Targeting PI3K in cancer treatment: A comprehensive review with insights from clinical outcomes

The phosphoinositide 3-kinase (PI3K) pathway plays a crucial role in cancer, including cell growth, survival, metabolism, and metastasis. Its major role in tumor growth makes it a key target for cancer therapeutics, offering significant potential to slow tumor progression and enhance patient outcomes. Gain-of-function mutations, gene amplifications, and the loss of regulatory proteins like PTEN are frequently observed in malignancies, contributing to tumor development and resistance to conventional treatments such as chemotherapy and hormone therapy. As a result, PI3K inhibitors have received a lot of interest in cancer research. Several kinds of small-molecule PI3K inhibitors have been developed, including pan-PI3K inhibitors, isoform-specific inhibitors, and dual PI3K/mTOR inhibitors, each targeting a distinct component of the pathway. Some PI3K inhibitors such as idelalisib, copanlisib, duvelisib, alpelisib, and umbralisib have received FDA-approval, and are effective in the treatment of breast cancer and hematologic malignancies. Despite promising results in preclinical and clinical trials, the overall clinical success of PI3K inhibitors has been mixed. While some patients may get substantial advantages, a considerable number of them acquire resistance as a result of feedback activation of alternative pathways, adaptive tumor responses, and treatment-emergent mutations. The resistance mechanisms provide barriers to the sustained efficacy of PI3K-targeted treatments. This study reviews recent advancements in PI3K inhibitors, covering their clinical status, mechanism of action, resistance mechanisms, and strategies to overcome resistance.

IGF1R activates FOXP3-β-catenin signaling to promote breast cancer development

PURPOSE

Forkhead box P3 (FOXP3), a key marker of regulatory T cells (Tregs), is crucial for Treg differentiation and development. Emerging evidence suggests that FOXP3 is also expressed in various tumor cells; however, its role in tumor progression remains controversial. This study aimed to elucidate the impact of FOXP3 on breast cancer development.

METHODS

Breast cancer cell lines, including HCC1937, HCC1806, Hs 578T, MDA-MB-231, and MCF-7, along with xenograft mouse models, to assess the effects of FOXP3 on cell proliferation and tumor growth. FOXP3 expression in human breast cancer samples was analyzed using quantitative PCR and immunohistochemistry analyses. Cell proliferation and invasion were evaluated through MTS and transwell assays, respectively. Chromatin immunoprecipitation (ChIP) assays were performed to determine FOXP3 binding to the β-catenin gene promoter.

RESULTS

FOXP3 expression was elevated in advanced breast cancer and correlates with poor clinical outcomes. FOXP3 directly binds to β-catenin gene promoter - 986 to - 1168 region to facilitate β-catenin transcription, consequently resulting in increased breast cancer cell proliferation, migration, and invasion in vitro and tumor growth in vivo. Furthermore, IGF1R activated FOXP3-β-catenin signaling to promote breast tumor growth. Moreover, elesclomol, a potent copper ionophore, significantly inhibited FOXP3 expression to suppress breast tumor growth.

CONCLUSION

This study indicates that FOXP3 plays an oncogenic role in breast cancer development and suggests that targeting IGF1R-FOXP3-β-catenin signaling may be a putative therapeutic strategy for human breast cancer treatment.

Exosomal dynamics: Bridging the gap between cellular senescence and cancer therapy

Cancer remains one of the most devastating diseases, severely affecting public health and contributing to economic instability. Researchers worldwide are dedicated to developing effective therapeutics to target cancer cells. One promising strategy involves inducing cellular senescence, a complex state in which cells exit the cell cycle. Senescence has profound effects on both physiological and pathological processes, influencing cellular systems through secreted factors that affect surrounding and distant cells. Among these factors are exosomes, small extracellular vesicles that play crucial roles in cellular communication, development, and defense, and can contribute to pathological conditions. Recently, there has been increasing interest in engineering exosomes as precise drug delivery vehicles, capable of targeting specific cells or intracellular components. Studies have emphasized the significant role of exosomes from senescent cells in cancer progression and therapy. Notably, chemotherapeutic agents can alter the tumor microenvironment, induce senescence, and trigger immune responses through exosome-mediated cargo transfer. This review explores the intricate relationship between cellular senescence, exosomes, and cancer, examining how different therapeutics can eliminate cancer cells or promote drug resistance. It also investigates the molecular mechanisms and signaling pathways driving these processes, highlighting current challenges and proposing future perspectives to uncover new therapeutic strategies for cancer treatment.

Interferon-Inducible ADAR1 p150 Is Essential for the Survival of Oral Squamous Cell Carcinoma

We identified ADAR1 as one of the top essential genes for oral squamous cell carcinoma (OSCC) survival from our genome-wide CRISPR/Cas9 screen in OSCC cell lines. In this study, we confirm that ADAR1-knockout (KO) inhibits cell viability and colony forming ability, and induces apoptosis. We report that IFN-β treatment sensitizes less-dependent cell lines to ADAR1 KO-induced cell lethality. Overexpression of ADAR1-p150, but not ADAR1-p110, rescued cell lethality upon ADAR1 KO, confirming that the IFN-inducible p150 is responsible for OSCC survival. Using a deaminase inactive mutant, we demonstrate that the editing function of ADAR1 is important for OSCC survival. Furthermore, we show that ADAR1 KO-induced cell death is mediated by both PKR and MDA5. We compute gene signatures of ADAR1 dependency in OSCC tumors, and found that those with high ADAR1 dependency score are associated with well or moderate differentiation, likely due to high PKR expression or activation. While a majority of ADAR1-dependent tumors exhibit a low T cell-inflamed gene expression profile, ADAR1 KO upregulates PD-L1, a marker of anti-PD1 response, indicating that ADAR1 inhibition may enhance immunotherapy response in OSCC. Collectively, these findings suggest that targeting ADAR1-p150 not only induces OSCC cell death but could induce a favorable response to anti-PD1.

Molecular genetic analysis of pulmonary benign metastasizing leiomyoma and intravenous leiomyomatosis: a comparative study using whole exome sequencing

OBJECTIVE

Benign Metastasizing Leiomyoma (BML) and Intravenous Leiomyomatosis (IVL) are rare uterine-derived smooth muscle tumors. Although both exhibit histologically benign and similar features, they demonstrate aggressive biological behaviors. Currently, molecular genetic studies on BML and IVL are limited, and no comparative research on their genetic variations has been reported. To investigate the genetic basis underlying their shared aggressive phenotypes, this study employs whole-exome sequencing (WES) to conduct a molecular genetic comparison between the two entities. The aim is to explore potential genetic variations that may reveal common pathological pathways shared by these diseases, thereby enhancing our understanding of the molecular mechanisms driving their invasiveness.

METHODS

A pulmonary BML case and an IVL case underwent analysis, with paraffin-embedded tumor tissues subjected to WES. Mutant genes were screened and comparatively analyzed between the two cases.

RESULTS

WES revealed 15 single nucleotide polymorphism (SNP) genetic mutations in the BML case: HFM1, SCN10A, HEXA, SLC7A14, TEP1, KCNJ12, KCNJ18, DNAJB12, ACOX3, ABCC2, RASA1, ALOX15B, TCIRG1, COL5A3, and MCCC2. In the IVL case, 18 mutant genes were observed: CADPS2, GPSM2, REEP4, KCNJ12, KCNJ18, DUSP15, PDE11A, TCIRG1, KLHL33, PAH, MYO18A, FBLN7, ATP7B, MYO7A, MLKL, LRP10, KRT15, and HEPH. The mutations were consistent across both samples in this case. Shared mutations in BML and IVL cases included TCIRG1, KCNJ12, and KCNJ18.

CONCLUSION

BML and IVL exhibit distinct gene mutations in tumor development, with certain shared mutations.

RPS27A as a potential clock-related diagnostic biomarker for myocardial infarction: Comprehensive bioinformatics analysis and experimental validation

BACKGROUND

The circadian system plays a crucial role in managing cardiovascular functions, with disturbances in this system associated with Myocardial Infarction (MI). Despite this connection, the exact mechanisms by which clock genes influence MI occurrence are not well-defined. This research focused on investigating the link between clock genes and MI.

METHODS

The authors examined MI microarray datasets (GSE151412 and GSE60993) from the GEO database, concentrating on Differentially Expressed Genes (DEGs) associated with the circadian system. To clarify critical biological functions and pathways, the authors performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Through Lasso regression, the authors pinpointed hub genes and confirmed their relevance using both the GSE66360 dataset and quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR). Furthermore, the authors conducted single-Gene Set Enrichment Analysis (GSEA) to reveal pathways linked to the hub gene. The analysis extended to exploring drug interactions and networks involving competing endogenous RNA (ceRNA).

