The implication of non-AUG-initiated N-terminally extended proteoforms in cancer

Dysregulated translation is a hallmark of cancer, and recent genome-wide studies in tumour cells have uncovered widespread translation of non-canonical reading frames that often initiate at non-AUG codons. If an upstream non-canonical start site is located within a frame with an annotated coding sequence (CDS), such translation events can lead to the production of proteoforms with altered N-termini (PANTs). Certain examples of PANTs from oncogenes (e.g. c-MYC) and tumour suppressors (e.g. PTEN) have been previously linked to cancer. We have performed a systematic computational analysis on recently identified non-AUG initiation-derived N-terminal extensions of cancer-associated proteins, and we discuss how these extended proteoforms may acquire new oncogenic properties. We identified a loss of stability for the N-terminally extended proteoforms of oncogenes TCF-4 and SOX2. Furthermore, we discovered likely functional short linear motifs within the N-terminal extensions of oncogenes and tumour suppressors (SOX2, SUFU, SFPQ, TOP1 and SPEN/SHARP) that could provide an explanation for previously described functionalities or interactions of the proteins. In all, we identify novel cases where PANTs likely show different localization, functions, partner binding or turnover rates compared to the annotated proteoforms. Therefore, we propose that alterations in the stringency of translation initiation, often seen under conditions of cellular stress, may result in reprogramming of translation to generate novel PANTs that influence cancer progression.

Research progress on estrogen receptor-positive/progesterone receptor-negative breast cancer

Breast cancer, which arises from the epithelial tissue of the breast, is one of the most common cancers affecting women worldwide. Its incidence and mortality rates have been increasing in both developed and developing countries. As a hormone-dependent cancer, breast cancer is classified into several molecular subtypes based on the expression of key markers: Estrogen Receptor (ER), Progesterone Receptor (PR), Human Epidermal Growth Factor Receptor 2 (HER-2), and Ki67. PR loss is associated with endocrine resistance and a poorer prognosis in breast cancer. Despite this, the underlying mechanisms of ER-positive/PR-negative (ER+PR-) breast cancer remain poorly understood. This study aims to review recent advancements in research on ER+PR- breast cancer, analyze its clinical characteristics and molecular mechanisms, and provide recommendations for more targeted therapeutic approaches.

A comprehensive transcriptome based meta-analysis to unveil the aggression nexus of oral squamous cell carcinoma

Lymph node metastasis in oral cancer (OC) complicates management due to its aggressive nature and high risk of recurrence, underscoring the need for biomarkers for early detection and targeted therapies. However, the drivers of this aggressive phenotype remain unclear due to the variability in gene expression patterns. To address this, an integrative meta-analysis of six publicly available transcriptomic profiles, categorized by lymph nodal status, is conducted. Key determinants of disease progression are identified through functional characterization and the TopConfects ranking approach of nodal associated differentially expressed genes (DEGs). To explore the critical nexus between lymph node metastasis and OC recurrence, significant metastatic genes were cross-analysed with literature-derived genes exhibiting aberrant methylation patterns in OC recurrence. Their clinical relevance and expression patterns were then validated in an external dataset from the TCGA head and neck cancer cohort. The analysis identified elevated expression of genes involved in extracellular matrix remodelling and immune response, while the expression of genes related to cellular differentiation and barrier functions was reduced, driving the transition to nodal positivity. The highest-ranked gene, MMP1, showed a log-fold change (LFC) of 4.946 (95 % CI: 3.71, 6.18) in nodal-negative samples, which increased to 5.899 (95 % CI: 4.80, 6.99) in nodal-positive samples, indicating consistent elevation across disease stages. In contrast, TMPRSS11B was significantly downregulated, with an LFC of -5.512 (95 % CI: -6.63, -4.38) in nodal-negative samples and -5.898 (95 % CI: -7.15, -4.64) in nodal-positive samples. Furthermore, MEIS1, down-regulated in nodal-positive status, was found to exhibit hypermethylation at CpG sites associated with OC recurrence. This study represents the first transcriptomic meta-analysis to explore the intersection of lymph node metastasis and OC recurrence, identifying MEIS1 as a potential key contributor. These comprehensive insights into disease trajectories offer potential biomarkers and therapeutic targets for future treatment strategies.

Case Series of Patients With FGFR1-Related Pheochromocytoma and Paraganglioma With a Focus on Biochemical, Imaging Signatures and Treatment Options

Pheochromocytoma and paraganglioma (together PPGL) are tumours with a high degree of heritability. Genetic landscape is divided into three clusters, cluster 1 (Krebs/pseudohypoxia signalling pathway), cluster 2 (kinase signalling pathway) and cluster 3 (Wnt signalling pathway). With increasing knowledge in the field of genetics, cluster-specific tumour characteristics, biochemical phenotype and imaging signatures are established in commonly found genes. The association of FGFR1 pathogenic mutations with PPGL have been recently described although its features are not yet well established. Here, we present four patients with PPGL who were found to have somatic FGFR1 pathogenic mutations. We discuss their clinical presentations, biochemical phenotypes, imaging signatures and treatment options that will be relevant for practicing physicians in managing these patients effectively.

Invasive Salmonella Typhimurium colonizes gallbladder and contributes to gallbladder carcinogenesis through activation of host epigenetic modulator KDM6B

Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.

