Search Results (245)

Background/Objectives: We aim to identify predictors of response to ICIs in patients with advanced solid tumors that exhibiting a TMB ≥ 10 mut/Mb. Methods: Patients treated with ICIs alone at Northwestern University between 1 January 2015 and 31 December 2020 were identified. Progression-free survival (PFS) and overall survival (OS) were calculated using the Kaplan–Meier method, and groups were compared using the log-rank test. Wilcoxon rank sum tests, chi-squared tests, and Fisher’s exact tests were used for univariable analyses evaluating the impact of clinical and genetic variables on response, with significance defined as p < 0.05. Results: A total of 117 patients were classified as ICI-sensitive (n = 88) or non-ICI-sensitive (n = 29). Among evaluable patients (n = 105), the overall response rate was 34% with 14% achieving a complete response. Median PFS and OS were 8.05 months and 26.8 months, respectively. Higher PFS rates were significantly linked to the ICI-sensitive tumor group (p = 0.009), absence of liver metastasis (p = 0.015), and no prior systemic treatment (p = 0.001) in both cohorts. In non-ICI-sensitive patients, a TMB of ≥15 mut/Mb correlated with improved outcomes (p = 0.012). Mutations in the MYC pathway (p = 0.03) and the MLL2 gene (p = 0.014) were associated with poorer responses, while mutations in the TERT gene were linked to better responses (p = 0.031). Conclusions: Patients without liver metastasis, mutations in TERT, and TMB ≥ 15 mut/Mb are associated with superior response, while mutations in the MYC pathway and MLL2 are associated with worse responses. Full article

Background. Medulloblastoma (MB) prognosis and response to therapy depend largely on genetic changes in tumor cells. Many genes and chromosomal abnormalities have been identified as prognostic factors, including amplification of MYC oncogenes, gains in 1q and 17q, deletions in 10q and 21p, or isochromosomes 17 (i(17)(q10)). The frequency of these abnormalities varies greatly between ethnic populations, but the frequency of specific abnormalities, such as MYCC and MYCN amplification, 17q gain, and deletions, in the Russian population is unknown. Objective: The aim is to study the frequency of MYCC and MYCN amplifications, 17q gain, and 17p deletion and determine their prognostic value in Russian patients with MB. Methods. This study was performed on MB cells obtained from 18 patients (12 boys and 6 girls, aged between 3 months and 17 years, with a median age of 6.5 years). Determination of cytogenetic aberrations was carried out using FISH assays with MYCC-SO, MYCN-SO, and MYCN-SG/cen2 probes, as well as cen7/p53 dual color probes and PML/RARα dual color probes (Abbott Molecular, USA). One-way ANOVA and Fisher’s F-test were used to compare the two groups. The differences were considered significant when p < 0.05. Results. In 77.7% of patients (14/18), the classical type of MB was present; in 16.7% (3/18), desmoplastic type; and in 5.6% (1/18), nodular desmoplasic types of neoplasms. Amplification of MYC genes was detected in 22.2% of Russian patients (n = 4 out of 18). Patients with MYC amplification had the worst overall survival (OS: 0% vs. 68%, p = 0.0004). Changes on the 17th chromosome were found in 58.3% of patients. Deletion of 17p occurred in 23.1%, and gain of 17q occurred in 46.2%. There were no significant differences in OS, clinical signs, or the presence of additional 17q material or 17p deletion among patients with MB. Conclusions: Amplification of the MYC gene is a predictor of poor overall survival to therapy and a high risk of metastatic relapse. This allows us to more accurately stratify patients into risk groups in order to determine the intensity and duration of therapy. Full article