RESULTS

The present analysis identified ten clock genes associated with circadian rhythms that showed differential expression between MI patients and healthy controls. Enrichment analysis suggested these genes' roles in pathways like the Gap junction and circadian rhythm pathways. Following Lasso regression and validation, RPS27A was identified as the main hub gene. GSEA further highlighted enriched pathways, such as mismatch repair. Additionally, immune infiltration analysis revealed notable differences in B-cell and CD4+ T-cell populations between the MI group and the control group.

CONCLUSION

The present findings suggest that the clock-related gene RPS27A is associated with MI, potentially influencing its development through circadian rhythm regulation. These results enhance the understanding of MI pathogenesis and may offer new avenues for therapeutic intervention.

Hydrogels in Endoscopic Submucosal Dissection for Gastrointestinal Cancers

Endoscopic Submucosal Dissection (ESD) has emerged as a pivotal technique for the minimally invasive treatment of early gastrointestinal cancers, offering benefits such as reduced trauma, lower complication rates, and cost-effectiveness. Despite its advantages, the selection of optimal biomaterials for submucosal injection poses significant challenges. Current materials used in clinical settings often suffer from rapid diffusion, requiring multiple injections and potentially causing localized inflammation. These issues underscore the importance of identifying more effective submucosal injection materials to minimize postoperative complications and enhance patient outcomes. Recent advancements have highlighted the potential of hydrogels in this context, favored for their ability to maintain mucosal elevation longer and support wound healing. This review comprehensively examines the development and application of hydrogels in ESD, focusing on their physicochemical properties, biocompatibility, and the clinical implications of their use. These issues discuss various formulations of hydrogels, their mechanisms of action, and comparative analyses with traditional materials. Furthermore, the review explores ongoing innovations and future perspectives in hydrogel research, aiming to catalyze further advancements in ESD techniques. STATEMENT OF SIGNIFICANCE: This review critically examines hydrogel technologies in endoscopic submucosal dissection for gastrointestinal cancers, highlighting their role in improving procedural outcomes and patient recovery. It explores hydrogels' ability to enhance mucosal elevation, reduce complications, and accelerate healing, offering insights into their transformative potential in medical treatments. The findings emphasize the development of innovative materials that could significantly advance clinical practices in gastrointestinal cancer management.

Establishment and characterization of patient-derived tongue squamous cell carcinoma cell lines

Oral squamous cell carcinoma (OSCC) is a common carcinoma in Indian population, wherein one-third of global OSCC cases are from India. The five-year survival rate is poor due to late diagnosis. Oral tongue squamous cell carcinoma (OTSCC) is the second-most common OSCC. An in vitro cell line model is a valuable tool to get a deeper understanding of the molecular mechanisms involved in therapy resistance and disease progression. We report establishment of three OTSCC cell lines from advanced stage treatment naïve Indian patient samples, such as ACOTSC120, ACOSTC132, and ACOTSC140. All three OTSCC cell lines showed epithelial morphology, which was confirmed by Keratin-14 staining. The cell lines showed in vitro spheroid-forming and in vivo tumorigenic potential. The STR of the cell lines ensured their human origin and novelty when compared to DSMZ cell line database. The karyotype of the cell lines showed aneuploidy and further confirmed their human origin. These cell lines showed the presence of cancer stem cell (CSCs) population, i.e., the ALDHbr/CD44+ population. These cell lines thus provide a model to help understand the biology of disease and its progression.

HES1 in cancer: a key player in tumorigenesis and its prognostic significance

The dysregulation of transcriptional regulators is a critical feature in the progression of many malignancies. Hairy and enhancer of split homolog-1 (HES1), a member of the basic helix-loop-helix (bHLH) gene family, has emerged as a key player in tumorigenesis due to its regulatory roles in multiple cellular pathways. This review aims to systematically explore the relevance of HES1 in cancer development, emphasizing its activation through major signaling pathways such as Notch, Hedgehog, hypoxia, and Wnt, and its contribution to advanced tumor progression. Numerous studies have demonstrated that HES1 upregulates genes associated with stemness, proliferation, and metastasis, and its expression correlates with poor clinicopathological features, including enhanced tumor proliferation, self-renewal, migration, metastasis, and drug resistance. Furthermore, HES1 has been frequently identified as a downstream effector of critical oncogenic pathways, further consolidating its role in aggressive cancers. Based on current evidence, HES1 holds promise as both a prognostic biomarker and a potential therapeutic target in various lethal malignancies. A deeper understanding of HES1's molecular mechanisms could pave the way for the development of targeted interventions aimed at improving cancer outcomes.

Predicting drug-gene relations via analogy tasks with word embeddings

Natural language processing is utilized in a wide range of fields, where words in text are typically transformed into feature vectors called embeddings. BioConceptVec is a specific example of embeddings tailored for biology, trained on approximately 30 million PubMed abstracts using models such as skip-gram. Generally, word embeddings are known to solve analogy tasks through simple vector arithmetic. For example, subtracting the vector for man from that of king and then adding the vector for woman yields a point that lies closer to queen in the embedding space. In this study, we demonstrate that BioConceptVec embeddings, along with our own embeddings trained on PubMed abstracts, contain information about drug-gene relations and can predict target genes from a given drug through analogy computations. We also show that categorizing drugs and genes using biological pathways improves performance. Furthermore, we illustrate that vectors derived from known relations in the past can predict unknown future relations in datasets divided by year. Despite the simplicity of implementing analogy tasks as vector additions, our approach demonstrated performance comparable to that of large language models such as GPT-4 in predicting drug-gene relations.

PANoptosis as a Two-Edged Sword in Colorectal Cancer: A Pathogenic Mechanism and Therapeutic Opportunity

The examination of PANoptosis in colorectal cancer is particularly important, as many tumor cells can evade apoptotic cell death while continuing to proliferate through inflammatory mediators and creating an immunosuppressive environment. The PANoptosome functions as a regulatory complex that unites proteins governing pyroptotic, apoptotic, and necroptotic pathways, rather than allowing distinct death pathways to compete. The expression and functional status of key molecules within the PANoptosome, such as ZBP1, RIPK1, RIPK3, CASP8, and ASC, may influence tumor viability and immune detection. The tumorigenic impact of PANoptosis is complex and predominantly manifests through chronic inflammation, immune response modulation, and changes in the tumor microenvironment. PANoptosis also aids in the defense against colon cancer by directly eradicating tumor cells and modifying the cellular environment. The expression profile of PANoptosis components may possess prognostic and predictive significance. The therapeutic ramifications of PANoptosis in colorectal cancer are now being investigated through many avenues. It provides an opportunity to develop targeted therapeutic techniques. In contrast, it may also be pertinent in conjunction with immunotherapy, as PANoptosis signifies an immunogenic type of cell death and may consequently enhance the anti-tumor immune response. A thorough comprehension of how these parameters influence PANoptosis is crucial for practical implementation.

Deciphering aging-associated prognosis and heterogeneity in gastric cancer through a machine learning-driven approach

Gastric cancer (GC) is a prevalent malignancy with a high mortality rate and limited treatment options. Aging significantly contributes to tumor progression, and GC was confirmed as an aging-related heterogeneous disease. This study established an aging-associated index (AAI) using a machine learning-derived gene panel to stratify GC patients. High AAI scores associated with poor prognosis and indicated potential benefits from adjuvant chemotherapy, while showing resistance to immunotherapy. Single-cell transcriptome analysis revealed that AAI was enriched in monocyte cells within the tumor microenvironment. Two distinct molecular subtypes of GC were identified through unsupervised clustering, leading to the development of a subtype-specific regulatory network highlighting SOX7 and ELK3 as potential therapeutic targets. Drug sensitivity analyses indicated that patients with high ELK3 expression may respond to FDA-approved drugs (axitinib, dacarbazine, crizotinib, and vincristine). Finally, a user-friendly Shiny application was created to facilitate access to the prognostic model and molecular subtype classifier for GC.

Two-pore-domain potassium channel Sandman regulates intestinal stem cell homeostasis and tumorigenesis in Drosophila melanogaster

Potassium channels regulate diverse biological processes, ranging from cell proliferation to immune responses. However, the functions of potassium homeostasis and its regulatory mechanisms in adult stem cells and tumors remain poorly characterized. Here, we identify Sandman, a two-pore-domain potassium channel in Drosophila, as an essential regulator for the proliferation of intestinal stem cells and malignant tumors, while dispensable for the normal development processes. Mechanistically, loss of sandman elevates intracellular K+ concentration, leading to growth inhibition. This phenotype is rescued by pharmacological reduction of intracellular K+ levels using the K+ ionophore. Conversely, overexpression of sandman triggers stem cell death in most regions of the midgut, inhibits tumor growth, and induces a Notch loss-of-function phenotype in the posterior midgut. These effects are mediated predominantly via the induction of endoplasmic reticulum (ER) stress, as demonstrated by the complete rescue of phenotypes through the co-expression of Ire1 or Xbp1s. Additionally, human homologs of Sandman demonstrated similar ER stress-inducing capabilities, suggesting an evolutionarily conserved relationship between this channel and ER stress. Together, our findings identify Sandman as a shared regulatory node that governs Drosophila adult stem cell dynamics and tumorigenesis through bioelectric homeostasis, and reveal a link between the two-pore potassium channel and ER stress signaling.