Efficacy of 2 different fibroblast growth factor receptor-inhibitors in a patient with extrahepatic cholangiocarcinoma harboring an FGFR2 mutation: a case report

Cholangiocarcinoma (CCA) is a type of cancer with few effective systemic therapies. Elucidation of the molecular landscape of the disease from genomic studies based on next-generation sequencing (NGS) has contributed to the introduction of new targeted therapies. One of these treatments consists of a class of small molecules that target members of the fibroblast growth factor receptors (FGFRs) family of receptor tyrosine kinases. We report here on a patient with a cholangiocarcinoma bearing an FGFR2 mutation. The patient was treated with 2 different FGFR inhibitors, as the first caused ocular toxicity. She obtained clinical benefits from both. This case illustrates the efficacy of FGFR inhibitors on cholangiocarcinoma with specific point mutations.

Current treatment landscape for patients with non-small cell lung cancer with common EGFR mutations

Common EGFR mutations including exon-19 deletions and the L858R point mutation in exon 21 constitute predominant actionable genomic alterations in individuals with non-small cell lung cancer (NSCLC). The introduction of EGFR tyrosine kinase inhibitors (TKIs) has fundamentally changed the treatment landscape for such patients by improving both progression-free survival (PFS) and overall survival (OS). Among EGFR-TKIs, third-generation agents such as osimertinib have shown marked efficacy and favorable safety profiles and have become the standard of care in the first-line setting. The combination of osimertinib with platinum-based chemotherapy has recently been shown to improve PFS compared with osimertinib monotherapy in the FLAURA2 trial. Similarly, the MARIPOSA trial demonstrated clinical benefit of the combination of the EGFR-MET bispecific antibody, amivantamab, with the third-generation EGFR-TKI, lazertinib, further supporting the use of combination therapies as first-line treatment for EGFR-mutated NSCLC. Despite these advances, however, challenges such as brain metastases remain substantial barriers to successful treatment outcomes. Management of patients with such metastases often requires a multidisciplinary approach that integrates systemic treatment with local interventions such as radiation therapy. Finally, circulating tumor DNA has emerged as a promising biomarker for real-time monitoring of treatment response and evolution of drug resistance mechanisms. Analysis of such biomarkers can facilitate dynamic and personalized therapeutic adjustments, potentially improving outcomes. This review provides a comprehensive overview of the latest clinical evidence supporting therapeutic advances in the management of EGFR-mutated NSCLC, emphasizing the importance of tailoring treatment strategies based on tumor biology, patient-specific factors, and evolving therapeutic options.

Targeting exon mutations in NSCLC: clinical insights into LAG-3, TIM-3 pathways, and advances in fourth-generation EGFR-TKIs

Lung cancer remains the second leading cause of cancer-related morbidity and mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for the majority of cases. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have become the standard first-line therapy for advanced NSCLC with EGFR mutations, offering significant improvements in progression-free survival (PFS), overall survival (OS), and objective response rate (ORR) compared to chemotherapy alone. Recent studies suggest that their effectiveness decreased with the emergence of acquired resistance, such as C797S and T790M. Immunotherapy alone also shows enhanced PFS and OS over chemotherapy; however, its applicability can be limited in cases with low programmed cell death ligand 1 (PD-L1) expression and result in immune-related adverse effects like those observed in retrospective, non-randomized studies. Emerging fourth-generation EGFR-TKIs, currently under clinical trials, show promising potential to address these resistance mechanisms. Advanced inhibitors, including BBT-176, BLU-945, and BLU-701, have effectively targeted resistant mutations and reduced disease progression. Studies have suggested that combining fourth-generation EGFR-TKIs with immunotherapies targeting novel pathways like LAG-3 and TIM-3 may enhance patient outcomes. Such combination regimens aim to optimize PFS, OS, and ORR while minimizing adverse effects and addressing the limitations of current therapies. This study explores the landscape of EGFR mutations, their clinical significance, and the integration of innovative fourth-generation EGFR-TKIs with immunotherapies, emphasizing the potential of precision medicine in advancing the management of EGFR-mutated NSCLC.

Evolving treatment for advanced Non-small cell lung cancer harbouring common EGFR activating mutations

A clinically important subgroup of non-small cell lung cancer (NSCLC) is driven by common mutations in the epidermal growth factor receptor (EGFR). Over the past decade, first-, second-, and third-generation EGFR tyrosine kinase inhibitors (TKIs) have substantially improved clinical outcomes, although acquired resistance inevitably emerges. In particular, the third-generation TKI osimertinib has demonstrated superior progression-free survival (PFS) and overall survival (OS) compared to earlier-generation TKIs in the frontline setting, yet median OS remains approximately three years in pivotal trials. Efforts to extend disease control have led to various upfront intensification strategies, including combining EGFR TKIs with antiangiogenics or chemotherapy (e.g., the FLAURA-2 trial), and pairing novel bispecific antibodies such as amivantamab with third-generation TKIs. Upon progression on third-generation EGFR TKIs, platinum-based chemotherapy remains the standard second-line treatment, albeit with modest response rates. Emerging therapies targeting MET amplification (e.g., savolitinib plus osimertinib), leveraging antibody-drug conjugates (e.g., patritumab deruxtecan), or adding immunotherapy and antiangiogenics have shown preliminary promise in overcoming resistance. Ongoing trials are assessing optimal treatment sequencing and the use of circulating tumor DNA (ctDNA) to guide therapy escalation or de-escalation. Ultimately, the evolving landscape of EGFR-mutant NSCLC underscores the need for refined biomarker-driven approaches and personalized regimens to achieve further gains in survival. In this review, we discuss these strategies in detail, highlighting current evidence and future directions for EGFR-mutant NSCLC treatment.