Gleason score (GS) is one of the best predictors of prostate cancer (PCa) aggressiveness; however, its biological features need to be elucidated. This study aimed to explore the biological characteristics of localized/locally advanced PCa stratified using in silico GS analysis. Biological features were analyzed using gene set variation analysis and the xCell algorithm with mRNA expression in two independent public databases: The Cancer Genome Atlas (TCGA) (n = 493; radical prostatectomy cohort) and GSE116918 (n = 248; radiation therapy cohort). GS levels were positively correlated with the activity levels of cell proliferation-related gene sets, including E2F targets, the G2M checkpoint, the mitotic spindle, and MYC targets v1 and v2 in both cohorts. Furthermore, GS levels were positively associated with the activity levels of immune-related gene sets and infiltrating fractions of immune cells, including CD4+ memory T cells, dendritic cells, M1 macrophages, and Th2 cells, in both cohorts. Notably, GS levels were positively associated with the score levels of homologous recombination defects, intratumor heterogeneity, fraction genome alteration, neoantigens, and mutation rates in the TCGA cohort. In conclusion, PCa with high GS levels was associated with cancer cell proliferation, immune cell infiltration, and high mutation rates, which may reflect worse clinical outcomes. Full article

Drought ranks among the key abiotic stresses that limit the growth and yield of grapevines (Vitis vinifera L.). Flavonols, a class of antioxidants commonly found in grapevines, play a crucial role in combating drought stress. In this study, we characterized the function and regulatory mechanism of the grapevine VviMYC4 in mediating flavonol biosynthesis in response to drought stress. VviMYC4 encodes a protein of 468 amino acids with conserved bHLH-MYC_N and bHLH domains. Phylogenetic analysis confirmed its homology with the grapevine VviMYC2 and similarity in function. The expression of VviMYC4 in ‘Cabernet Sauvignon’ grapevine seedling leaves increased initially and then decreased during prolonged drought stress. The homologous and heterologous transformation of VviMYC4 in grape suspension cells, Arabidopsis plants, tobacco leaves, and grapevine leaves demonstrated its ability to positively regulate flavonol biosynthesis and accumulation by promoting the expression of flavonol-related genes, thereby enhancing the drought tolerance of transgenic plants. Furthermore, VviMYC4 could bind to specific E-box sites on the promoters of VviF3H and VviFLS to improve their activities. This study highlights VviMYC4 as a pivotal positive regulator of drought tolerance in grapevines and proposes that VviMYC4 enhances the antioxidant and reactive oxygen species (ROS) scavenging abilities of grapevines in challenging environments and improves their stress resilience by mediating flavonol biosynthesis. Our findings offer crucial candidate genes and valuable insights for the molecular breeding of grapevine drought resistance. Full article

Cancer stem cells (CSCs) are described as a subpopulation of cells with capabilities of self-renewal, chemoresistance, and invasiveness. CSCs reside in tumor niches and can be studied in vitro through their enrichment in spheroids (Stem). Molecular iodine (I₂) induces apoptosis and differentiation in various cancer cells. I₂ can activate peroxisome proliferator-activated receptors type gamma (PPARγ), and its pathways are associated with its oxidant/antioxidant capacity. This work aimed to compare the effect of I₂ supplementation in progenitor and CSC populations with low (MCF-7 and S-K-NAS) and high invasiveness (MDA-MB231 and SK-N-BE2) in mammary and neuroblastoma (NB) cell lines. Results showed that the CSC population enriched by the spheroid culture overexpressed stem messengers CD44, SOX2, and NMYC and exhibited the highest mitochondrial metabolism (membrane mitochondrial potential and O₂⁻). The presence of I₂ increases PPARγ expression and induces apoptosis through the Bax/Bcl2 index in all populations but silences NMYC expression and reduces mitochondrial metabolism in Stem NB. I₂ also enhances the expression of nuclear erythroid factor 2 (Nrf2) in all populations, but the target antioxidant superoxide dismutase 2 (SOD2) is only elevated in progenitor cells. In contrast, the mitophagy inductors PTEN-induced putative kinase 1 (Pink1) and microtubule-associated protein1 light chain3 alpha (LC3) were overexpressed in Stem populations. I₂-preselected SK-N-BE2 populations exhibited minor implantation and invasion capacities in the in vivo zebrafish model. These data indicate that I₂ interferes with viability, implantation, and invasion capacity in all cell lines, but the molecular mechanisms vary depending on the progenitor or Stem condition. Full article

