Normal Tissue Research Articles

RGS4 promotes the progression of gastric cancer through the focal adhesion kinase/phosphatidyl-inositol-3-kinase/protein kinase B pathway and epithelial-mesenchymal transition.

Regulator of G protein signaling (RGS) proteins participate in tumor formation and metastasis by acting on the α-subunit of heterotrimeric G proteins. The specific effect of RGS, particularly RGS4, on the progression of gastric cancer (GC) is not yet clear. To explore the role and underlying mechanisms of action of RGS4 in GC development. The prognostic significance of RGS4 in GC was analyzed using bioinformatics based public databases and verified by immunohistochemistry and quantitative polymerase chain reaction in 90 patients with GC. Function assays were employed to assess the carcinogenic impact of RGS4, and the mechanism of its possible influence was detected by western blot analysis. A nude mouse xenograft model was established to study the effects of RGS4 on GC growth in vitro. RGS4 was highly expressed in GC tissues compared with matched adjacent normal tissues. Elevated RGS4 expression was correlated with increased tumor-node-metastasis stage, increased tumor grade as well as poorer overall survival in patients with GC. Cell experiments demonstrated that RGS4 knockdown suppressed GC cell proliferation, migration and invasion. Similarly, xenograft experiments confirmed that RGS4 silencing significantly inhibited tumor growth. Moreover, RGS4 knockdown resulted in reduced phosphorylation levels of focal adhesion kinase, phosphatidyl-inositol-3-kinase, and protein kinase B, decreased vimentin and N-cadherin, and elevated E-cadherin. High RGS4 expression in GC indicates a worse prognosis and RGS4 is a prognostic marker. RGS4 influences tumor progression via the focal adhesion kinase/phosphatidyl-inositol-3-kinase/protein kinase B pathway and epithelial-mesenchymal transition.

Long Non-Coding RNA LINC01123 Facilitates Cholangiocarcinoma Aggravation by Targeting miR-641.

Cholangiocarcinoma (CCA) is a malignant and insidious tumor that is tricky to treat. Long non-coding RNA (LncRNA) LINC01123 is a biomolecule that influences cancer progression by regulating gene expression via influencing the regulatory function of microRNAs in gene expression. Therefore, this study investigated the connection between LINC01123 and CCA and explored the underlying mechanism. The objective of this study was to provide valuable information on the management of CCA. Tumor and normal paracancer tissue samples in this study were collected from 128 CCA patients. To measure LINC01123 and miR-641 expression characteristics, quantitative reverse transcription-polymerase chain reaction was used. To explore the biological functions of LINC01123 and miR-641 in CCA cells, cell counting Kit-8 (CCK-8) and transwell migration and invasion assays were used. The mechanism was investigated using dual luciferase reporter assays and rescue experiments. This study found that the expression levels of LINC01123 were higher in CCA tissues and cells than in normal tissues and cells. LINC01123 promoted the proliferation, migration and invasion ability of CCA cells and consequently became an indicator of lymph node metastasis and advanced TNM stage in CCA. Moreover, the expression of miR-641 was negatively correlated with the expression of LINC01123. LINC01123 affected CCA progression by downregulating miR-641. There was an upregulation of LINC01123 in CCA tumor tissues and cells. LINC01123 promoted CCA aggravation by targeting miR-641. LINC01123 could be the target of future treatment for CCA.

Single-molecule localisation microscopy (SMLM) is feasible in human and animal formalin fixed paraffin embedded (FFPE) tissues in medical renal disease

AimsEstablishment of a protocol for routine single-molecule localisation microscopy (SMLM) imaging on formalin fixed paraffin embedded (FFPE) tissue using medical renal disease including minimal change disease (MCD) and focal segmental...

Implementing Mutational Epidemiology on a Global Scale: Lessons from Mutographs.

The Mutographs Cancer Grand Challenge team aimed to discover unknown causes of cancer through mutational epidemiology, an alliance of cancer epidemiology and somatic genomics. By generating whole-genome sequences from thousands of cancers and normal tissues from more than 30 countries on five continents, it discovered unsuspected mutagenic exposures affecting millions of people, raised the possibility that some carcinogens act by altering forces of selection in tissue microenvironments rather than by mutagenesis, and demonstrated changes to the direction of somatic evolution in normal cells of the human body in response to exogenous exposures and noncancer diseases. See related article by Bressan et al., p. 16 See related article by Bhattacharjee et al., p. 28 See related article by Goodwin et al., p. 34.