Biologics for novel driver altered non-small cell lung cancer: potential and pitfalls

Precision medicine has revolutionized clinical paradigm of lung cancer (LC) patients optimizing therapeutical options on the basis of molecular fingerprinting of tumor cells. The advent of the genomic era contributed to the widespread diffusion of sequencing technologies laying the basis for the approval of an increasing number of clinically relevant predictive biomarkers in clinical settings. In the rapidly evolving scenario of predictive biomarkers, mandatory testing genes demonstrated a statistically significant clinical benefit in LC patients elected to molecular tests, but emerging biomarkers are under investigation to raise the bar in the clinical management of LC patients. To date, promising IHC-based predictive biomarkers emerged as potentially integrative tools in the panel of clinically approved biomarkers. On this basis, genomic, transcriptomic and proteomic data are gaining ground toward "3D" biology" supporting the need of a multidimensional analysis of tumor cells to clinically stratify LC patients. Here we sought to overview the most promising biomarkers investigated in clinical trials to be integrated into diagnostic panel of predictive biomarkers tools for NSCLC patients.

High-grade Endometrial Carcinomas With Solid Basaloid Morphology and Geographic Necrosis Lacking Definitive Pilomatrix-like Features: Clinicopathologic Characteristics Including Aggressive Behavior and Novel Molecular Events

High-grade endometrioid carcinomas occasionally demonstrate solid basaloid morphology with geographic necrosis (SB-GN). This pattern is among the defining features of pilomatrix-like high-grade endometrioid carcinoma (PiMHEC), a recently proposed tumor type which is additionally characterized by the presence of shadow cells, abnormal beta-catenin/ CTNNB1 mutations, strong CDX2 expression, and poor outcomes. Clinicopathologic overlap between PiMHEC and other high-grade endometrial cancers with SB-GN has not been established. We screened 300 endometrial carcinomas on tissue microarray for SB-GN histology and performed a detailed whole-section morphologic review, immunohistochemical analysis, and next-generation sequencing on all cases bearing this pattern. Four (1.3%) demonstrated SB-GN. All 3 with clinical follow-up had extremely aggressive behavior despite being MMR-deficient; in contrast, only 27% of other MMR-deficient high-grade carcinomas recurred. One SB-GN case met most of the previously outlined diagnostic criteria for PiMHEC including abnormal beta-catenin/ CTNNB1 (p.S37P variant) and strong CDX2 expression; notably, however, shadow cells were absent. This case also demonstrated a KRAS p.A59T pathogenic variant. The other 3 cases also lacked shadow cells; the 2 with sequencing data bore no CTNNB1 abnormalities but showed likely oncogenic variants involving the pilomatrixoma-associated gene FGFR2. All 3 cases with molecular results also bore somatic Notch pathway ( NOTCH1/NOTCH2/NOTCH3 ) variants. The single case treated with immunotherapy showed complete and sustained response with regression of bone metastases despite abnormal beta-catenin/ CTNNB1 , which has been associated with immunotherapeutic resistance. These data suggest that the SB-GN pattern may connote a poor prognosis even in the absence of overt pilomatrix-like differentiation, and that novel molecular events may have implications for the treatment of these tumors.

Comprehensive Genomic Profiling of Indian Patients With Lung Cancer

PURPOSE

Genomic profiling has revolutionized non-small cell lung cancer (NSCLC) therapy, but molecular data on Indian patients with NSCLC are limited.

MATERIALS AND METHODS

We analyzed next-generation sequencing (NGS) data of 5,219 Indian patients with lung cancer, tested between May 2022 and August 2023 at CORE Diagnostics, a commercial laboratory in India. Using the PulmoCORE gene panel, we targeted 13 key genes (ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, RET, ROS1, TP53, and NTRK) for DNA and RNA sequencing. PD-L1 was tested by immunohistochemistry.

RESULTS

Median patient age was 62 years, and 62.5% were male. Common histologies included adenocarcinoma (57.1%), NSCLC not otherwise specified (19.3%), and squamous cell carcinoma (7%). Genomic alterations were detected in 80.6% patients according to the PulmoCORE panel; 64.2% patients had actionable alterations in at least one of the nine biomarkers with Food and Drug Administration-approved targeted therapies, that is, EGFR, KRAS, ALK, ROS1, BRAF, NTRK1/2/3, MET, RET, and ERBB2. Common alterations included TP53 (37%), EGFR (34.1%), and KRAS (13.3%), ALK (8.8%), and others below 5%. Alterations were more common in adenocarcinoma (76.4%) than in patients with squamous cell carcinoma (29.9%). Sex and age influenced mutation prevalence, with EGFR mutations more common in females and KRAS in males, while ALK, ROS1, and RET fusions were prevalent in younger adults. Most genomic alterations were mutually exclusive, although 25% patients had co-occurring mutations. PD-L1 positivity was higher in males (28.3%) and more common in patients with squamous cell carcinoma (34.2%).