Exploring the antitumorigenic properties of agro-food byproducts: A comprehensive scientific review

Natural byproducts have garnered significant attention for their potential antitumorigenic properties. The current scenario sketched by the goals of circular economy approaches the research towards the utilization of agro-waste biomasses as valuable source of biological active metabolites. This comprehensive scientific review explores the various mechanisms through which these natural compounds exert anticancer effects, including apoptosis induction, cell cycle arrest, inhibition of angiogenesis, and suppression of metastasis. The review highlights key bioactive molecules such as polyphenols, flavonoids, alkaloids, and terpenoids, examining their molecular interactions with cancer cells. Furthermore, the potential of these natural byproducts as adjuvant therapies in combination with conventional treatments is discussed. By summarizing recent advancements and identifying future research directions, this review underscores the promise of natural byproducts from as a source of novel anticancer agents. A specific section is dedicated to outline the role of innovative materials, such as nanoparticles, hydrogels, and biopolymers, that are being developed to enhance the delivery and efficacy of active components. These carriers offer improved stability, targeted delivery, and controlled release of natural compounds, maximizing their therapeutic potential while minimizing side effects.

Comprehensive review and in silico analysis of the role of noncoding RNAs in retinoblastoma: A step-toward ncRNA precision

Noncoding RNAs (ncRNAs) have greatly revolutionized our understanding of gene regulation and its main role in oncogenesis, particularly in retinoblastoma (RB), the most prevalent type of intraocular malignancy in children. Despite recent significant therapeutic advances, the prognosis for RB remains unclear owing to late diagnosis and resistance to conventional treatments. This review comprehensively explores the multiple roles of ncRNAs-microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and PIWI-interacting RNAs (piRNAs)-in RB pathogenesis. miRNA dysregulation serves as the initial cascade for modulating cell proliferation, apoptosis, and metastasis. Similarly, lncRNAs demonstrate dual behavior, functioning either as oncogenic drivers or tumor suppressors by interacting with several molecular targets and interacting with different signaling pathways, such as the PI3K/Akt and Wnt/β-catenin pathways. Additionally, circRNAs, owing to their persistent stability and unique ability to act as miRNA sponge main binding sites, affect various normal physiological processes, influencing tumor progression and chemoresistance. Emerging data also highlight the intricate crosstalk between piRNAs and other ncRNAs in retinal homeostasis and oncogenesis, with promising future implications for their utility as diagnostic biomarkers in liquid biopsy types. This comprehensive review consolidates the latest knowledge on the molecular mechanisms of noncoding RNAs (ncRNAs) in retinoblastoma (RB), along with in silico analysis of ncRNA-gene interactions, providing a guide for precision medical approaches. However, future research should aim to utilize ncRNAs as a vital clinical tool to improve the early diagnosis, prognosis, and targeted treatment of RB.

Machine learning approaches reveal methylation signatures associated with pediatric acute myeloid leukemia recurrence

Acute myeloid leukemia (AML) is a severe hematological malignancy characterized by high recurrence rates, especially in pediatric patients, highlighting the need for reliable prognostic markers. This study proposes methylation signatures associated with AML recurrence using computational methods. DNA methylation data from 696 newly diagnosed and 194 relapsed pediatric AML patients were analyzed. Feature selection algorithms, including Boruta, least absolute shrinkage and selection operator, light gradient boosting machine, and Monte Carlo feature selection, were employed to screen and rank methylation sites strongly correlated with AML recurrence. Incremental Feature Selection was performed to evaluate these results, and optimal subsets were identified using Decision Tree and Random Forest methods. Several important methylation features, such as modifications in SLC45A4, S100PBP, TSPAN9, PTPRG, ERBB4, and PRKCZ, emerged from the intersection of all feature selection algorithms. Functional enrichment analysis indicated these genes participate in biological processes, including calcium-mediated signaling and regulation of binding. These findings are consistent with existing literature, suggesting that identified methylation features likely contribute to AML progression through alterations in gene expression levels. Therefore, this study provides a valuable reference for enhancing recurrence risk prediction models in AML and clarifying disease pathogenesis, as well as offering broader insights into mechanisms underlying other major diseases.

CK2: The master regulator in tumor immune-microenvironment - A crucial target in oncotherapy

A constitutively active serine/threonine kinase, casein kinase 2 (CK2) is involved in several physiological functions, such as DNA repair, apoptosis, and cell cycle control. New research emphasizes how critical CK2 is to the immune system's dysregulation in the tumor immune-microenvironment (TIME). The inhibition of immunological responses, including the downregulation of immune effector cells and the elevation of immunosuppressive proteins that aid in the development of tumor and immune evasion, has been linked to CK2 overexpression. CK2 maintains an immunosuppressive milieu that impedes anti-tumor immunity by encouraging the expressions and activities of immune checkpoint markers, regulating cytokines release, and boosting immune-suppressive cells such as regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs) to maintain immune evasion. It is a promising target for cancer treatment due to its complex role in immune regulation and oncogenic pathways. In this study, we address the therapeutic perspectives of targeting CK2 in oncotherapy and investigate the mechanisms by which it controls immunological responses in the TME. This review, comprehending the function of CK2 in immune suppression can facilitate the creation of innovative treatment approaches aimed at augmenting anti-tumor immunity and enhancing immunotherapy effectiveness.

Caspases: structural and molecular mechanisms and functions in cell death, innate immunity, and disease

Caspases are critical regulators of cell death, development, innate immunity, host defense, and disease. Upon detection of pathogens, damage-associated molecular patterns, cytokines, or other homeostatic disruptions, innate immune sensors, such as NLRs, activate caspases to initiate distinct regulated cell death pathways, including non-lytic (apoptosis) and innate immune lytic (pyroptosis and PANoptosis) pathways. These cell death pathways are driven by specific caspases and distinguished by their unique molecular mechanisms, supramolecular complexes, and enzymatic properties. Traditionally, caspases are classified as either apoptotic (caspase-2, -3, -6, -7, -8, -9, and -10) or inflammatory (caspase-1, -4, -5, and -11). However, extensive data from the past decades have shown that apoptotic caspases can also drive lytic inflammatory cell death downstream of innate immune sensing and inflammatory responses, such as in the case of caspase-3, -6, -7, and -8. Therefore, more inclusive classification systems based on function, substrate specificity, or the presence of pro-domains have been proposed to better reflect the multifaceted roles of caspases. In this review, we categorize caspases into CARD-, DED-, and short/no pro-domain-containing groups and examine their critical functions in innate immunity and cell death, along with their structural and molecular mechanisms, including active site/exosite properties and substrates. Additionally, we highlight the emerging roles of caspases in cellular homeostasis and therapeutic targeting. Given the clinical relevance of caspases across multiple diseases, improved understanding of these proteins and their structure-function relationships is critical for developing effective treatment strategies.

Epigenetic mechanisms involved in hepatocellular carcinoma development and progression

Hepatocellular carcinoma (HCC) typically develops in the context of chronic liver disease, where prolonged hepatocyte exposure to inflammation drives the synergistic accumulation of genetic and epigenetic alterations. Epigenetic regulation encompasses multiple mechanisms that govern the transcription machinery accessibility to DNA. This process is regulated by the addition and removal of covalent marks on chromatin, which can either affect DNA-histone interactions or serve as scaffolds for other proteins, among other mechanisms. Recent research has revealed that epigenetic alterations can disrupt chromatin homeostasis, redirecting transcriptional regulation to favour cancer-promoting states. Consequently, these alterations play a pivotal role in the acquisition of cancer hallmarks and provide insights into several biological processes involved in hepatocarcinogenesis. This review highlights the key epigenetic mechanisms underlying the development, progression and dissemination of HCC, with a particular focus on DNA methylation and histone post-translational modifications. This knowledge is relevant for guiding the development of innovative therapeutic approaches based on epigenetic modulators.

LncRNA HOTAIR Interaction With WTAP Promotes m6A Methyltransferase Complex Assembly and Posterior Capsule Opacification Formation by Increasing THBS1

Purpose

To explore the role of long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A) in posterior capsule opacification (PCO) and their underlying mechanisms.

