophagosomes. The protein levels of PINK1, Parkin, OPTIN, P62, and NDP52 in uterine tissue from AM mice were noticeably increased, accompanied by a considerable upregulation of ROS levels compared to the control group. In addition, cells in the AM group showed remarkably elevated mitophagy and invasion potentials compared to the control group. In contrast, the cell invasion ability decreased following PINK1 knockdown using the RNA interference technique. The high levels of PINK1-mediated mitophagy have been found in AM. The upregulation in mitophagy contributes to mitochondrial damage, which may result in the abnormal invasion characteristic of AM.

Serum Pentaxin 3 (PTX3) Promotes NLRP3 Inflammasome and Pyroptosis in Patients with Up-Regulated Myasthenia Gravis.

Myasthenia gravis (MG) is an autoantibodies-mediated autoimmune disease with the complications of neuromuscular junction transmission. In this study, we aimed to investigate the molecular regulatory roles of pentaxin 3 (PTX3) in patients and in animal model with MG and to explore its underlying mechanism. Patients with MG were identified and enrolled at our designated hospital and animal model was utilized for the proposed study. Enzyme-linked immunosorbent assay (ELISA) kit were used to quantify the IL-1β, IL-6, INF-γ, IL-17, TNF-α, anti-TAChR IgG/IgG1/IgG2b/IgG2c levels. Serum PTX3 expression level in patients with MG was up-regulated as compared to normal. Furthermore, we found increased expression level of mRNA and protein product of PTX3 in the mice with MG. PTX3 promoted inflammation, pyroptosis in patients as well as in the MG mouse model. In addition, PTX3 induced the STAT3/NLRP3 inflammasome and promoted gene synthesis of STAT3. We found that METTL3-mediated m6A modification decreases PTX3 stability. Our study suggests that the PTX3 is associated with the enhancement of inflammation and pyroptosis through regulating the STAT3/NLRP3 inflammasome signaling pathway at the early stage of the disease. The pro-inflammatory PTX3 facilitates the development of MG and it can be used as a potantial MG-associated diagnostic biomarker for MG.

Potential Significance of CTPS1 in Multiple Myeloma

Introduction With the increasing interest to the metabolism of multiple myeloma (MM), a number of metabolic genes and their associated regulatory networks are essential for MM progression. Our team's prior work indicated that high expression of metabolism-related gene CTPS1 (CTP synthase 1) correlated with poor prognosis of MM. However, the mechanism of CTPS1 in MM is unknown. Methods The difference in CTPS1 expression level in patients with plasma cell malignancies, various stages, and drug-resistant recurrence was examined using publicly available data. MM cell lines were engineered to overexpress or knockdown CTPS1. RNA-seq was used to unbiased interrogate the downstream effector genes modulated by CTPS1. Severe immunodeficient NRG-SGM mice expressing humanized myeloid cytokines were used to determine the effect of CTPS1 on MM proliferation in vivo. Results CTPS1 expression levels varied substantially in various plasma cell malignancies. High CTPS1 expression was associated with shorter overall survival and progression-free survival in newly diagnosed MM patients. Moreover, there was a strong correlation between CTPS1 and sex, albumin, β2 microglobulin, lactate dehydrogenase, and ISS/R-ISS stage. In vitro, CTPS1 overexpressing cells proliferated more quickly than CTPS1 knockdown cells. NRG-SGM3 mouse experiments demonstrated that tumor growth was significantly accelerated in vivo in the CTPS1 overexpression group. In the pharmacological experiment, CTPS1 overexpression group's sensitivity to 20 nM bortezomib reduced, but CTPS1 down-knocked group's sensitivity to 20 nM bortezomib rose. CTPS1 was also shown to be involved in metabolism and synthesis, notably mRNA metabolism, DNA metabolism, chromosomal combination, cell cycle, spliceosome, and cellular senescence. Furthermore, Myc was found to be tightly connected to CTPS1 in both MM cell lines and newly diagnosed MM. Conclusions This study found that increased CTPS1 expression is associated with a poor prognosis and reduced sensitivity to bortezomib in MM. Additionally, CTPS1 upregulated Myc-signaling genes, which promoted progression of MM.

Diagnostic Utility of Proteogenomic Analysis for Inherited Bone Marrow Failure Syndrome