CONCLUSION

Broad molecular profiling is important to detect actionable alterations in Indian patients with lung cancer, for delivering optimal personalized precision medicine. Our study underscores the fact that NGS should be routinely done before planning therapy in Indian patients with advanced lung cancer.

Pharmacological effects of osimertinib on a chicken chorioallantoic membrane xenograft model with the EGFR exon-19-deleted advanced NSCLC mutation

Non-small cell lung cancer (NSCLC) affects 10-50% of patients with epidermal growth factor receptor (EGFR) mutations. Osimertinib is a third-generation EGFR tyrosine kinase inhibitor (TKI) that radically changes the outcome of patients with tumors bearing EGFR sensitizing or EGFR T790M resistance mutations. However, resistance usually occurs, and new therapeutic combinations need to be explored. The chorioallantoic membrane (CAM) xenograft model is ideal for studying aggressive tumor growth and the responses to complex therapeutic combinations due to its vascularization and complex microenvironment. This study aims to demonstrate the relevance of analyzing a complex therapeutic response to osimertinib treatment, especially through advanced transcriptomic analysis with the CAM model, which has been limited thus far. We engrafted HCC827 cells (EGFR p.E746_A750del) into the CAM model and treated them with various osimertinib doses for 7 days. The study involved supervised multivariate discrimination and ontology analysis of human transcriptional data. We found that CDX tumor growth inversely correlated with osimertinib dosage, with a notable 35% tumor weight reduction at 10 μm. Transcriptomic analysis revealed that osimertinib reduces EGFR pathway activity and its effectors, and dampens chemotaxis, immune recruitment and angiogenesis, indicating that effectiveness extends beyond cellular mechanisms to the tissue level. This was supported by a 15% reduction in blood vessels around the xenograft in osimertinib-treated cases. This study is the first to demonstrate that ontological analysis of transcriptomic data in the CAM model aligns with clinical observations, highlighting the relevance of this methodology for understanding and ameliorating the efficacy of targeted therapy in NSCLC.

KMT2A facilitates the epithelial-to-mesenchymal transition and the progression of ovarian cancer

Epithelial-mesenchymal transition (EMT) plays critical roles in cancer progression and metastasis. Thus, the exploration of the molecular mechanism regulating EMT would provide potential opportunities for the therapy of metastatic ovarian cancer (OC). Herein, we investigated the putative role of KMT2A in modulating EMT and metastasis in OC. The expression of KMT2A in OC was detected by Western blot and immunohistochemistry and its relationship with clinicopathological factors was analyzed. The effect of KMT2A on the biological behavior of OC cells was examined. Moreover, the expressions of EMT-associated proteins were detected in vivo and vitro by Western blot, immunofluorescence, and immunohistochemistry. KMT2A was highly expressed in OC cell lines and tissues and was positively correlated with advanced International Federation of Gynecology and Obstetrics (FIGO) stage, pathological grade, and metastasis. KMT2A overexpression was correlated with poor prognosis. Suppression of KMT2A inhibited OC cells proliferation, migration, and invasion and induced their apoptosis in vitro and vivo. In contrast, the ectopic expression of KMT2A had the opposite effects. Furthermore, KMT2A knockdown inhibited TGF-β-induced EMT in OC and reduced the phosphorylation levels of Smad2. Taken together, these observations demonstrate that KMT2A could promote the malignant behavior of OC by activating TGF-β/Smad signaling pathway and may be a potential prognostic biomarker and therapeutic target for OC.

Differences between lung adenocarcinoma and lung squamous cell carcinoma: Driver genes, therapeutic targets, and clinical efficacy

With the rapid advancements in second-generation gene sequencing technologies, a growing number of driver genes and associated therapeutic targets have been unveiled for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). While they are clinically classified as non-small cell lung cancer (NSCLC), they display distinct genomic features and substantial variations in clinical efficacy, underscoring the need for particular attention. Hence, this review provides a comprehensive overview of the latest advancements in driver genes, epigenetic targets, chemotherapy, targeted therapy, and immunotherapy for LUAD and LUSC. Additionally, it delves into the distinctions in signaling pathways and pivotal facets of clinical management specific to these two categories of lung cancer. Moreover, we furnish pertinent details regarding clinical trials pertaining to driver genes and epigenetics, thus establishing a theoretical foundation for the realization of precision treatments for LUAD and LUSC.

Validation of ion mobility spectrometry - mass spectrometry as a screening tool to identify type II kinase inhibitors of FGFR1 kinase

RATIONALE

The protein kinase FGFR1 regulates cellular processes in human development. As over-activity of FGFR1 is implicated with cancer, effective inhibitors are in demand. Type I inhibitors, which bind to the active form of FGFR1, are less effective than type II inhibitors, which bind to the inactive form. Screening to distinguish between type I and type II inhibitors is required.

METHODS

X-ray crystallography was used to indicate whether a range of potential inhibitors bind to the active or inactive FGFR1 kinase conformation. The binding affinity of each ligand to FGFR1 was measured using biochemical methods. Electrospray ionisation - ion mobility spectrometry - mass spectrometry (ESI-IMS-MS) in conjunction with collision-induced protein unfolding generated a conformational profile of each FGFR1-ligand complex. The results indicate that the protein's conformational profile depends on whether the inhibitor is type I or type II.