Methods

The localization of lncRNAs and proteins was analyzed using fluorescence in situ hybridization and immunofluorescence staining. RNA m6A quantification, RNA immunoprecipitation, co-immunoprecipitation, MeRIP-seq, MeRIP-qPCR, western blotting, wound healing, and Transwell assays were applied to elucidate the underlying mechanisms.

Results

The levels of lncRNA HOX transcript antisense intergenic RNA (HOTAIR) and m6A methylation increased significantly during epithelial-mesenchymal transition (EMT) in lens epithelial cells (LECs). HOTAIR promoted EMT and m6A methyltransferase activity but had no effect on methyltransferase activity and was not modified by m6A. Nevertheless, HOTAIR interacted with WT1-associated protein (WTAP), a key m6A writer protein, facilitating WTAP-mediated recruitment of METTL3-METTL14 heterodimers and enhancing m6A modification. The HOTAIR/WTAP complex elevated m6A levels, thrombospondin 1 (THBS1) expression, and EMT in LECs.

Conclusions

LncRNA HOTAIR enhances the assembly of the WTAP/METTL3/METTL14 complex and promotes EMT in LECs by upregulating m6A modification and THBS1 expression. Targeting the HOTAIR/WTAP/THBS1 pathway may prevent or treat PCO.

Prioritization of potential drug targets in ovarian-related diseases: Mendelian randomization and colocalization analyses

OBJECTIVE

To identify key genes and potential drug targets for ovarian-related diseases through genome-wide Mendelian randomization (MR) and colocalization analyses.

DESIGN

We conducted a comprehensive two-sample MR analysis to estimate the causal effects of blood expression quantitative trait loci (eQTLs) on ovarian-related diseases, followed by colocalization analyses to verify the robustness of the expression instrumental variables (IVs). Phenome-wide association studies (PheWAS) were also performed to evaluate the horizontal pleiotropy of potential drug targets and possible side effects.

SUBJECTS

Large cohorts of European ancestry.

EXPOSURE

The exposure in this study was the genetic variants (eQTLs) associated with gene expression levels, considered a form of lifelong exposure. Expression quantitative trait loci data were obtained from the eQTLGen Consortium, encompassing 16,987 genes and 31,684 cis-eQTLs derived from blood samples of healthy individuals of European ancestry.

MAIN OUTCOME MEASURES

The primary outcome measures were the identification of genes causally associated with ovarian-related diseases and the validation of these genes as potential therapeutic targets.

RESULTS

Our study revealed that specific genes such as CD163L1, PPP3CA, MTAP, F12, NRM, BANK1, ZNF66, GNA15, and SLC6A9 were associated with ovarian endometriosis, ovarian cysts, and polycystic ovarian syndrome. Through MR and colocalization analyses, we identified potential drug targets, including CTNNB1, PTPN7, and ABCB4, with strong evidence of colocalization with ovarian-related diseases. Sensitivity analyses confirmed the robustness of our findings, showing no evidence of horizontal pleiotropy or heterogeneity.

CONCLUSION

This research highlights the significance of precision medicine approaches in identifying genetic factors underlying ovarian-related diseases and provides a foundation for developing targeted therapies, enhancing diagnostic accuracy, and improving treatment strategies for ovarian-related diseases.

HPV-Mediated Radiosensitivity in Oropharyngeal Squamous Cell Carcinoma: Molecular Mechanisms and Cellular Pathways

PURPOSE OF REVIEW

While the oncogenic potential of HPV has been well-established in other disease sites (e.g. cervix, vulva, anus), it is increasingly evident that a significant proportion of oropharyngeal cancer cases are related to the virus. Although considerable progress has been made in the understanding of this disease with respect to its underlying biology and clinical behavior, numerous questions persist. From a therapeutic standpoint, HPV-positive oropharyngeal cancer has been shown to be more radiosensitive than HPV-negative disease. However, how HPV mediates this radiosensitivity is relatively uncertain.

RECENT FINDINGS

Given that it has been firmly established that patients with HPV-positive oropharyngeal cancer have a significantly improved prognosis as a result of their exquisite response to radiation and can be treated with less-than-standard doses, logical questions pertain to how HPV confers this benefit to infected patients. Although the exact reason for the improved radiosensitivity of HPV-positive oropharyngeal carcinoma is unclear, multiple theories have been proposed. Indeed, it is likely that no single explanation exists for the increased radiosensitivity, and instead, HPV likely exerts its influence through a cascade of activated pathways at both the cellular level and tumor microenvironment. As will be discussed in this review, the proposed mechanisms for HPV-induced radiation response have generally centered on the disruption of such cellular pathways as DNA repair, cell cycle checkpoints, metabolic-induced stress, immunology, and cancer stem cells. Given that HPV-positive oropharyngeal cancer is increasingly recognized as a public health problem, the search to better understand its unique biological radiosensitivity has important societal and treatment-related implications.

Key roles of ubiquitination in regulating critical regulators of cancer stem cell functionality

The ubiquitin (Ub) system, a ubiquitous presence across eukaryotes, plays a crucial role in the precise orchestration of diverse cellular protein processes. From steering cellular signaling pathways and orchestrating cell cycle progression to guiding receptor trafficking and modulating immune responses, this process plays a crucial role in regulating various biological functions. The dysregulation of Ub-mediated signaling pathways in prevalent cancers ushers in a spectrum of clinical outcomes ranging from tumorigenesis and metastasis to recurrence and drug resistance. Ubiquitination, a linchpin process mediated by Ub, assumes a central mantle in molding cellular signaling dynamics. It navigates transitions in biological cues and ultimately shapes the destiny of proteins. Recent years have witnessed an upsurge in the momentum surrounding the development of protein-based therapeutics aimed at targeting the Ub system under the sway of cancer stem cells. The article provides a comprehensive overview of the ongoing in-depth discussions regarding the regulation of the Ub system and its impact on the development of cancer stem cells. Amidst the tapestry of insights, the article delves into the expansive roles of E3 Ub ligases, deubiquitinases, and transcription factors entwined with cancer stem cells. Furthermore, the spotlight turns to the interplay with pivotal signaling pathways the Notch, Hedgehog, Wnt/β-catenin, and Hippo-YAP signaling pathways all play crucial roles in the regulation of cancer stem cells followed by the specific modulation of Ub-proteasome.

A Comprehensive Review on LncRNAs/miRNAs-DNMT1 Axis in Human Cancer: Mechanistic and Clinical Application

Cancer constitutes a significant public health concern, and addressing the challenge of cancer holds paramount importance and requires immediate attention. Epigenetic alterations, encompassing DNA methylation, have emerged as pivotal contributors to the development of diverse cancer types. These modifications exert their influence by modulating chromatin structure, gene expression patterns and other nuclear processes, thereby influencing cancer pathogenesis. Over the last two decades, an increasing body of evidence has established the involvement of DNA methyltransferase 1 (DNMT1) in various aspects of cancer development, including tumorigenesis, aggressiveness and treatment response. Furthermore, non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are increasingly recognised as significant modulators in diverse biological processes, encompassing metastasis, apoptosis, cell proliferation and differentiation. Several recent studies have elucidated the intricate relationship between epigenetic machinery, specifically DNMT1, and the expression of ncRNAs in the context of cancer. In this review, we provide a comprehensive overview of the interaction between DNMT1 and ncRNAs in cancer pathogenesis. Furthermore, we discuss the important role of the ncRNAs-DNMT1 axis in cancer stem cells and cancer therapy resistance as critical issues in cancer therapy. Finally, we demonstrate that herbal medicine and synthetic RNA molecules regulate DNMT1 activity and hold great promise in cancer treatment.

Investigation of urinary miRNA profile changes in amphotericin B-induced nephrotoxicity in C57BL/6 mouse, Sprague-Dawley rats and Beagle dogs

MicroRNA (miRNAs) have been associated with drug-induced kidney injury (DIKI). However, there are few reports on the utility of miRNAs, when monitoring for nephrotoxicity across multiple species. The purpose of this study was to assess the value of urinary miRNA profile changes as renal safety biomarkers, when monitoring for kidney injury in investigative toxicology studies. To this end, we evaluated urine miRNA expression levels in response to amphotericin B (AmpB)-induced nephrotoxicity in mice, rats, and dogs. The results showed that 35 miRNAs were significantly differentially expressed across the 3 species in response to the induced renal injuries. Dogs showed the highest number of miRNAs with significant changes. miR-205-5p and miR-31-5p were the most consistently altered miRNA biomarkers across all 3 species. In rodents, these 2 miRNAs were the most sensitive markers and showed comparable or better sensitivities than the previously published urine protein biomarkers with the same nephrotoxicant. In dogs, none of the upregulated miRNAs were as sensitive as urine clusterin protein as observed in a previously published study with AmpB. Taken together, these miRNAs could complement the more established urinary protein biomarkers in monitoring DIKI in mice, rats, and dogs. To our knowledge, this is the first report that demonstrates the comparative utility of urinary miRNAs for the early detection of DIKI across 3 nonclinical animal models.