Bioinformatics Analysis Reveals Microrchidia Family Genes as the Prognostic and Therapeutic Markers for Colorectal Cancer.

The aim of this study is to examine the role of the microrchidia (MORC) family, a group of chromatin remodeling proteins, as the therapeutic and prognostic markers for colorectal cancer (CRC). MORC protein family genes are a highly conserved nucleoprotein superfamily whose members share a common domain but have distinct biological functions. Previous studies have analyzed the roles of MORCs as epigenetic regulators and chromatin remodulators; however, the involvement of MORCs in the development and pathogenesis of CRC was less examined. The current work examined the role of the MORCs as the therapeutic and prognostic markers for CRC. The expressions and prognostic significance of MORC family genes in CRC were explored. The role of these genes in tumor immunity was comprehensively analyzed in terms of their functions in immune cell infiltration, tumor microenvironment (TME), and their interaction with immune regulatory genes such as immunosuppressive genes, immune checkpoints and immunostimulatory genes. The relations between MORC family genes, tumor mutation burden (TMB), DNA, mismatch repair (MMR), RNA methylation, microsatellite instability (MSI), and drug sensitivity were investigated using the R statistical software. The expressions of MORC4 in 150 CRC tissues and 60 paracancer tissues were detected by immunohistochemical method. CRC cell proliferation, migration, and invasion were measured by cell counting kit-8 (CCK-8), scratch assay, and transwell cell invasion assay. The expressions of MORC2 and MORC4 were significantly upregulated, whereas those of MORC1 and MORC3 were noticeably downregulated in CRC in comparison to their expressions in normal colorectal mucosal tissues. Patients with high-expressed MORC2 showed a more unfavorable prognosis than those with a low MORC2 level. Functional annotation analysis identified 100 MORC family genes with the most significant negative or positive correlations to diabetic cardiomyopathy, amyotrophic lateral sclerosis, oxidative phosphorylation, Huntington's disease, thermogenesis, Parkinson's disease, olfactory transduction, Alzheimer's disease, prion disease. MORC3 expression was positively correlated with Stromal score, Immune score and ESTIMATE score, while MORC2 expression was negatively related to the three scores in CRC, these correlations were not statistically significant. Additionally, the MORC family genes were significantly positively correlated with tumor-infiltrating immune cells such as T helper cells and exhibited close relations to some immunosuppressive genes such as CXCR4 and PVR, immunostimulatory genes such as TGFBR1, KDR, and CD160 as well as some immune checkpoint genes. It was found that the expressions of some members of MORC family genes were positively correlated with DNA methylation, MSI, TMB, MMRs, and drug sensitivity in CRC and that the mRNA and protein levels of MORC4 were remarkably upregulated in CRC tissues than in adjacent normal tissues (P<0.05). In the MORC4 knockdown group, DLD-1 cell proliferation was more inhibited than in the negative control (NC) and siRNA groups (P<0.05). Furthermore, the migratory capacity of DLD-1 cells and the number of cells crossing the basement membrane in the MORC4 knockdown group were reduced compared to the NC and siRNA groups (all P<0.05). The expressions of MORC family genes were significantly different in CRC samples, which was related to the immune cell infiltration and prognosis of CRC. Thus, the MORC family genes were considered as markers for indicating the clinical immunotherapy and prognostic outcome of CRC.

Upregulated PCAT-1 predicts poor prognosis and reduced immune cell infiltration in head and neck squamous cell carcinoma through the miR-145-5p / FSCN-1 axis.