The N-Myc Downstream Regulated Gene 1 (NDRG1) protein, a member of a family of four, has emerged as a key regulator of various physiological and pathological processes. Extensive knowledge has been gained on the modulation of NDRG1 expression during endoplasmic reticulum stress, autophagy, and hypoxia. Moreover, new functions have emerged in recent years. Notably, NDRG1 regulates cell differentiation, metabolism, autophagy and vesicular transport. This has raised interest in the molecular mechanisms that control the cellular levels and activity of NDRG1. A series of studies have shown that NDRG1 can be finely regulated at the transcriptional, post-transcriptional, and translational levels. In addition, processes that mediate protein degradation and clearance also play key roles. Furthermore, three different NDRG1 proteoforms with distinct functions have been identified. An important question is the extent to which these proteoforms contribute to the regulation of cellular functions. Given the growing clinical interest in NDRG1, this review provides an overview of the regulatory mechanisms that control NDRG1 abundance, helping to deepen our understanding of the complex mechanisms underlying protein regulation. Full article

Background: Small heat shock proteins (sHsps), particularly Hsp20 family members, are pivotal for plant thermotolerance and abiotic stress adaptation. However, their evolutionary dynamics and functional roles in Lycium barbarum (goji berry), a commercially significant stress-tolerant crop, remain uncharacterized. This study aims to comprehensively identify LbHsp20 genes, delineate their evolutionary patterns, and decipher their regulatory mechanisms under heat stress to accelerate molecular breeding of resilient cultivars. Methods: Forty-three LbHsp20 genes were identified from the goji genome using HMMER and BLASTP. Phylogenetic relationships were reconstructed via MEGA-X (maximum likelihood, 1000 bootstraps), while conserved motifs and domains were annotated using MEME Suite and InterProScan. Promoter cis-elements were predicted via PlantCARE. Heat-responsive expression profiles of candidate genes were validated by qRT-PCR in two contrasting lines (N7 and 1402) under 42 °C treatment. Results: The LbHsp20 family clustered into 14 subfamilies, predominantly cytoplasmic (subfamilies I–VII). Chromosomal mapping revealed a tandem duplication hotspot on Chr4 (12 genes) and absence on Chr9, suggesting lineage-specific gene loss. All proteins retained the conserved α-crystallin domain (ACD), with 19 members harboring the ScHsp26-like ACD variant. Promoters were enriched in stress-responsive elements (HSE, ABRE, MYC). Heat stress induced significant upregulation (>15-fold in LbHsp17.6A and LbHsp18.3) in N7, whereas 1402 showed weaker induction (<5-fold). Subfamily specific divergence was observed, with cytoplasmic subfamily I genes exhibiting the strongest heat responsiveness. Conclusions: This study unveils the evolutionary conservation and functional diversification of LbHsp20 genes in L. barbarum. The tandem duplication-driven expansion on Chr4 and subfamily specific expression patterns underpin their roles in thermotolerance. These findings establish a foundation for engineering climate-resilient goji varieties. Full article

We have generated a vector that enables the removal of plasmids coding for truncated proteins. This vector expresses a protein of interest in the yeast Saccharomyces cerevisiae from a galactose-inducible promoter. The gene of interest is fused in-frame to a downstream sequence coding for phosphoribosylanthranilate isomerase (PRAI), which catalyses the third step in tryptophan biosynthesis. As a consequence, only the full-length protein of interest renders the host cell tryptophan prototrophic, allowing for selection against cells expressing truncated proteins. Our proof-of-principle study demonstrates that PRAI is functional when fused C-terminally to a protein, robustly rendering cells tryptophan prototrophic. The N-terminal GST tag and C-terminal myc tag allow for tag-mediated protein purification, co-precipitation studies, determination of relative expression levels, as well as validation of full-length expression of the protein via Western blotting. Full article