Promising protein biomarkers for early gastric cancer: clinical performance of combined detection

OBJECTIVES

In the early stage of gastric cancer (GC), identifying cancer-specific biomarkers is a key step in the disease screening process. This study aims to explore the clinical value of five novel protein biomarkers and their combination (5 MP) for GC early diagnosis.

METHODS

The candidate biomarkers were mined from TCGA, GTEx, and CPTAC databases. The clinical value of the five biomarkers and 5 MP in the early diagnosis from healthy control, benign gastric disease (BGD), precancerous lesions (PLGC), early GC (EGC), and GC was evaluated by receiver operator characteristic curve (ROC), the area under the curve (AUC), sensitivity, specificity, and accuracy.

RESULTS

Five candidate biomarkers, COL10A1, GKN1, GKN2, LIPF, and REG4, were mined from TCGA, GTEx, and CPTAC databases. In the training cohort, the five proteins were confirmed to be differentially expressed in the serum of control, BGD, EGC, and GC. COL10A1 has the highest AUC of a single protein in control vs. EGC (0.857). GKN2 has the highest AUC of a single protein in BGD vs. EGC (0.822). 5 MP has an AUC of 0.890 in Control vs. EGC, and 0.854 in BGD vs. EGC. In the validation cohort, 5 MP has an AUC of 0.834 in PLGC vs. GC, and 0.839 in PLGC vs. EGC.

CONCLUSIONS

Our findings suggest that COL10A1, GKN1, GKN2, LIPF, and REG4 are useful non-invasive serum biomarkers for GC diagnosis. Combination detection (5 MP) has enhanced early diagnosis of GC and distinguishing between benign and malignant gastric diseases.

Copy Number Gains of VPS72 Drive De Novo Lipogenesis and Hepatocarcinogenesis via ATF3/mTORC1/SREBP1 Axis

Hepatocellular carcinoma (HCC) is the predominant form of primary liver cancer and a major contributor to cancer-related mortality globally. Central to its pathogenesis is the dysregulation of lipid metabolism in hepatocytes, leading to abnormal lipid accumulation. Our bioinformatics analysis has identified the histone acetyltransferase complex subunit VPS72 as being associated with HCC, yet the precise molecular mechanisms through which VPS72 contributes to hepatocarcinogenesis remain poorly understood. Our analysis of extensive HCC patient cohorts identifies a significant proportion with VPS72 copy number gains, which are strongly linked to adverse prognostic outcomes. By integrating RNA-Seq, ChIP-Seq, ATAC-seq, and experimental validation, we show that VPS72 overexpression activates mTORC1 signaling, subsequently promoting lipid synthesis and driving HCC progression. We further uncover that VPS72 modulates the epigenetic landscape by enhancing DNA methylation at the ATF3 promoter, resulting in ATF3 repression and subsequent activation of mTORC1. This study elucidates a novel regulatory axis that links dysregulated lipid metabolism with HCC progression, highlighting potential epigenetic and metabolic targets for therapeutic intervention.

Unravelling the Impact of Outer Membrane Protein, OmpA, From S. Typhimurium on Aberrant AID Expression and IgM to IgA Class Switching in Human B-Cells

Salmonella enterica serovar Typhimurium is a Gram-negative bacterium that causes gastrointestinal infection and poses significant public health risks worldwide. This study aims to explore how S. Typhimurium manipulates B-cell function through outer membrane protein A (OmpA). We investigate the effect of OmpA on Raji human B-cells, leading to the induction of activation-induced cytidine deaminase (AID) protein, which plays an important role in generating antibody diversity in B-cells, via initiating the process of somatic hypermutation (SHM) and class switch recombination (CSR). Our key findings demonstrate that OmpA is crucial for inducing aberrant AID expression in B-cells, leading to increased CSR. Interestingly, the increased AID expression was likely due to overexpression of cMYC, an activator for AID expression. Not only was the expression of cMYC elevated, but its occupancy on the aicda locus was raised. Furthermore, increased AID expression induced CSR events, specifically switching to IgA. In summary, our study suggests that OmpA plays a potential role in modulating B-cell regulation and controlling the adaptive immune system. These functional attributes of OmpA implicate its potential as a therapeutic target for combating S. Typhimurium pathogenesis.

Bioinformatics Analysis of Cancer Related CBP Mutations on Copper Ion and Drug Binding

In cancer biology, copper-binding proteins (CBPs) possess a wide range of roles that impact various aspects of tumour development and progression. Modifications in CBPs in malignancy may have an enormous effect on cellular processes essential for the development and growth of cancers. We utilised bioinformatics approaches to separate down CBPs in the cancer proteome, and 32 proteins have been determined to be putative CBPs. Twelve of these proteins were associated with a likelihood of metastatic spread from primary to secondary cancer regions. Results indicated that the point mutation causes structural and functional changes in the proteins. Point mutations also alter the Cu2+/+ binding sites and drug molecules' binding affinity for CBPs. The majority of mutations disrupt copper binding sites in CBPs, based on subsequent mutation studies focused on proteins P61769:B2MG (Beta-2-microglobulin) and P42684:ABL2 (Tyrosine kinase protein ABL2) due to their high and low expression profile respectively, in various cancer types. The copper ion binding sites and drug-binding affinity for B2MG and ABL2 highlighted in the case study represent the impact of point mutation on the proteins. This study highlighted the possible effect of mutations in CBPs, representing that the point mutations disrupt the intramolecular interactions of the proteins and simultaneously alter the other molecules' binding affinity.

USP2-induced upregulation of LEF1 through deubiquitination relieves osteoporosis development by promoting the osteogenic differentiation of bone marrow mesenchymal stem cells

BACKGROUND

Bone marrow mesenchymal stem cells (BMSCs) exhibit therapeutic potential for osteoporosis through their differentiation into osteoblasts. Here, we investigated the role and mechanism of lymphoid enhancer-binding factor 1 (LEF1) in regulating osteogenic differentiation of human BMSCs (hBMSCs).

METHODS

hBMSCs were exposed to the specific medium to induce their osteogenic differentiation. The ovariectomy (OVX)-induced osteoporotic mouse model was constructed. LEF1 and USP2 mRNA expression was analyzed by quantitative PCR, and protein levels were detected by immunohistochemistry and immunoblotting. Cell proliferation was assessed by CCK-8 assay. Alkaline phosphatase (ALP) expression and activity assay and Alizarin Red staining were used to evaluate osteogenic differentiation. LEF1 protein stability analysis and co-immunoprecipitation (Co-IP) assay were performed to test the USP2/LEF1 interaction.

RESULTS

During hBMSC osteogenic differentiation, LEF1 and USP2 levels were increased in hBMSCs. Inhibiting LEF1 or USP2 diminished the proliferation and osteogenic differentiation of hBMSCs in vitro. Mechanistically, USP2 stabilized LEF1 protein by mediating LEF1 deubiquitination. Increased expression of LEF1 reversed USP2 knockdown-imposed suppression on proliferation and osteogenic differentiation of hBMSCs. Moreover, increased USP2 expression reduced bone loss and enhanced osteogenic differentiation in OVX mice. Additionally, LEF1 and USP2 were downregulated in the bone marrow of patients with osteoporosis.

CONCLUSION

Our findings provide the first demonstration of the USP2/LEF1 cascade that enhances the osteogenic differentiation of hBMSCs, broadening the field for the development of BMSCs as effective agents in osteoporosis therapy.

CDC6 as early biomarker for myocardial infarction with acute cellular senescence and repair mechanisms

We aimed to the exploration of genes related to the cell cycle and the mechanisms of cardiac cell repair and senescence post-MI. The sequencing dataset of myocardial infarction in mice (GSE161427) was downloaded from the Gene Expression Omnibus (GEO) database, yielding 894 upregulated differentially expressed genes (DEGsup). Additionally, 494 senescence-related genes (SRGs) were obtained from the CellAge database. The overlapping differentially expressed genes (DEupSGs) between these two sets were identified using the R software. WGCNA using the GSE59867 dataset revealed a highly related module to MI. The intersection of core genes from the purple module and DEupSGs yielded 12 genes. Through machine learning and PPI analysis, two target genes related to MI and cellular senescence were identified: CDC6 and PLK1. ROC curve analysis using the MI animal myocardial sample dataset GSE775 and the patient blood sample dataset GSE60993 indicated that CDC6 expression has high diagnostic value for MI and cellular senescence, with differential expression levels at various times post-infarction.These results show that CDC6 is specifically upregulated in the early stages of MI, and both in vivo and ex vivo model results are consistent with bioinformatics findings. Additionally, overexpression of CDC6 in the early oxygen-glucose deprivation (OGD) model in vitro increased the expression of genes mediating cardiac repair. Interestingly, when ABT263 was used to clear senescent cells, the expression of genes mediating repair in primary cardiac cells decreased, suggesting that acute ischemic hypoxia early on, CDC6-mediated acute cardiac cell senescence may promote early cardiac repair. This finding may provide new insights into the monitoring and assessment of cardiac cell senescence and repair in the early stages of MI.