Background: Inherited bone marrow failure syndrome (IBMFS)-a heterogeneous group of disorders characterized by marked cytopenia in one hematopoietic cell lineage-may progress to pancytopenia and make the patient susceptible to hematological malignancies or solid tumors. No clinically useful screening tests have been established for IBMFS, with a few exceptions, including the chromosome fragility test in Fanconi anemia (FA) and telomere length measurement in dyskeratosis congenita (DC). Therefore, high-throughput sequencing is widely used for not only clinical diagnosis of IBMFS but also screening applications; however, a significant number of patients remain genetically undiagnosed. Recent technological advances in in-depth data-independent acquisition proteomic analysis have enabled comprehensive quantitative analysis of &amp;gt;9000 proteins, including very low-abundant proteins. Integration of proteomic analysis with genomic information has been performed in brain tumors and acute leukemia, showing the potential to bridge the gap between genetic information and clinical validation; however, to our knowledge, proteogenomics in IBMFS has not been fully evaluated thus far. Herein, an omics analysis of patients with various IBMFS was performed to assess the diagnostic utility of in-depth proteomic techniques. Methods: We performed an omics analysis of the discovery cohort of 60 patients with IBMFS for in-depth proteomic analysis, targeted capture DNA sequencing, and RNA sequencing. For non-targeted proteomic analysis, digested peptides from the peripheral blood mononuclear cell samples were processed using a Q Exactive HF-X (Thermo Fisher Scientific, Waltham, MA, USA) data-independent acquisition mass spectrometer. Furthermore, diagnostic proteomic analyses targeting several IBMFS-related proteins were performed on a developmental cohort (417 samples; IBMFS [n = 229], aplastic anemia [n = 75], myelodysplastic syndrome/acute myeloid leukemia [n = 113], and healthy controls [n = 27]) using an Orbitrap Exploris 480 mass spectrometer (ThermoFisher Scientific) equipped with an EVOSEP ONE system (EVOSEP, Odense, Denmark). This study was approved by the ethics committee of the Nagoya University Graduate School of Medicine. Results: Non-targeted proteomic analysis was performed on 74 samples obtained from 60 patients with IBMFS and 14 healthy controls. Unsupervised clustering identified eight independent proteomic clusters (C1-C8), with ribosomal pathway-associated protein expression specifically downregulated in C1 and C2. Patients with Diamond-Blackfan anemia, Shwachman-Diamond syndrome (SDS), FA, ADH5/ALDH2 deficiency, and DC were enriched in C1, C2/C8, C3/C4, C6, and C7 clusters, respectively. In particular, among the 74 samples, four patients with ADH5/ALDH2 deficiency showed significantly reduced ADH5 protein expression, whereas the remaining patients showed normal expression, with 100% diagnostic concordance. In addition, 6 of 74 samples had significantly decreased SBDS protein expression, including two patients with monoallelic pathogenic variants in the SBDS gene. This suggested that proteomic analysis may play a complementary role to genetic analysis. To provide a large-scale rapid screening system for IBMFS in a practical clinical setting, targeted proteomic analysis was performed using a small panel of ADH5, SBDS, and GAPDH proteins in a developmental cohort of 417 patients. We demonstrated the significantly decreased SBDS protein expression levels in patients with SDS ( P = 4.98 × 10 -9). ADH5 protein expression levels were also significantly reduced in ADH5/ALDH2 deficiency ( P = 1.66 × 10 -6). Regarding the diagnostic tests, the sensitivity and specificity values were 85.7% and 93.4% for SDS, and 100.0% and 97.5% for ADH5/ALDH2 deficiency, respectively, indicating the sufficient performance to identify patients who required early diagnosis and therapeutic intervention. Conclusion: We performed the first proteogenomic analysis of patients with IBMFS and identified eight independent proteomic clusters associated with IBMFS subtypes and characteristic pathways. Furthermore, the clinical application of targeted proteomic assays constructed from these results may help diagnose and screen IBMFS, including SDS and ADH5/ALDH2 deficiency, for which appropriate clinical screening tests are lacking.

Identification of immunological characteristics and cuproptosis-related molecular clusters in primary Sjögren's syndrome

BackgroundPrimary Sjögren's syndrome (pSS) is a chronic systemic autoimmune disease characterized by lymphocyte infiltration of the exocrine glands. The typical clinical symptoms of pSS include dryness of the mouth (xerostomia) and eyes (xerophthalmia), fatigue, and joint pain. Cuproptosis is a recently identified mode of programmed cell death that leads to the progression of multiple diseases, and the precise etiology and pathophysiology of pSS remain unknown. Consequently, the aim of our study was to explore cuproptosis-related molecular clusters and identify key genes in pSS. MethodGene expression profiles of the peripheral blood in the GSE84844 dataset were downloaded to identify the expression characteristics of cuproptosis regulators and immune cell infiltration. Subsequently, further exploration was conducted on the clusters involving cuproptosis-related genes (CRGs) and the corresponding immune cell infiltration, and the WGCNA algorithm was applied to explore the cluster-specific differentially expressed genes. Finally, the best machine prediction model was selected for candidate hub cuproptosis-associated genes and the accuracy of predictive efficiency was verified by the salivary gland in an external dataset (GSE143153) and enzyme-linked immunosorbent assay. ResultThrough a comparison of patients with pSS and controls, 7 CRGs and 4 types of immune cells were identified. Immune cell infiltration revealed significant immune heterogeneity in three cuproptosis-related molecular clusters in pSS. The random forest machine model showed the best discriminatory performance (area under the receiver operating characteristic curve (AUC) = 1.000) and built a predictive model based on 5 genes, which demonstrated satisfactory performance (AUC = 0.70) in the GSE143153 dataset. Based on serum samples, EED (AUC = 0.557), CBL (AUC = 0.635), and NFU1 (AUC = 0.655) showed lower expression levels in patients with pSS (p = 0.037, p = 0.000, p = 0.000, respectively). ConclusionIn this study, we systematically analyzed the association between pSS and cuproptosis, established a predictive model that screened for high-risk genes linked to the advancement of pSS, and explored the pathogenic mechanisms and novel therapeutic strategies for pSS, targeting EED, CBL and NFU1.