Objective: Non-small cell lung cancer (NSCLC) remains one of the most significant contributors to cancer-related mortality. This investigation explores the influence and underlying mechanisms of the USP1 inhibitor SJB2-043 on A549 cells, with the aim of advancing the development of anti-NSCLC therapeutics. Methods: Publicly available databases were utilized to assess USP1 expression and its association with the progression of NSCLC. Gene expression variations were ascertained through RNA sequencing, followed by the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway enrichment evaluations. Various doses of SJB2-043 were administered to A549 cells to evaluate its impact on cell multiplication, motility, apoptosis, and the cell cycle using CCK-8 assays, colony formation, wound healing, flow cytometry, and Western blotting (WB). Results: USP1 was found to be overexpressed in NSCLC specimens and linked to adverse prognosis. Treatment with SJB2-043 markedly inhibited A549 cell proliferation and migration, diminished clonogenic potential, and triggered apoptosis in a dose-dependent manner. Modifications in the cell cycle were observed, showing an elevated percentage of cells in the G2 phase while exhibiting a parallel decline in the G₁ phase. WB examination demonstrated diminished protein levels of N-cadherin, CyclinB₁, CDK1, C-myc, Bcl-2, p-ERK/ERK, p-p38/p38, p-JNK/JNK, p-AKT/AKT, and p-mTOR/mTOR, alongside an upregulation of E-cadherin, ZO-1, occludin, p53, Bax, p-β-catenin/β-catenin, and GSK3β. Conclusions: SJB2-043 exerts a suppressive effect on A549 cell proliferation, migration, and epithelial–mesenchymal transition while enhancing apoptosis. These cellular effects appear to be mediated through the inhibition of the MAPK, Wnt/β-catenin, and PI3K/AKT/mTOR signaling cascades, in addition to modulation of the cell cycle. Full article

Objective: Non-small cell lung cancer (NSCLC) is a major cause of cancer-related deaths worldwide. This study investigated the effects and mechanisms of the USP7 inhibitor GNE-6776 on human NSCLC A549 and H1299 cells, providing insights for anti-NSCLC drug development. Methods: USP7 expression was analyzed in lung cancer tissue using data from public databases. RNA sequencing and functional enrichment analyses were conducted to explore differentially expressed genes (DEGs) and potentially related pathways. A549 and H1299 cells were treated with GNE-6776 at different concentrations, and its effects on cell proliferation, migration, invasion, apoptosis, mitochondrial membrane potential, and cell cycle were evaluated. Changes in protein expression following GNE-6776 treatment were assessed by Western blot. A xenograft tumor model in nude mice was used to evaluate the in vivo effects of GNE-6776. Results: GNE-6776 inhibited the proliferation, migration, and invasion of A549 and H1299 cells, induced apoptosis, and caused cells to arrest in the G1 phase in a concentration-dependent manner. GNE-6776 decreased the mitochondrial membrane potential, suppressed epithelial-mesenchymal transition (EMT) markers, and downregulated the PI3K/AKT/mTOR and Wnt/β-catenin signaling pathways. GNE-6776 significantly inhibited tumor growth without affecting body weight, reduced expression of CDK6, C-myc, and N-cadherin, and increased GSK3β expression in tumor tissue. Conclusions: In summary, GNE-6776 demonstrated potent anti-tumor activity in NSCLC both in vitro and in vivo. GNE-6776 suppresses NSCLC cell proliferation, invasion, and migration while promoting apoptosis by inhibiting the EMT and modulating the PI3K/AKT/mTOR and Wnt/β-catenin pathways. These findings support its potential as a therapeutic agent for treating NSCLC. Full article