RESULTS

X-ray crystallography confirmed which of the kinase inhibitors bind to the active or inactive form of FGFR1 kinase. Collision-induced unfolding combined with ESI-IMS-MS showed distinct differences in the FGFR1 folding landscape for type I and type II inhibitors. Biochemical studies indicated a similar range of FGFR1 affinities for both types of inhibitors, thus providing confidence that the conformational variations detected using ESI-IMS-MS can be interpretated unequivocally and that this is an effective screening method.

CONCLUSIONS

A robust ESI-IMS-MS method has been implemented to distinguish between the binding mode of type I and type II inhibitors by monitoring the conformational unfolding profile of FGFR1. This rapid method requires low sample concentrations and could be used as a high-throughput screening technique for the characterisation of novel kinase inhibitors.

Flavokawain a induces cell cycle arrest through CDT1-dependent p27 regulation and synergizes with venetoclax in acute myeloid leukemia

The poor prognosis of patients with acute myeloid leukemia (AML) is largely ascribed to the deficiency of persistently effective therapies. Despite the recent approval of targeted drugs such as the BCL-2 inhibitor venetoclax, the clinical benefit is limited due to the development of resistance. The use of natural products is emerging as a feasible strategy to treat malignant diseases including AML. Flavokawain A (FKA) is a naturally occurring chalcone isolated from the root of kava and possesses extensive antitumor activities. The therapeutic potential of FKA in AML remains unknown. In the present study, we found that treatment with FKA reduced the viability in four AML cell lines in dose- and time-dependent manners. The anti-AML activity of venetoclax was significantly potentiated by FKA. Mechanistically, FKA induced G1 phase arrest in AML cells along with CDT1 downregulation and p27 upregulation. Knockdown of CDT1 increased the expression of p27, leading to the inhibition on cell viability. Both p27 upregulation and viability inhibition caused by FKA was partially rescued by CDT1 overexpression. The therapeutic effect of FKA alone or in combination with venetoclax was verified in primary blasts from AML patients, further strengthening the clinical relevance of the current study. Therefore, our data suggest that FKA can be considered as a potential therapeutic agent in the treatment of AML.

AKT1 as a therapeutic target for platinum-resistant SOX2 positive ovarian cancer cells

Ovarian cancer remains the most lethal gynecological malignancy, largely owing to its chemotherapy resistance and high recurrence rate. Emerging evidence has linked the aberrant expression of SOX2, a transcription factor that is important in the development and maintenance of stem cell state, with chemoresistance and poor prognosis of ovarian cancer patients. In this study, we aimed to elucidate the mechanisms that drive aberrant SOX2 expression in ovarian cancer cells. By examining multiple ovarian cancer cell lines and a panel of clinical tumor samples, we observed a broad overexpression of SOX2 in ovarian cancer cell lines and tumors. To identify signaling pathway(s) that drives SOX2 overexpression in ovarian cancer cells, we screened a set of small-molecule kinase inhibitors that target 30 major cellular kinases. Among the top hits identified are AKT inhibitors. We demonstrated that inhibition or knockdown of AKT1 can drastically downregulate SOX2 protein level, impairs the growth and stemness of SOX2-positive ovarian cancer cells, and markedly sensitize SOX2-positive ovarian cancer cells to platinum drugs. Mechanically, we found that AKT1 drives SOX2 overexpression primarily by enhancing its protein stability and does so by phosphorylating SOX2 at threonine 116. Altogether, our study reveals an underlying mechanism that drives SOX2 overexpression in ovarian cancer and underscores pharmacological inhibition of AKT1 as a potential therapeutic strategy to sensitize SOX2-positive ovarian cancer to platinum drugs.

Genomic, socio-environmental, and sequencing capability patterns in the surveillance of SARS-CoV-2 in Latin America and the Caribbean up to 2023

Latin America and the Caribbean (LAC) have been one of the most strongly impacted regions by the Coronavirus disease 2019 (COVID-19) emergency, with more than 83 million reported infections and 1.7 million deaths until December 2023, intensifying economic and social inequalities. This study aimed to provide information to the regional SARS-CoV-2 surveillance programs by determining genomic, socio-environmental, and sequencing capacity patterns associated with the circulation of the virus in Latin America up to 2023. Data from 24 countries in LAC were analyzed using public databases up to December 2023. A sampling of SARS-CoV-2 sequences from cases in the region enabled a phylogenomic study to elucidate the temporal distribution of various variants of concern (VOCs), mutations, and recombinants. Also, we identified differences in sequencing capabilities in LAC. Additionally, correlation and generalized linear model (GLM) analyses were conducted to explore potential associations between 89 socio-environmental variables and five COVID-19 indicators at the country level. The phylogenomic analyses revealed a diversity of variants with the predominance of some during specific periods, mainly VOCs and some recombinant cases, and a mutation rate of 8.39 × 10-4 substitutions per site per year, which are in line with other regions of the world. Besides, a low sequencing rate in LAC (on average 0.7% of cases) and incomplete databases in several countries were identified. In the analysis of indicators, correlations between 9 socio-environmental indicators and four COVID-19 variables associated with cases, deaths, and diagnostic tests related to the virus in the region, although not for sequencing percentages. This study provides information about the development of COVID-19 disease in LAC in terms of the viral genome, sequencing capabilities, and the region's complex socio-environmental conditions. Therefore, emphasis must be placed on implementing an integrated epidemiological surveillance approach to strengthen public health infrastructure and improve cooperation and preparedness for future infections affecting this region.