Construction of a prognostic model and identification of key genes in liver hepatocellular carcinoma based on multi-omics data

Liver hepatocellular carcinoma (LIHC) strongly contributes to global cancer mortality, highlighting the need for a deeper understanding of its molecular mechanisms to enhance patient prognosis and treatment approaches. We aimed to investigate the differential expression of immunogenic cell death-related genes (ICDRGs) and cellular senescence-related genes (CSRGs) in LIHC and their effects on patient prognosis. We combined the GSE25097, GSE46408, and GSE121248 datasets by eliminating batch effects and standardizing the data. After processing, 16 genes were identified as ICDR&CSR differentially expressed genes (ICDR&CSRDEGs), including UBE2T, HJURP, PTTG1, CENPA, and FOXM1. Gene set enrichment analysis indicated a strong enrichment of these genes in pre-Notch expression and processing. Gene set variation analysis revealed 20 pathways with significant differences between the LIHC and control groups. Mutation analysis identified TP53 as the most commonly mutated gene in LIHC samples. A prognostic risk model integrating 12 ICDR&CSRDEGs was developed, showing high precision at 1 year but diminished accuracy at 2 and 3 years. Our constructed prognostic risk model provides valuable insights for predicting patient outcomes and may guide future therapeutic interventions targeting these specific genes. Further research is needed to explore the mechanistic roles of these genes in LIHC progression and treatment response.

Thiolutin, a novel NLRP3 inflammasome inhibitor, mitigates IgA nephropathy in mice

NLRP3 inflammasome plays a key role in IgA Nephropathy (IgAN) pathogenesis. Thiolutin (THL) is an NLRP3 inflammasome inhibitor with anti-inflammatory effects, but its role in IgAN is unclear. This study aimed to evaluate the protective efficacy of THL in IgAN mice, alongside assessing its inhibitory mechanisms. IgAN was induced by administration of bovine serum albumin combined with Staphylococcal Enterotoxin B in mice, followed by THL treatment. Kidney injury biomarkers, inflammatory cytokines, histological changes and the NLRP3 inflammasome pathway were assessed. The effect of THL on pyroptosis and action site on inflammasome was examined in J774A.1 cells, and co-immunoprecipitation was used to study specific protein interactions. In IgAN mice, THL treatment significantly reduced renal dysfunctional markers and histological injury without affecting hepatic function, accompanied by decreased serum IgA levels, renal IgA deposition and pro-inflammatory cytokine accumulation via regulating the mRNA and protein expression of key inflammasome components. It also attenuated pyroptosis and NLRP3 inflammasome activation instead of priming in macrophages, via disturbing the combination of NLRP3 with apoptosis-associated speck-like protein and NIMA-Related Kinase 7. THL has significant anti-inflammatory and renal protective effects in IgAN via inhibiting the NLRP3 inflammasome pathway. Its selective impact on the activation and assembly of the inflammasome, without affecting priming, highlights its potential as a targeted therapeutic agent in IgAN management.

Identification of key hub genes associated with anti-gastric cancer effects of lotus plumule based on machine learning algorithms

BACKGROUND

Lotus plumule and its active components have demonstrated inhibitory effects on gastric cancer (GC). However, the molecular mechanism of lotus plumule against GC remains unclear and requires further investigation.

AIM

To identify the key hub genes associated with the anti-GC effects of lotus plumule.

METHODS

This study investigated the potential targets of traditional Chinese medicine for inhibiting GC using weighted gene co-expression network analysis and bioinformatics. Initially, the active components and targets of the lotus plumule and the differentially expressed genes associated with GC were identified. Subsequently, a protein-protein interaction network was constructed to elucidate the interactions between drug targets and disease-related genes, facilitating the identification of hub genes within the network. The clinical significance of these hub genes was evaluated, and their upstream transcription factors and downstream targets were identified. The binding ability of a hub gene with its downstream targets was verified using molecular docking technology. Finally, molecular docking was performed to evaluate the binding affinity between the active ingredients of lotus plumule and the hub gene.

RESULTS

This study identified 26 genes closely associated with GC. Machine learning analysis and external validation narrowed the list to four genes: Aldo-keto reductase family 1 member B10, fructose-bisphosphatase 1, protein arginine methyltransferase 1, and carbonic anhydrase 9. These genes indicated a strong correlation with anti-GC activity.

CONCLUSION

Lotus plumule exhibits anti-GC effects. This study identified four hub genes with potential as novel targets for diagnosing and treating GC, providing innovative perspectives for its clinical management.

Promising Gastric Cancer Biomarkers-Focus on Tryptophan Metabolism via the Kynurenine Pathway

Currently, gastric cancer treatment remains an enormous challenge and requires a multidisciplinary approach. Globally, the incidence and prevalence of gastric cancer vary, with the highest rates found in East Asia, Central Europe, and Eastern Europe. Early diagnosis is critical for successful surgical removal of gastric cancer, but the disease often develops asymptomatically. Therefore, many cases are diagnosed at an advanced stage, resulting in poor survival. Metastatic gastric cancer also has a poor prognosis. Therefore, it is urgent to identify reliable molecular disease markers and develop an effective medical treatment for advanced stages of the disease. This review summarizes potential prognostic or predictive markers of gastric cancer. Furthermore, the role of tryptophan metabolites from the kynurenine pathway as prognostic, predictive, and diagnostic factors of gastric cancer is discussed, as this metabolic pathway is associated with tumor immune resistance.

Ubiquitination of transcription factors in cancer: unveiling therapeutic potential

Transcription factors, pivotal in gene expression regulation, are essential in cancer progression. Their function is meticulously regulated by post-translational modifications, including ubiquitination. This process, which marks proteins for degradation, can either enhance or inhibit the function of transcription factors, contingent on the context. In cancers, dysregulated ubiquitination of transcription factors contributes to the hallmark of uncontrolled growth and survival of tumors. For example, tumor suppressors such as p53 might be degraded prematurely due to abnormal ubiquitination, causing genomic instability. On the other hand, oncogenic transcription factors may gain stability via ubiquitination, thus facilitating tumorigenesis. Targeting the ubiquitin-proteasome system (UPS) therefore could be a viable therapeutic approach in cancer. Emerging treatments aim to block the ubiquitination of oncogenic transcription factors or to stabilize tumor suppressors. This review underscores the critical impact of transcription factor-altered ubiquitination on cancer progression. Additionally, it outlines innovative therapeutic approaches that involve inhibitors or drugs directed at specific ubiquitin E3 ligases and deubiquitinases (DUBs) that regulate transcription factor activity.

PITX1 as a grading, prognostic and tumor-infiltrating immune cells marker for chondrosarcoma: a public database-based immunoassay and tissue sample analysis

Background

Chondrosarcoma (CHS) is a rare bone cancer originating from chondrocytes, with high-grade cases associated with high mortality rates. However, the prognostic factors and therapeutic targets for CHS have not been studied.

Methods

Graded gene differential analysis was conducted on 97 CHS tissues to identify genes associated with CHS grading. Additionally, we performed GO and KEGG enrichment analyses of the differentially-expressed genes (DEGs), as well as GSEA analysis, differential expression analysis, survival analysis, and univariable and multifactorial COX analysis of paired-like homology structural domain transcription factor 1 (PITX1). Furthermore, our findings investigated the relationship between tumor-infiltrating immune cells (TICs) in CHS tumors using CIBERSORT to calculate proportions and differences. Our findings also explored the associations among gene expression patterns, survival prognosis, TICs, and immune checkpoints across various cancer types. Finally, immunohistochemical staining was carried out on self-collected clinical samples to assess PITX1 expression levels and correlate them with clinical information.

Results

Gene differential expression analysis revealed a strong correlation between PITX1 expression and tumor grade. GO, KEGG enrichment, and GSEA analysis demonstrated the association of PITX1 with cell proliferation-related processes, such as cell cycle regulation and mitosis, and differentiation-related processes, such as RNA processing. PITX1 expression was associated with tumor stage and survival outcomes. Immunoassay indicated a positive correlation between PITX1 levels and TICs, immune checkpoints, and graded TICs. Pan-cancer analysis confirmed the differential expression of the PITX1 gene across multiple cancers, impacting survival prognosis, TIC patterns, and immune checkpoint regulation. Lastly, our 75 collection of clinical patient tissue samples exhibited varying levels of PITX1 expression across different cancer grades while also demonstrating a significant association with tumor differentiation and metastasis.