Background/Objectives: Colorectal cancer (CRC) arises from the epithelial lining of the colon or rectum, often following a progression from benign adenomatous polyps to malignant carcinoma. Screening modalities such as colonoscopy, faecal immunochemical tests (FIT), and FIT-DNA are critical for early detection and prevention, but non-invasive methods lack sensitivity to polyps and early CRC. Chromosome conformations (CCs) are potent epigenetic regulators of gene expression. We have previously developed an epigenetic assay, EpiSwitch^®®, that employs an algorithmic-based CCs analysis. Using EpiSwitch^®® technology, we have shown the presence of cancer-specific CCs in peripheral blood mononuclear cells (PBMCs) and primary tumours of patients with melanoma and prostate cancer. EpiSwitch^®®-based commercial tests are now available to diagnose prostate cancer with 94% accuracy (PSE test) and response to immune checkpoint inhibitors across 14 cancers with 85% accuracy (CiRT test). Methods/Results/Conclusions: Using blood samples collected from n = 171 patients with CRC, n = 44 patients with colorectal polyps and n = 110 patients with a ‘clear’ colonoscopy we performed whole Genome DNA screening for CCs correlating to CRC diagnosis. Our findings suggest the presence of two eight-marker CC signatures (EpiSwitch^®® NST) in whole blood that allow diagnosis of CRC and precancerous polyps, respectively. Independent validation cohort testing demonstrated high accuracy in identifying colorectal polyps and early versus late stages of CRC with an exceptionally high sensitivity of 79–90% and a high positive prediction value of 60–84%. Linking the top diagnostic CCs to nearby genes, we have built pathways maps that likely underline processes contributing to the pathology of polyp and CRC progression, including TGFβ, cMYC, Rho GTPase, ROS, TNFa/NFκB, and APC. Full article

Background/Objectives: Hypoxia-inducible factor-1α (HIF-1α) is a transcription factor that plays a crucial role in various physiological and pathological processes of the ovary. However, the timing of HIF-1α expression and its specific biological function in the follicular development of the human ovary remain unclear. Therefore, in this study, we aimed to examine whether HIF-1α and its downstream gene, N-myc downstream-regulated gene 1 (NDRG1), exhibit stage-specific expression during the follicular development process in the human ovary. Methods: We used ovarian tissues from eight women with regular menstrual cycles who were not undergoing hormonal treatment. We investigated HIF-1α and NDRG1 expression and localization using immunohistochemistry. Further, we transfected human ovarian granulosa (KGN) cells with HIF-1α small interfering RNA (siRNA) to investigate the influence of HIF-1α on NDRG1 expression and progesterone synthesis. Results: The immunohistochemical analysis of human ovarian tissues revealed that HIF-1α was localized in the cytoplasm of granulosa cells (GCs) at both the primary and secondary follicular stages. Conversely, in tertiary and later developmental stages, HIF-1α was observed exclusively in the nucleus of GCs. Furthermore, while NDRG1 was not detected in primary follicles, it was present in all GCs beyond the tertiary stage. Notably, transfection of KGN cells with HIF-1α siRNA significantly decreased NDRG1 expression, at both the mRNA and protein levels, and in progesterone synthesis. Conclusion: Our results indicate that HIF-1α and NDRG1 are integral to follicular development and the early luteinization of pre-ovulatory follicles. Full article