LncRNA PCAT-1 is known to promote cancer proliferation, invasion, and metastasis. However, its significance in HNSCC is not fully understood. This research investigates how the PCAT-1 / miR-145-5p / FSCN-1 axis promote HNSCC. We analyzed the gene expression patterns on 238 fresh-frozen samples, comparing tumors with their normal adjacent tissues (NATs). HNSCC samples showed higher PCAT-1 and FSCN-1 expression compared to NATs (p < 0.001 and p < 0.001, respectively). In contrast, miR-145-5p expression was markedly downregulated compared to NATs (p < 0.001). Notably, ROC curve analysis revealed exceptional diagnostic power, with an AUC of 0.83 for PCAT-1, 0.95 for miR-145-5p, and 0.91 for FSCN-1. Pearson correlation analysis unveiled a significant positive correlation between PCAT-1 and FSCN-1 expression levels (r = 0.084, p < 0.001) and negative correlations between FSCN-1 and miR-145-5p (r = -0.710, p < 0.001) as well as between PCAT-1 and miR-145-5p (r = -0.759, p < 0.001). Distinct molecular profiles were observed in the levels of PCAT-1, miR-145-5p, and FSCN-1 between HPV (-) and HPV ( +) 16 and 18 genotypes (p = 0.007, p = 0.027, and p = 0.002). MiR-145-5p expression showed significant differences between HPV (-) and HPV ( +) other genotypes (p = 0.035). FSCN-1 expression showed notable distinctions between HPV ( +) 18 & 16 and HPV ( +) other genotypes (p = 0.031). Elevated levels of lncRNA PCAT-1 promote HNSCC through the miR-145-5p/FSCN-1 axis and are associated with poor prognosis and reduced immune cell infiltration levels.

Integrating machine learning with mendelian randomization for unveiling causal gene networks in glioblastoma multiforme

BackgroundGlioblastoma multiforme (GBM) is a highly aggressive brain cancer with poor prognosis and limited treatment options. Despite advances in understanding its molecular mechanisms, effective therapeutic strategies remain elusive due to the tumor’s genetic complexity and heterogeneity.MethodsThis study employed a comprehensive analysis approach integrating 113 machine learning algorithms with Mendelian Randomization (MR) analysis to investigate the molecular underpinnings of GBM. Five publicly available gene expression datasets were analyzed to identify differentially expressed genes (DEGs) associated with GBM. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify GBM-related gene modules. Further, gene set enrichment and variation analyses were conducted to explore the biological pathways involved. The machine learning models were evaluated using Receiver Operating Characteristic (ROC) curves and confusion matrices to assess their predictive accuracy, with the best-performing model validated across external datasets. MR analysis was performed to establish causal relationships between genetically predicted gene expression levels and GBM outcomes.ResultsThe study identified 286 DEGs between GBM and adjacent normal tissues across five datasets. WGCNA highlighted the yellow module as the most relevant to GBM, containing key genes such as KLHL3, FOXO4, and MAP1A. Of the 113 machine learning models tested, Ridge regression achieved the highest area under the curve (AUC) of 0.92, demonstrating robust predictive accuracy. Validation using external datasets confirmed the model's reliability, with a classification accuracy of 89.5% in the training set and 85.3% in the validation sets. MR analysis provided strong evidence of a causal relationship between the expression levels of the identified genes and GBM risk.ConclusionsThis study demonstrates the power of combining machine learning and Mendelian Randomization to uncover novel genetic markers for GBM. The identified genes offer promising potential as biomarkers for GBM diagnosis and therapy, providing new avenues for personalized treatment strategies.

Identification of Immune Infiltration-Associated CC Motif Chemokine Ligands as Biomarkers and Targets for Colorectal Cancer Prevention and Immunotherapy.

Colorectal cancer (CRC) is the third most common cancer globally, with limited effective biomarkers and sensitive therapeutic targets. An increasing number of studies have highlighted the critical role of tumor microenvironment (TME) imbalances, particularly immune escape due to impaired chemokine-mediated trafficking, in tumorigenesis and progression. Notably, CC chemokines (CCLs) have been shown to either promote or inhibit angiogenesis, metastasis, and immune responses in tumors, thereby influencing cancer development and patient outcomes. However, the diagnostic and prognostic significance of CCLs in CRC remains unclear. In this study, multiple online tools for bioinformatics analyses were utilized. The findings revealed that the mRNA expression levels of CCL3, CCL4, and CCL26 were significantly elevated in CRC tissues compared to normal tissues, whereas CCL2, CCL5, CCL11, CCL21, and CCL28 mRNA levels were markedly downregulated. Additionally, dysregulation of CCL4, CCL5, and CCL21 was strongly associated with clinical staging, and elevated levels of CCL4, CCL11, and CCL28 were linked to significantly prolonged survival in CRC patients. Functional enrichment analysis indicated that the cellular roles of CCLs were predominantly associated with the chemokine, Wnt, and Toll-like receptor signaling pathways, as well as protein kinase activity. Furthermore, transcriptional regulation of most CCLs involved RELA and NFKB1. Key downstream targets included members of the SRC family of tyrosine kinases (HCK, LYN, and LCK), serine/threonine kinases (ATR and ATM), and others such as CSNK1G2, NEK2, and CDK2. Moreover, CCLs (CCL2, CCL3, CCL4, CCL5, CCL11, CCL21, and CCL28) exhibited strong correlations with major infiltration-related immune cells, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. In conclusion, our study provides novel insights into the potential utility of CCLs as biomarkers and therapeutic targets for CRC prevention and immunotherapy.