Conclusion

PITX1 is a novel biomarker for distinguishing between high-grade and low-grade CHS, serving as a prognostic indicator for patients with this condition and presenting a promising target for immunotherapy. These findings offer innovative insights into the treatment of CHS.

Splicing factor SF3B4 acts as a switch in cancer cell senescence by regulating p21 mRNA stability

SF3B4, a splicing factor known to regulate mRNA expression and function, is upregulated in various cancers. Despite its potential significance, the mechanisms through which SF3B4 regulates nonsense-mediated mRNA decay (NMD) and cancer cell senescence remain poorly understood. This study explores the underlying mechanisms by which SF3B4 modulates mRNA stability through the NMD pathway and elucidates its role in switching cancer cells between growth and senescence. We demonstrate that SF3B4 deficiency leads to decreased cancer cell proliferation, increased senescence-associated β-galactosidase (SA-β-Gal) activity, p53-independent upregulation of p21 expression, and ultimate induction of cell senescence. We further show that SF3B4 recruits essential NMD factors, including UPF1, MAGOH, and RNPS1, which facilitate mRNA decay of the crucial senescence regulator, p21. Conversely, SF3B4 depletion results in the dissociation of these factors from the 3'UTR of p21 mRNA, thereby enhancing its stability. Collectively, our results suggest that SF3B4 critically regulates p21 expression at the post-transcriptional level, providing insights into the novel role of SF3B4 in regulating p21 mRNA stability, interacting with key NMD factors, and modulating cancer cell senescence.

Molecular signatures bidirectionally link myocardial infarction and lung cancer

Myocardial Infarction (MI) and lung cancers are major contributors to mortality worldwide. While seemingly diverse, the two share common risk factors, such as smoking and hypertension. There is a pressing need to identify bidirectional molecular signatures that link MI and lung cancer, in order to improve clinical outcomes for patients. In this study, we identified common differentially expressed genes between MI and lung cancer. Specifically, we identified 1,496 upregulated and 1,482 downregulated genes in the MI datasets. By focusing on the 1,000 most upregulated and downregulated genes in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC), we identified 35 genes that are common across MI, LUAD, and LUSC. Functional enrichment analysis revealed shared biological processes, such as "inflammatory response" and "cell differentiation." The Cox proportional hazards model demonstrated a significant association between the shared genes and overall survival in lung cancer patients, as well as with smoking history in these patients. In addition, a machine learning model based on the expression of the shared genes distinguished MI patients from controls, achieving an AUROC of 0.72 and an AUPRC of 0.86. Finally, based on drug repurposing analysis, we proposed FDA-approved drugs potentially targeting the upregulated genes as novel therapeutic options for the co-occurring conditions of MI and lung cancer. Overall, our findings highlight the similarities in molecular makeup between lung cancer and MI.

Helicobacter pylori CagA and Cag type IV secretion system activity have key roles in triggering gastric transcriptional and proteomic alterations

Colonization of the human stomach with cag pathogenicity island (PAI)-positive Helicobacter pylori strains is associated with increased gastric cancer risk compared to colonization with cag PAI-negative strains. To evaluate the contributions of the Cag type IV secretion system (T4SS) and CagA (a secreted bacterial oncoprotein) to gastric molecular alterations relevant for carcinogenesis, we infected Mongolian gerbils with a Cag T4SS-positive wild-type (WT) H. pylori strain, one of two Cag T4SS mutant strains (∆cagT or ∆cagY), or a ∆cagA mutant for 12 weeks. Histologic staining revealed a biphasic distribution of gastric inflammation severity in WT-infected animals and minimal inflammation in animals infected with mutant strains. Atrophic gastritis (a premalignant condition), dysplasia, and gastric adenocarcinoma were only detected in WT-infected animals with high inflammation scores. Transcriptional profiling, liquid chromatography-tandem mass spectrometry analysis of micro-extracted tryptic peptides, and imaging mass spectrometry revealed more than a thousand molecular alterations in gastric tissues from WT-infected animals with high inflammation scores compared to uninfected tissues and few alterations in tissues from other groups of infected animals. Proteins with altered abundance in animals with severe Cag T4SS-induced inflammation mapped to multiple pathways, including the complement/coagulation cascade and proteasome pathway. Proteins exhibiting markedly increased abundance in tissues from H. pylori-infected animals with severe inflammation included calprotectin components, proteins involved in proteasome activation, polymeric immunoglobulin receptor (PIGR), interferon-inducible guanylate-binding protein (GBP2), lactoferrin, lysozyme, superoxide dismutase, and eosinophil peroxidase. These results demonstrate key roles for CagA and Cag T4SS activity in promoting gastric mucosal inflammation, transcriptional alterations, and proteomic alterations relevant to gastric carcinogenesis.IMPORTANCEHelicobacter pylori colonizes the stomachs of about half of humans worldwide, and its presence is the primary risk factor for the development of stomach cancer. H. pylori strains isolated from humans can be broadly classified into two groups based on whether they contain a chromosomal cag pathogenicity island, which encodes a secreted effector protein (CagA) and components of a type IV secretion system (T4SS). In experiments using a Mongolian gerbil model, we found that severe gastric inflammation and gastric transcriptional and proteomic alterations related to gastric cancer development were detected only in animals infected with a wild-type H. pylori strain containing CagA and an intact Cag T4SS. Mutant strains lacking CagA or Cag T4SS activity successfully colonized the stomach without inducing detectable pathologic host responses. These findings illustrate two different patterns of H. pylori-host interaction.

Mechanisms of HDACs in cancer development

Histone deacetylases (HDACs) are a class of epigenetic regulators that play pivotal roles in key biological processes such as cell proliferation, differentiation, metabolism, and immune regulation. Based on this, HDAC inhibitors (HDACis), as novel epigenetic-targeted therapeutic agents, have demonstrated significant antitumor potential by inducing cell cycle arrest, activating apoptosis, and modulating the immune microenvironment. Current research is focused on developing highly selective HDAC isoform inhibitors and combination therapy strategies tailored to molecular subtypes, aiming to overcome off-target effects and resistance issues associated with traditional broad-spectrum inhibitors. This review systematically elaborates on the multidimensional regulatory networks of HDACs in tumor malignancy and assesses the clinical translation progress of next-generation HDACis and their prospects in precision medicine, providing a theoretical framework and strategic reference for the development of epigenetic-targeted antitumor drugs.

Recent advances in small molecule inhibitors of deubiquitinating enzymes

Proteins play a pivotal role in maintaining cellular homeostasis. Their degradation primarily orchestrated through the ubiquitin-proteasome system (UPS) and cellular autophagy. Dysfunction of the UPS is associated with various human diseases, including cancer, autoimmune disorders, and neurodegenerative conditions. Consequently, the UPS has emerged as a promising therapeutic target. Deubiquitinases (DUBs) have garnered significant attention as potential targets for therapeutic intervention due to their role in modulating protein stability and function. This review focuses on recent advancements of DUBs, particularly their relevance in the UPS and their potential as drug targets. Notably, inhibitors targeting specific DUBs, such as USP1, USP7, USP14, and USP30 have shown promise in preclinical and clinical studies for cancer therapy. Additionally, DUB inhibitors have been involved in novel therapeutic approaches lately, including as targets for proteolysis-targeting chimeras (PROTACs) or as tools in deubiquitinase-targeting chimeras (DUBTACs).

Wnt signaling pathways in biology and disease: mechanisms and therapeutic advances

The Wnt signaling pathway is critically involved in orchestrating cellular functions such as proliferation, migration, survival, and cell fate determination during development. Given its pivotal role in cellular communication, aberrant Wnt signaling has been extensively linked to the pathogenesis of various diseases. This review offers an in-depth analysis of the Wnt pathway, detailing its signal transduction mechanisms and principal components. Furthermore, the complex network of interactions between Wnt cascades and other key signaling pathways, such as Notch, Hedgehog, TGF-β, FGF, and NF-κB, is explored. Genetic mutations affecting the Wnt pathway play a pivotal role in disease progression, with particular emphasis on Wnt signaling's involvement in cancer stem cell biology and the tumor microenvironment. Additionally, this review underscores the diverse mechanisms through which Wnt signaling contributes to diseases such as cardiovascular conditions, neurodegenerative disorders, metabolic syndromes, autoimmune diseases, and cancer. Finally, a comprehensive overview of the therapeutic progress targeting Wnt signaling was given, and the latest progress in disease treatment targeting key components of the Wnt signaling pathway was summarized in detail, including Wnt ligands/receptors, β-catenin destruction complexes, and β-catenin/TCF transcription complexes. The development of small molecule inhibitors, monoclonal antibodies, and combination therapy strategies was emphasized, while the current potential therapeutic challenges were summarized. This aims to enhance the current understanding of this key pathway.