The molecular link between stress and carcinogenesis and the positive outcomes of stress intervention in cancer therapy have recently been well documented. Cancer stem cells (CSCs) facilitate cancer malignancy, drug resistance, and relapse and, hence, have emerged as a new therapeutic target. Here, we aimed to investigate the effect of three previously described antistress compounds (triethylene glycol, TEG; Withanone, Wi-N, and Withaferin A, Wi-A) on the stemness and differentiation characteristics of cancer cells. Breast carcinoma, glioblastoma, and neuroblastoma cells were treated with a non-toxic concentration of TEG (0.1%), Wi-N (5 µM), and Wi-A (0.1 µM) in 2D and 3D cultures. The results demonstrated that TEG, Wi-N, and Wi-A suppressed the stemness properties, which was linked with their inhibition of epithelial–mesenchymal transition (EMT) signaling. In particular, Wi-N and TEG caused a stronger reduction in the self-renewal capability of CSCs than Wi-A, as evidenced by a tumor spheroid formation assay and analyses of stemness-related genes (ALDH1, CD44, NANOG, CD133, SOX2). Furthermore, TEG and Wi-N caused the differentiation of cancer cells. Each of these was supported by (i) the upregulation of KRT18, KRT19, E-cadherin, and downregulation of vimentin in breast carcinoma; (ii) increased levels of GFAP, MAP2, and PSD-95 in astrocytoma; and (iii) increased NeuN, GAP-43, and NF200 levels in neuroblastoma. Furthermore, a reduction in cancer progression-related proteins (PI3K, N-myc) was recorded in treated cells. Our results suggest that TEG and Wi-N may be recruited to target cancer cell stemness and differentiation therapy. Full article

High-grade B-cell lymphoma with 11q aberration (HGBCL-11q) is a rare germi-nal centre lymphoma characterised by a typical gain/loss pattern on chromo-some 11q but without MYC translocation. It shares some features with Burkitt lymphoma (BL), HGBCLs and germinal centre-derived diffuse large B-cell lym-phoma, not otherwise specified (GCB-DLBCL-NOS). Since microRNA expression in HGBCL-11q remains unknown, we aimed to identify and compare the mi-croRNA expression profiles in HGBCL-11q, BL and in GCB-DLBCL-NOS. Next-generation sequencing (NGS)-based microRNA profiling of HGBCL-11q (n = 6), BL (n = 8), and GCB-DLBCL-NOS without (n = 3) and with MYC rearrange-ment (MYC-R) (n = 7) was performed. We identified sets of 39, 64, and 49 mi-croRNAs differentiating HGBCL-11q from BL, and from GCB-DLBCL-NOS without MYC-R, respectively. The expression levels of miR-223-3p, miR-193b-3p, miR-29b-3p, and miR-146a-5p consistently differentiated HGBCL-11q from both BL, GCB-DLBCL-NOS without MYC-R. In addition, HGBCL-11q presented greater heterogeneity in microRNA expression than BL. The expression profile of MYC-regulated microRNAs differed in HGBCL-11q and in BL, while also clearly distinguishing HGBCL-11q and BL from GCB-DLBCL-NOS. The microRNA pro-file of HGBCL-11q differs from those of BL and GCB-DLBCL-NOS, exhibiting greater heterogeneity compared to BL. The microRNA profile further supports that HGBCL-11q is a distinct subtype of B-cell lymphoma. Full article

Cancer is a leading cause of death, so continuous efforts into cancer therapy are imperative. In tumor cells, telomerase and oncogene activity are key points for uncontrolled cell growth. Targeting these processes with ligands that inhibit telomerase and/or reduce oncogene expression has been identified as a promising cancer therapy. This study evaluated the selectivity and affinity of the silver^II complex of 5,10,15,20-tetrakis(N-methyl-4-pyridinium)porphyrin (AgTMPyP) to stabilize DNA sequences capable of forming G4 structures mimicking the telomeric and oncogene regions, using spectroscopic, biochemical methods and in vitro assays. The tetracationic silver complex was compared with the free base, H₂TMPyP, and the zinc^II complex, ZnTMPyP. The results obtained from UV-Vis and fluorescence methods pointed to a great affinity and good selectivity of AgTMPyP to G4 structures, especially for the oncogene MYC. In general, an increase in the ability of the studied ligands for ¹O₂ generation when interacting with oncogenic and telomeric G4 sequences was found. The results of the PCR stop assays proved that AgTMPyP has the ability to inhibit Taq polymerase. Additionally, in vitro assays demonstrated that the silver^II complex exhibits low cytotoxicity against HaCaT— an immortalized, non-tumorigenic, skin keratinocytes cell line—and, although nonexclusive, AgTMPyP shows nuclear co-localization. Full article