Novel combination therapy targeting oncogenic signaling kinase P21 activated Kinase-1 and chemotherapeutic drugs against triple negative breast cancer.

Most of the triple negative phenotype or basal-like molecular subtypes of breast cancers are associated with aggressive clinical behaviour and show poor disease prognosis. Current treatment options are constrained, emphasizing the need for novel combinatorial therapies for this particular tumor subtype. Our group has demonstrated that functionally active p21 activated kinase 1 (PAK1) exhibits significantly higher expression levels in clinical triple negative breast cancer (TNBC) samples compared to other subtypes, as well as adjacent normal tissues. Low PAK1 expression in TNBC was significantly linked to better prognosis, with improved overall survival (OS, p=0.00236) and relapse-free survival (RFS, p=0.0314), as shown by GOBO analysis. To confirm the role of PAK1 as a therapeutic target and to discover novel synergistic chemotherapy drug combinations, we conducted a drug combination screen using triple negative breast cancer cell lines and a mouse metastatic tumor cell line. We identified the combined inhibition of PAK1 inhibitor, NVS-PAK1 with doxorubicin/paclitaxel/methotrexate as a synergistic novel therapeutic approach for treating metastatic TNBC to improve overall survival. This study also indicated a reduction in the effective dosage of the chemotherapeutic drug when combined with NVS-PAK1. Our study demonstrates that combining NVS-PAK1 with each of the chemotherapeutic drugs' doxorubicin, paclitaxel, and methotrexate resulted in decreased colony formation, reduced wound healing capability, and diminished migratory and invasive potential in both TNBC cell lines and 4T1 in vitro. These findings were further validated in orthotopic mouse mammary tumors, confirming that simultaneous PAK1 inhibition alongside chemotherapy significantly enhanced anti-tumor efficacy and reduced metastasis.

Migrasome-related prognostic signature TSPAN4 correlates with immune infiltrates and metabolic disturbances in hepatocellular carcinoma.

We aim to comprehensively analyze and validate the prognostic efficacy of tetraspanin 4 (TSPAN4) and several other migrasome-related markers in hepatocellular carcinoma (HCC). The expression, diagnostic, and prognostic efficacy of five migrasome-related genes in HCC were analyzed using several databases. Five pairs of adjacent non-tumor tissues and HCC tissues were used to validate the expression. The prognostic efficacy of TSPAN4 was validated in a HCC cohort. TSPAN4 was knocked down in Huh-7 cells, EdU, and CCK-8, and wound healing assays were conducted to analyze its effects on cell proliferation and migration. In addition, transcriptomic sequencing was used to identify differentially expressed genes. Compared with those in normal tissues, four genes (TSPAN4, PIGK, NDST1, and CPQ) were elevated in liver hepatocellular carcinoma (LIHC), but not TSPAN7. Of these, only elevated TSPAN4 predicted unfavorable prognosis of HCC patients. The expression and prognostic efficacy of TSPAN4 were further confirmed in a HCC cohort (97 patients); and patients in the TSPAN4high group showed unfavorable overall survival (log-rank P = 0.0055). Functional analysis showed that TSPAN4 knockdown significantly suppressed cell migration, but not cell proliferation. Moreover, TSPAN4 knockdown induced disturbances of the metabolic pathways, mainly pentose and glucuronate interconversions. TPSAN4 is a promising prognostic and therapeutic target for HCC treatment and may be involved in the metabolic pathways that affect disease progression.

Epidemiology of the most Prevalent Cancers in Ninewa between 2017–2021

Purpose. Cancer is characterized by abnormal cell growth resulting from uncontrolled cell division. These cells spread and form metastatic lesions in normal tissues, leading to loss of tissue and organ function. Cancer is one of the most life-threatening diseases worldwide that develops in humans. regardless of sex, ethnicity, or nationality.Material and methods. Here, we conducted a retrospective study to collect data on the various types of cancers prevalent in Ninewa, Iraq, between 2017–2021, using hospital records pooled in the Iraq Cancer Registry. We focused on the top 10 most notable cancers prevalent in humans.Results. Our study revealed that number of novel cancer cases and mortality rates have been increasing annually between 2017– 2021. Females had higher rates of cancer occurrence than males. The most prevalent cancers in Ninewa were breast cancer in women and lung cancer in men. Leukemia was the most common pediatric cancer. Furthermore, this study reported that lung cancer had the highest mortality rate in Ninewa, followed by breast cancer.Conclusion Our study provides a statistical overview on cancer cases in the Ninewa governorate, and will be useful to clinicians, faculty members and other professionals in the medical field.

Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1-Alpha in Endometriosis: Expression, Regulation, and Potential Role.

The present study was designed to comprehensively analyze the expression profiles of peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α), estrogen-related receptor-α (ERRα), estrogen receptor-β (ERβ), interleukin-6 (IL-6), cysteinyl-aspartic acid-specific protease-3 (caspase-3), and cysteinyl-aspartic acid-specific protease-9 (caspase-9) in endometriosis tissues. It also aimed to elucidate the hitherto unclarified role of PGC-1α in the processes of proliferation, apoptosis, and gene expression regulation of human endometrial stromal cells, thereby providing novel insights and identifying potential molecular targets for advancing endometriosis treatment modalities. A total of 49 ectopic endometrial tissue samples and 50 normal endometrial tissue samples were meticulously collected from patients who underwent gynecological surgeries in the People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine in Fuzhou, China, between January 2022 and January 2023. Immunohistochemistry was used to detect protein expression levels. Human primary endometrial stromal cells were transfected and grouped for in-depth analysis. Real-time quantitative polymerase chain reaction (RT-qPCR) was utilized to measure gene expression, the cell counting kit 8 (CCK-8) assay was employed to evaluate cell proliferation, and the lactate dehydrogenase (LDH) method was used to determine cell death. In endometriosis tissues, compared with normal endometrial tissues, the expression levels of PGC-1α, ERRα, and IL-6 were significantly increased. The expression of ERβ was also elevated, while the expression levels of caspase-3 and caspase-9 were decreased. In cell experiments, after transfection with interference plasmids to reduce PGC-1α expression, the expression levels of ERRα and ERβ were decreased, the expression of IL-6 was increased, and the expression levels of caspase-3 and caspase-9 were augmented. Conversely, after transfection with overexpression plasmids to enhance PGC-1α expression, the expression levels of ERRα and ERβ were elevated, the expression of IL-6 was diminished, and the expression levels of caspase-3 and caspase-9 were decreased. Moreover, when PGC-1α expression was interfered with by siRNA, cell proliferation was attenuated (albeit not statistically significant), and cell apoptosis was enhanced. Overexpression of PGC-1α promoted cell proliferation and inhibited cell apoptosis. PGC-1α potentially plays a crucial role in the pathogenesis of endometriosis by regulating ERRα, ERβ, IL-6, and apoptosis-related factors. This study provides a strong theoretical foundation and a novel direction for developing endometriosis treatment strategies. To the best of our knowledge, it is the first to systematically explore the relationship between PGC-1α and these key factors in endometriosis, filling a knowledge gap. Future studies are needed to further dissect its mechanism and realize its clinical application potential.

Leveraging explainable AI and large-scale datasets for comprehensive classification of renal histologic types

Recently, as the number of cancer patients has increased, much research is being conducted for efficient treatment, including the use of artificial intelligence in genitourinary pathology. Recent research has focused largely on the classification of renal cell carcinoma subtypes. Nonetheless, the broader categorization of renal tissue into non-neoplastic normal tissue, benign tumor and malignant tumor remains understudied. This gap in research can primarily be attributed to the limited availability of extensive datasets including benign tumor and normal tissue in addition to specific type of renal cell carcinoma, which hampers the ability to conduct comprehensive studies in these broader categories. This research introduces a model aimed at classifying renal tissue into three primary categories: normal (non-neoplastic), benign tumor, and malignant tumor. Utilizing digital pathology while slide images (WSIs) from nephrectomy specimens of 2,535 patients from multiple institutions, the model provides a foundational approach for distinguishing these key tissue types. The study utilized a dataset of 12,223 WSIs comprising 1,300 WSIs of normal tissue, 700 WSIs of benign tumors, and 10,223 WSIs of malignant tumors. Employing the ResNet-18 architecture and a Multiple Instance Learning approach, the model demonstrated high accuracy, with F1-scores of 0.934 (CI: 0.933–0.934) for normal tissue, 0.684 (CI: 0.682–0.687) for benign tumors, and 0.878 (CI: 0.877–0.879) for malignant tumors. The overall performance was also notable, achieving a weighted average F1-score of 0.879 (CI: 0.879–0.880) and a weighted average area under the receiver operating characteristic curve of 0.969 (CI: 0.969–0.969). This model significantly aids in the swift and accurate diagnosis of renal tissue, encompassing non-neoplastic normal tissue, benign tumor, and malignant tumor.