Cell-type-specific subtyping of epigenomes improves prognostic stratification of cancer

BACKGROUND

Most molecular classifications of cancer are based on bulk-tissue profiles that measure an average over many distinct cell types. As such, cancer subtypes inferred from transcriptomic or epigenetic data are strongly influenced by cell-type composition and do not necessarily reflect subtypes defined by cell-type-specific cancer-associated alterations, which could lead to suboptimal cancer classifications.

METHODS

To address this problem, we here propose the novel concept of cell-type-specific combinatorial clustering (CELTYC), which aims to group cancer samples by the molecular alterations they display in specific cell types. We illustrate this concept in the context of DNA methylation data of liver and kidney cancer, deriving in each case novel cancer subtypes and assessing their prognostic relevance against current state-of-the-art prognostic models.

RESULTS

In both liver and kidney cancer, we reveal improved cell-type-specific prognostic models, not discoverable using standard methods. In the case of kidney cancer, we show how combinatorial indexing of epithelial and immune-cell clusters define improved prognostic models driven by synergy of high mitotic age and altered cytokine signaling. We validate the improved prognostic models in independent datasets and identify underlying cytokine-immune-cell signatures driving poor outcome.

CONCLUSIONS

In summary, cell-type-specific combinatorial clustering is a valuable strategy to help dissect and improve current prognostic classifications of cancer in terms of the underlying cell-type-specific epigenetic and transcriptomic alterations.

Senescence-related Genes as Prognostic Markers for STEMI Patients: LASSO Regression-Based Bioinformatics and External Validation

The prognostic value of differentially expressed senescence-related genes(DESRGs) in ST-segment elevation myocardial infarction(STEMI) patients is unclear. We used GEO2R to identify DESRGs from GSE60993 and performed functional enrichment analysis. We built an optimal prognostic model with LASSO penalized Cox regression via GSE49925. We evaluated the model with survival analysis, ROC curve, decision curve analysis, nomogram, and external validation with plasma samples. We created a prognostic signature with three dysregulated DESRGs (CDC25B, FKBP5, and ECHDC3) and two clinical variables (serum creatinine, Gensini score). The signature stratified patients into low- and high-risk groups and showed strong predictive performance within two years. The external validation confirmed the survival difference between the groups. We identified three DESRGs that were differentially expressed and prognostic in STEMI patients. The model incorporating three DESRGs showed promising prediction and utility for stratifying patients and estimating survival risk in STEMI patients.

Silencing LINC01547 induces hepatocellular carcinoma cell apoptosis and metastasis inhibition via the ADAR1/FAK and miR-146b-5p/RAC1 axes

Growing research indicates that long noncoding RNAs (lncRNAs) are pivotal in the development and advancement of hepatocellular carcinoma (HCC). Our research pinpointed LINC01547 as a notable lncRNA that was significantly downregulated in Hep3B cells treated with bufotalin, whereas it exhibited elevated expression levels in HCC tumor tissues. Further study found that silencing LINC01547 markedly suppressed proliferation, induced apoptosis, and inhibited migration and invasion in Hep3B and HepG2 cells. LINC01547 knockdown reduced ADAR1 expression, which led to apoptosis and suppressed metastasis via inhibition of the FAK signaling pathway. Additionally, silencing LINC01547 upregulated miR-146b-5p, which in turn decreased RAC1 levels, further promoting apoptosis and inhibiting metastasis in HCC cells. In vivo, a Hep3B tumor-bearing mouse model confirmed the antitumor effects of LINC01547 silencing. Our findings demonstrate that LINC01547 regulates HCC cell apoptosis and metastasis through the ADAR1/FAK and miR-146b-5p/RAC1 pathways, suggesting that LINC01547 may serve as a biomarker and potential therapeutic target for HCC.

Advancements in immunotherapy for gastric cancer: Unveiling the potential of immune checkpoint inhibitors and emerging strategies

Gastric cancer (GC) is linked to high morbidity and mortality rates. Approximately two-thirds of GC patients are diagnosed at an advanced or metastatic stage. Conventional treatments for GC, including surgery, radiotherapy, and chemotherapy, offer limited prognostic improvement. Recently, immunotherapy has gained attention for its promising therapeutic effects in various tumors. Immunotherapy functions by activating and regulating the patient's immune cells to target and eliminate tumor cells, thereby reducing the tumor burden in the body. Among immunotherapies, immune checkpoint inhibitors (ICIs) are the most advanced. ICIs disrupt the inhibitory protein-small molecule (PD-L1, CTLA4, VISTA, TIM-3 and LAG3) interactions produced by immune cells, reactivating these cells to recognize and attack tumor cells. However, adverse reactions and resistance to ICIs hinder their further clinical and experimental development. Therefore, a comprehensive understanding of the advancements in ICIs for GC is crucial. This article discusses the latest developments in clinical trials of ICIs for GC and examines combination therapies involving ICIs (targeted therapy, chemotherapy, radiotherapy), alongside ongoing clinical trials. Additionally, the review investigates the tumor immune microenvironment and its role in non-responsiveness to ICIs, highlighting the function of tumor immune cells in ICI efficacy. Finally, the article explores the prospects and limitations of new immunotherapy-related technologies, such as tumor vaccines, nanotechnologies, and emerging therapeutic strategies, aiming to advance research into personalized and optimized immunotherapy for patients with locally advanced gastric cancer.

Discovery and evaluation of novel Benzohydroxamic acid-indole derivatives as dual inhibitors of ADAM17 and HDAC2 with antitumor activity

Hepatocellular carcinoma (HCC) has garnered significant attention from researchers due to its high recurrence rate and invasive characteristics. The design of drugs with dual-target combined effects represents a promising strategy in cancer treatment. Our observations suggest that ADAM17 and HDAC may inhibit the unfavorable prognostic signaling pathway Notch1 in HCC through distinct mechanisms, thereby suppressing tumor cell proliferation and metastasis. Consequently, this study utilized the ADAM17 inhibitor ZLDI-8 as a lead compound and developed a series of dual ADAM17/HDAC2 inhibitors by integrating strategies such as backbone leaping and pharmacophore fusion. We assessed the anti-hepatocellular carcinoma activity of these compounds, focusing on their anti-proliferative, pro-apoptotic, and anti-metastatic properties. Notably, ZSNI-21 effectively inhibited the proliferation of Bel-7402 cells and demonstrated significant anti-metastatic capabilities against HCC-LM3 cells, with its targeting confirmed. Additionally, its in vivo safety was validated. To date, there have been no reports on dual ADAM17/HDAC2 inhibitors, marking this as a novel endeavor.

Phospholipase D6 activates Wnt/β-catenin signaling through mitochondrial metabolic reprogramming to promote tumorigenesis in colorectal cancer

Phospholipase D6 (PLD6) is a critical enzyme involved in mitochondrial fusion with a key role in spermatogenesis. However, the role of PLD6 in cancer remains unknown. Notably, Wnt signaling, energy metabolism and mitochondrial function show complex interactions in colorectal cancer (CRC) progression. Here we found that PLD6 is highly expressed in CRC and positively correlated with poor prognosis. We present a novel function of PLD6 in activating Wnt/β-catenin signaling by enhancing mitochondrial metabolism. PLD6 depletion suppresses the oncogenic properties of CRC cells and impairs mitochondrial respiration, leading to reduced mitochondrial length, membrane potential, calcium levels and reactive oxygen species. PLD6 depletion also disrupts mitochondrial metabolic reprogramming by inhibiting the tricarboxylic acid cycle and mitochondrial oxidative phosphorylation, resulting in altered intracellular levels of citrate and acetyl-CoA-both key modulators of Wnt/β-catenin activation. PLD6-mediated acetyl-CoA production enhances β-catenin stability by promoting its acetylation via the acetyltransferases CREB-binding protein and P300/CREB-binding-protein-associated factor. Consequently, PLD6 ablation reduces cancer stem cell-associated gene expression downstream of Wnt/β-catenin signaling, suppressing stem-like traits and chemoresistance to 5-fluorouracil. Furthermore, PLD6 depletion attenuates CRC tumorigenesis in both subcutaneous and orthotopic tumor models. Overall, PLD6 acts as an oncogenic switch by promoting mitochondria-mediated retrograde signaling, thereby regulating Wnt signaling in CRC.