Mendelian randomization study on the causal relationships among fasting blood glucose, plasma proteins, and squamous cell lung cancer

BACKGROUND

Squamous cell lung cancer (SQCLC) represents the second most common subtype of lung cancer (LC) with characteristics of treatment resistance. Plasma proteins often influence levels of fasting blood glucose (FBG), consequently impacting LC. However, the precise role of FBG in this association remains unclear.

OBJECTIVE

To investigate the causal relationships of FBG with LC and its subtypes, plasma proteins, and SQCLC, as well as the mediating role of FBG.

METHODS

Mendelian randomization (MR) analysis was employed to assess the causal associations of FBG with LC and its subtypes, plasma proteins and SQCLC, and plasma proteins and FBG, using the two-step MR approach with the primary method being Inverse Variance Weighted (IVW). Protein-Protein Interaction (PPI) network was utilized to identify hub genes of plasma proteins causally linked to SQCLC.

RESULTS

FBG was a risk factor for SQCLC (OR: 1.376, 95% CI 1.017-1.862, P = 0.038) but had no significant causal associations with LC and other subtypes (P > 0.05). Furthermore, 54 plasma proteins had significant causal associations with SQCLC (P < 0.05). EEF2 K (OR: 1.111, 95% CI 1.015-1.216, P = 0.023) and SSR1 (OR: 0.546, 95% CI 0.487-0.613, P < 0.001) were identified as a risk and protective factor for FBG, respectively. Mediation analysis indicated a significant negative mediating effect of FBG in the causal relationship between SSR1 and SQCLC (B = - 0.193, 95% CI - 0.312-0.074, P = 0.001), with a mediation proportion of 44.4%.

CONCLUSION

Our study revealed FBG as a risk factor for SQCLC and demonstrated the mediating role of FBG in the causal association between SSR1 and SQCLC.

Prevalence of EGFR Mutations in Vietnamese Patients with Resected Early Stage Non-Small Cell Lung Cancer: EARLY-EGFR Study

Introduction

Comprehensive profiling of mutations in the EGFR gene is vital for selecting patients eligible for EGFR targeted therapies.

Methods

We investigated the prevalence of EGFR mutations and treatment patterns in patients with early stage non-small cell lung cancer (NSCLC) in Vietnam as a part of EARLY-EGFR (Clinical Trial Identifier: NCT04742192), a global, real-world study. Consecutive patients with surgically resected stage IA-IIIB, non-squamous NSCLC were diagnosed from August 2021 to June 2022 and were prospectively enrolled from November 2021 to July 2022.

Results

A total 200 patients (age: median [range], 60.0 [30.0-80.0] years) were enrolled from 3 centers; 56.0% were males and 64.0% never smoked. The prevalence of EGFR mutations was 51.0% (102/200) including deletions in exon-19 (49.0%) and exon-21 L858R mutations (33.3%). Females (73.9%, 65/88), patients aged ≥60 years (52.5%, 53/101), nonsmokers (61.2%, 63/103) and those with stage I (55.8%, 67/120) had higher prevalence of EGFR mutations. Multivariate analysis (adjusted odds ratio [aOR]) showed EGFR mutations to be significantly associated (p < 0.05) with female gender (aOR = 5.90), age ≥60 years (aOR = 1.05), and stage III disease (vs stage I) (aOR = 0.30).

Conclusion

These results underscore the need for EGFR testing early in management algorithm of NSCLC in Vietnam to identify patients eligible for targeted therapy in concordance with international guidelines.

Downregulation of GFPT2 enhances cisplatin chemotherapy sensitivity in STK11/KRAS mutant non-small cell lung cancer by regulating the hexosamine biosynthesis pathway, resisting tumor growth

OBJECTIVE

To explore the role of GFPT2 in the sensitivity of STK11/KRAS lung cancer cells to cisplatin chemotherapy, and its underlying mechanism.

MATERIALS & METHODS

A549 and H460 cells were used to analyze the effect of GFPT2 on cisplatin chemotherapy sensitivity, as both carry KRAS mutations and H460 has LKB1 inactivation mutations, meeting the requirements of a KRAS/LKB1 co mutant tumor model. The levels of UDP-GlcNAc, OGT, OGA, and O-GlcNAc in the HBP pathway were also determined. To verify the potential role of HBP, we added OGT inhibitors. In vivo, we constructed a nude mouse model bearing A549 tumor to further validate the results of in vitro cell experiments.

RESULTS

GFPT2 silencing can significantly inhibit cell proliferation, invasion, and migration, promote cell apoptosis, and enhance the effect of cisplatin (p < 0.05). After OSMI-1 processing, GFPT2 enhances O-GlcNAc modification levels via the OGT-mediated HBP, thereby decreasing the sensitivity of STK11/KRAS mutant cells to cisplatin chemotherapy. In addition, GFPT2 silencing enhances the chemotherapy sensitivity of cisplatin and inhibits tumor growth, while overexpression of GFPT2 weakens this effect (p < 0.05). The above results provide new targets and combination therapy options for the clinical treatment of KRAS/LKB1 mutant lung cancer.