Synchronous Interference of Dual Metabolic Pathways Mediated by H2S Gas/GOx for Augmenting Tumor Microwave Thermal Therapy.

Sublethal tumor cells have an urgent need for energy, making it common for them to switch metabolic phenotypes between glycolysis and oxidative phosphorylation (OXPHOS) for compensatory energy supply; thus, the synchronous interference of dual metabolic pathways for limiting energy level is essential in inhibiting sublethal tumor growth. Herein, a multifunctional nanoplatform of Co-MOF-loaded anethole trithione (ADT) and myristyl alcohol (MA), modified with GOx and hyaluronic acid (HA) was developed, namely, CAMGH. It could synchronously interfere with dual metabolic pathways including glycolysis and OXPHOS to restrict the adenosine triphosphate (ATP) supply, achieving the inhibition to sublethal tumors after microwave (MW) thermal therapy. Under low-power MW irradiation, CAMGH induced certain tumor thermal damage while ensuring the safety of the surrounding normal tissues. The loaded GOx consumed glucose in tumors, undoubtedly blocking the main energy supply pathway, the glycolytic pathway. Then, H2O2 generated from GOx reacted with Co2+ to produce cytotoxic ·OH, combining with the released H2S from ADT to co-obstruct OXPHOS and then synergy with the above glycolysis blocking for a more effective ATP inhibition. The powerful depletion of ATP caused significant suppression of damage resistance protein upregulated after thermal stimulation, i.e., HSP90, and then the activation of caspase-3, achieving the simultaneous reversal of heat resistance and apoptosis resistance. Altogether, the CAMGH-based synchronous interference of dual metabolic pathways shows the potential to break down tumor self-repair, presenting an alternative strategy to enhance the therapeutic effect of tumor MW thermal therapy.

SUGT1 is a prognostic biomarker and is associated with immune infiltrates in ovarian cancer

BackgroundOvarian cancer (OC) is a prevalent gynecological malignancy with a relatively dismal prognosis. The SGT1 homolog (SUGT1) protein, which interacts with heat shock protein 90 and is essential for the G1/S and G2/M transitions, was formerly thought to be a cancer promoter, but its precise role in OC remains unknown.MethodsWe conducted a comprehensive bioinformatics analysis of SUGT1 expression in patients with OC compared with their normal controls, including the data from the cancer genome atlas (TCGA), genotype–tissue expression (GTEx) databases, gene ontology (GO) analysis, Kyoto Encylopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analysis (GSEA), single sample gene set enrichment analysis (ssGSEA). In addition, Kaplan–Meier (KM) analysis, univariate and multivariate Cox analyses were applied to investigate the prognostic role of SUGT1 in ovarian cancer. Furthermore, we validated the expression of SUGT1 in OC and normal tissues through immunohistochemistry.ResultsSUGT1 was significantly overexpressed in OC than in normal tissues. In addition, the GO, KEGG and GSEA analysis revealed that SUGT1 was associated with the functions related to immunoglobulin complex, antigen binding, immunoglobulin receptor binding, among others. Besides, ssGSEA demonstrated a positive correlation between SUGT1 expression and the abundance of T central memory cells, natural killer cells, and T gamma delta cells, although it showed a negative association with activated dendritic cells, cytotoxic cells, T cells, and T helper 1 cells. Subsequently, KM survival analysis revealed that high SUGT1 expression indicated a shorter overall survival, disease specific survival and progression free interval in OC patients. Univariate and multivariate Cox regression revealed that SUGT1 could serve as an independent risk factor for prognosis of patients with OC.ConclusionsAll these results of this study show that SUGT1 is an important molecular component in immune infiltration in OC and may have a new significant prognostic role in OC.