CONCLUSION

Our study found that inhibiting GFPT2 can enhance the chemotherapy sensitivity of cisplatin to STK11/KRAS/LKB1 mutant NSCLCs cells through the OGT mediated HBP pathway, filling a key gap in the chemotherapy resistance mechanism of KRAS/LKB1 mutant lung cancer.

The Current Roadmap of Lung Cancer Biology, Genomics and Racial Disparity

Globally, lung cancer is the most prevalent cause of cancer-related death. There are two large histological groups of lung cancer: small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC). Based on histopathological and molecular features, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) are the two major histologic subtypes of NSCLC. Various epidemiological and environmental factors are linked with an increased risk of lung cancer. However, these risk factors show disparities in patients with divergent racial and ethnic backgrounds. Interestingly, different populations were found to harbor distinct molecular features as evidenced by variations in genetic mutation profiles. Moreover, diverse histological and molecular progression patterns are identified in lung cancer, which could be crucial in improving diagnosis, prognosis, and therapeutic planning. In concert with a plethora of nuclear genetic alterations, mitochondrial alteration, epigenetic reprogramming, microbial dysbiosis, and immune alteration signatures have been identified in various lung cancer types. This review article provides a comprehensive overview of screening tests and the treatment strategies for NSCLC and SCLC, including surgery, radiation therapy, chemotherapy, targeted therapies, and immunotherapies. Through the unification of these diverse aspects, this review article aspires to a complete understanding of lung cancer's genomics, biology, microbial landscapes, and racial disparity and seeks to understand the essential role of racial and ethnic factors in lung cancer occurrence and treatment.

Identification of Driver Mutations and Risk Stratification in Lung Adenocarcinoma via Liquid Biopsy

BACKGROUND

Liquid biopsy using plasma cfDNA has been established as a tool for informing the management of advanced-stage NSCLC. However, its effectiveness in early lung cancer detection, including the identification of high-risk cases, remains to be determined.

METHODS

We analyzed plasma cfDNA and matched tumors from 117 stage I-IV lung adenocarcinoma cases and compared the variants identified across all stages using the Oncomine Precision Assay on the GenexusTM next-generation sequencing platform.

RESULTS

Cancer-specific mutations were detected in plasma from approximately 72% (84/117) of cases (all stages), with detection rates increasing by stage. Concordance between cfDNA and tumor tissue also increased with stage 0% (stage I), 19% (stage II), 45% (stage III), and 75% (stage IV). KRAS mutations were concordant in approximately 22% (6/27) of stage II and 46% (11/24) of stage III cases. Clinically important EGFR variants showed concordance in 11% (1/9) of stage II and 80% (8/10) in stage III/IV cases. Actionable mutations, targetable with FDA-approved drugs, were detected in 11% (4/37) of stage II, 27% (12/45) of stage III, and 55% (4/9) of stage IV cases, underscoring the potential of liquid biopsy for early detection of therapeutic targets. Moreover, co-occurring mutations with varying actionability were identified more frequently in plasma than in tumor tissues. Plasma detection of clinically important KRAS and EGFR variants was mostly associated with advanced-stage disease, suggesting the presence of these variants in plasma as a potential indication of disease progression.

CONCLUSIONS

Liquid biopsy holds promise for identifying high-risk lung adenocarcinoma cases and serves as a complementary diagnostic tool in advanced stages, enhancing disease management strategies.

SPI1 activates mitochondrial unfolded response signaling to inhibit chondrocyte senescence and relieves osteoarthritis

Chondrocyte senescence is a critical pathological hallmark of osteoarthritis (OA). Aberrant mechanical stress is considered a pivotal determinant in chondrocyte aging; however, the precise underlying mechanism remains elusive. Our findings demonstrate that SPI1 plays a significant role in counteracting chondrocyte senescence and inhibiting OA progression. SPI1 binds to the PERK promoter, thereby promoting its transcriptional activity. Importantly, PERK, rather than GCN2, facilitates eIF2α phosphorylation, activating the mitochondrial unfolded protein response (UPRmt) and impeding chondrocyte senescence. Deficiency of SPI1 in mechanical overload-induced mice leads to diminished UPRmt activation and accelerated OA progression. Intra-articular injection of adenovirus vectors overexpressing SPI1 and PERK effectively mitigates cartilage degeneration. In summary, our study elucidates the crucial regulatory role of SPI1 in the pathogenesis of chondrocyte senescence by activating UPRmt signaling through PERK, which may present a novel therapeutic target for treating OA. SPI1 alleviates the progression of OA by inhibiting mechanical stress-induced chondrocyte senescence through mitochondrial UPR signaling.