Elevated expression of let-7b-3p enhances aggressiveness of larynx squamous cell carcinoma cells

Aims: Larynx squamous cell carcinoma (LSCC) is the second most common head and neck malignancy. While let-7b-3p has been shown to have a role in cancer progression in malignancies, there is no research examining the association between LSCC and let-7b-3p. This study aimed to investigate the expression status of let-7b-3p and the potential roles of this microRNA (miRNA) in LSCC. Methods: Using quantitative real-time polymerase chain reaction (qRT-PCR), we examined the expression status of let-7b3p in 36 LSCC samples and the neighboring normal tissues. Then, the let-7b-3p miRNA mimic was transfected into Hep-2 cells via lipofectamine 2000 reagents. Cell viability was determined using the cell viability detection (CVDK-8) kit, and cell migration was evaluated with the scratch assay. To identify differentially expressed genes (DEGs) in larynx cancer GSE137308 and GSE130605 datasets were downloaded and reanalyzed using Gene Expression Omnibus (GEO2R) tool. Potential target genes of let-7b-3p were investigated in the miRNA target prediction and functional annotation database (miRDB). Shared genes between geo datasets and miRDB results were identified and the relationship between these genes and LSCC was investigated in the literature. Results: We demonstrated that the expression levels of let-7b-3p was significantly upregulated in LSCC tumor tissues in comparison to the corresponding normal tissues. Mimic let-7b-3p transfection enhanced Hep-2 cell proliferation and migration. In vitro and bioinformatics analysis showed that overexpression of let-7b-3p can enhance the larynx cancer cell proliferation and migration through MYBPC1. Conclusion: It was evaluated that let-7b-3p/MYBPC1 axis could potentially affect the LSCC process. Let-7b-3p has the potential to be a biomarker for LSCC, therefore, the let-7b-3p/ MYBPC1/LSCC relationship should be elucidated with new studies.

Self-Sustained Biophotocatalytic Nano-Organelle Reactors with Programmable DNA Switches for Combating Tumor Metastasis.

Metastasis, the leading cause of mortality in cancer patients, presents challenges for conventional photodynamic therapy (PDT) due to its reliance on localized light and oxygen application to tumors. To overcome these limitations, a self-sustained organelle-mimicking nanoreactor is developed here with programmable DNA switches that enables bio-chem-photocatalytic cascade-driven starvation-photodynamic synergistic therapy against tumor metastasis. Emulating the compartmentalization and positional assembly strategies found in living cells, this nano-organelle reactor allows quantitative co-compartmentalization of multiple functional modules for the designed self-illuminating chemiexcited PDT system. Within the space-confined nanoreactor, biofuel glucose is converted to hydrogen peroxide (H2O2) which enhances luminol-based chemiluminescence (CL), consequently driving the generation of photochemical singlet oxygen (1O2) via chemiluminescence resonance energy transfer. Meanwhile, hemoglobin functions as a synchronized oxygen supplier for both glucose oxidation and PDT, while also exhibiting peroxidase-like activity to produce hydroxyl radicals (·OH). Crucially, the nanoreactor keeps switching off in normal tissues, with on-demand activation in tumors through toehold-mediated strand displacement. These findings demonstrate that this nanoreactor, which is self-sufficient in light and oxygen and precise in striking tumors, presents a promising paradigm for managing highly metastatic cancers.

Bioinformatics analysis of ferroptosis-related hub genes and immunoinfiltration in myocardial ischemia/reperfusion following heart transplantation

BackgroundIschemia/reperfusion (I/R) is an inevitable pathophysiological process during heart transplantation, and ferroptosis is an important pathogenic mechanism. Unlike other modes of cell death, ferroptosis depends on the accumulation of iron within the cell and the oxidative degradation of polyunsaturated fatty acids. Dysregulation of this pathway has been linked to the progression of multiple pathological conditions, making it an attractive target for therapeutic intervention. Therefore, this study aims to explore the effect of ferroptosis on I/R during heart transplantation.MethodsGEO2R was applied to identify differentially expressed genes (DEGs) obtained from GSE50884 data, which was involved in I/R and heart transplantation. And ferroptosis-related DEGs (FRDEGs) were screened by venn diagram with ferroptosis-related genes downloaded from FerDb database. FRDEGs was enriched and analyzed by GO and KEGG, and hub genes related to ferroptosis were screened by Cytoscape software and database STRING. Additionally, considering the relationship between ferroptosis and immunity, CIBERSORTx was to analyze the infiltration of 22 kinds of immune cells in I/R during heart transplantation, and the correlation between each immune cell and the expression of FRDEGs was also discussed. Finally, the mouse model of heart transplantation with I/R was constructed, and the hub genes was verified by RT-qPCR and western blot.Results12 FRDEGs were identified out of 327 DEGs in GSE50844, which were mainly involved in ferroptosis and other pathways. Three hub genes (SLC7A11, PSAT1, ASNS) were obtained by the degree algorithm of cytohubba plug-in. Immunoinfiltration analysis showed that 16 of 22 immune cells changed, and the immune score of heart transplantation with I/R was higher than that without I/R. In addition, hub genes exhibited significant correlation with Eosinophils, NK cells resting, Dendritic cells resting, NK cells activated and T cells CD4 memory activated. We verified the expression of SLC7A11, PSAT1 and ASNS was higher than that in normal tissues using RT-qPCR and western blot in mouse models of heart transplantation with I/R, companied by ferroptosis aggravated is involved.ConclusionsIn short, ferroptosis is involved in I/R injury during heart transplantation, which is related to immune cell infiltration. Three hub genes (SLC7A11, PSAT1 and ASNS) identified in this study provide therapeutic targets for ameliorating I/R injury in heart transplantation.

Research on the mechanism of eugenol in the treatment of liver cancer based on network pharmacology, molecular docking technology, and in vitro experiments.

Eugenol, a phenolic natural product with diverse pharmacological activities, remains unexplored in liver cancer. Using network pharmacology, we investigated eugenol's therapeutic mechanisms in liver cancer. We obtained eugenol's molecular structure from PubChem and screened its targets using similarity ensemble approach in Swiss Target Predictiondatabases. Overlapping genes with liver cancer-related genes from GeneCards were identified. Protein-protein interaction networks, Gene Ontology annotations, and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted. A target-pathway network revealed eugenol's interaction with 122 liver cancer-related genes. Molecular docking confirmed eugenol's high affinity for mitochondrial nicotinamide adenine dinucleotide, reduced form (NADH) dehydrogenase 1 (MT-ND1), AKT1, NDUFB7, and NADH dehydrogenase (complex I) subunit S3 (NDUFS3). Expression levels of these targets in normal liver and liver cancer tissues were examined using GEPIA2 and HPA databases. The CCK-8 assay and colony formation assay demonstrated that eugenol significantly inhibited the proliferation of hepatocellular carcinoma cells. Western blot analysis confirmed that eugenol upregulated MT-ND1 while downregulating the expression of targets such as AKT1, NDUFB7, and NDUFS3. Furthermore, it was found that eugenol could influence the expression of the AKT1 target through the AKT/p70 S6K pathway. This study provides new insights into the potential mechanisms of eugenol in liver cancer and offers novel perspectives for network-based liver cancer research.

Comprehensive discovery and functional characterization of the noncanonical proteome.

The systematic identification and functional characterization of noncanonical translation products, such as novel peptides, will facilitate the understanding of the human genome and provide new insights into cell biology. Here, we constructed a high-coverage peptide sequencing reference library with 11,668,944 open reading frames and employed an ultrafiltration tandem mass spectrometry assay to identify novel peptides. Through these methods, we discovered 8945 previously unannotated peptides from normal gastric tissues, gastric cancer tissues and cell lines, nearly half of which were derived from noncoding RNAs. Moreover, our CRISPR screening revealed that 1161 peptides are involved in tumor cell proliferation. The presence and physiological function of a subset of these peptides, selected based on screening scores, amino acid length, and various indicators, were verified through Flag-knockin and multiple other methods. To further characterize the potential regulatory mechanisms involved, we constructed a framework based on artificial intelligence structure prediction and peptide‒protein interaction network analysis for the top 100 candidates and revealed that these cancer-related peptides have diverse subcellular locations and participate in organelle-specific processes. Further investigation verified the interacting partners of pep1-nc-OLMALINC, pep5-nc-TRHDE-AS1, pep-nc-ZNF436-AS1 and pep2-nc-AC027045.3, and the functions of these peptides in mitochondrial complex assembly, energy metabolism, and cholesterol metabolism, respectively. We showed that pep5-nc-TRHDE-AS1 and pep2-nc-AC027045.3 had substantial impacts on tumor growth in xenograft models. Furthermore, the dysregulation of these four peptides is closely correlated with clinical prognosis. Taken together, our study provides a comprehensive characterization of the noncanonical proteome, and highlights critical roles of these previously unannotated peptides in cancer biology.