Expression of CREB3L1 blocks key cancer pathways and suppresses metastasis of lung squamous cell carcinoma cells

Lung cancer is the leading cause of death due to cancer, with higher mortality rates than cancers of the colon, breast and prostate combined. About one quarter of lung cancers are lung squamous cell carcinomas (LUSC), with a five-year survival rate of only 16 %. We discovered that the majority of LUSCs have reduced expression of a key transcription factor CREB3L1 (cAMP responsive element binding protein 3 like 1), known to function as a metastasis suppressor in breast, bladder and ovarian cancers. In this report, we set out to determine if CREB3L1 functions as a metastasis suppressor in LUSCs. A differential gene expression analysis showed that ectopic expression of CREB3L1 in NCI-H2170 and NCI-1703 cells caused significant reductions in many signaling pathway genes involved in promoting cell viability, survival, migration and angiogenesis. Expression of CREB3L1 was able to reduce cell migration and anchorage-independent growth in soft agar in NCI-H2170, NCI-H1703 and NCI-H226 LUSC cells. Expression of CREB3L1 had less impact on the growth of primary xenograft tumors for NCI-H2170 and NCI-H1703 cells, the latter of which formed atypical masses filled with blood. In contrast, xenografts of NCI-H226 expressing CREB3L1 showed significant reductions in primary tumor growth. Finally, in a mouse metastasis assay, expression of CREB3L1 in NCI-H2170 cells significantly reduced the formation of liver metastases and in NCI-H226 cells, lung metastases, as compared to their respective CREB3L1-deficient parental LUSC cells. Taken together, these results strongly support a role for CREB3L1 as a metastasis suppressor in lung squamous cell carcinoma cells.

The Predictive Roles of Tumour Markers, Hemostasis Assessment, and Inflammation in the Early Detection and Prognosis of Gallbladder Adenocarcinoma and Metaplasia: A Clinical Study

Gallbladder carcinoma (GBC) is one of the most aggressive malignancies of the biliary tract, often originating from chronic inflammation associated with gallstones and cholecystitis. Persistent inflammation plays a pivotal role in the development of preneoplastic changes, such as metaplasia, which may progress to malignancy. Despite its relatively low incidence, GBC is characterized by a poor prognosis due to late-stage diagnosis, highlighting the urgent need for improved early detection strategies. This study aimed to assess the diagnostic and prognostic significance of CA 19-9 and CEA levels in patients with gallbladder lesions, while also evaluating systemic inflammation and hemostatic dysregulation. A retrospective analysis was conducted on patients diagnosed with gallbladder lesions, with histopathological confirmation of adenocarcinoma and metaplasia. Laboratory assessments included serum levels of tumour markers, inflammatory markers such as CRP, and key hemostatic parameters, including thrombocyte count, prothrombin time (PT), activated partial thromboplastin time (aPTT), and fibrinogen levels. A predictive scoring model was developed using the cutoff values of CA 19-9 and CEA to assess their combined diagnostic potential. Among the patients studied, 48.9% had an initial diagnosis of chronic cholecystitis, while 32.2% presented with acute cholecystitis. Adenocarcinoma was identified in 6.7% of cases after histopathological examination, predominantly in females over 65 years old with acute cholecystitis. Metaplasia was detected in 7.8% of cases, primarily in elderly females with chronic cholecystitis. Laboratory findings revealed significantly elevated levels of CA 19-9, CEA, AFP, and CA-125 in patients with adenocarcinoma. Additionally, abnormalities in hemostatic parameters, including increased fibrinogen levels and alterations in thrombocyte count, were observed in patients with malignancy. A combined predictive score using CA 19-9 and CEA demonstrated strong potential for detecting adenocarcinoma and metaplasia, improving diagnostic accuracy. Our findings emphasize the clinical importance of integrating tumour markers, inflammatory biomarkers, and hemostatic parameters in the evaluation of gallbladder lesions associated with chronic inflammation. The combined assessment of these factors enhances early detection, facilitates malignancy risk stratification, and improves prognostic evaluation, particularly in patients with metabolic and cardiovascular comorbidities.

Genetic predictors of unexpected recurrence in low-risk endometrial cancer: A comprehensive genomic analysis reveals FGFR2 as a risk factor and a rare fatal POLE-mutated recurrence

OBJECTIVE

Endometrial cancer is the most common gynecological malignancy in high-income countries. While early-stage endometrial cancer generally has a favorable prognosis, a small proportion of low-risk patients experience unexpected recurrence. This study aimed to identify molecular factors contributing to recurrence in stage 1 A grade 1-2 low-risk endometrioid endometrial cancer.

METHODS

We performed next-generation sequencing (NGS) on tumor samples from 19 patients who experienced recurrence despite favorable clinicopathological features and compared them with six control patients without recurrence. Results were also compared to a matched cohort of low-risk endometrial cancers from The Cancer Genome Atlas (TCGA) database.

RESULTS

Mutations in PTEN, PIK3CA, ARID1A, and FGFR2 were the most frequent in the recurrence group. FGFR2 mutations were exclusive to the recurrence group (9/19, 47.4 %) and absent in the non-recurrent group (0/6), a difference approaching statistical significance (p = 0.0571). FGFR2 mutations were also significantly more prevalent in the recurrence cohort compared to the TCGA low-risk cohort (p = 0.0039). Prominent FGFR2 missense mutations included S252W, K659E, and N549K, which may drive oncogenesis and tumor progression. Among the recurrence group, a rare POLE-mutated tumor recurred unexpectedly and proved fatal, highlighting the potential for poor outcomes even in typically favorable molecular subtypes.

CONCLUSION

FGFR2 mutations may play a role in tumor recurrence in a subset of low-risk endometrial cancers, underscoring the importance of molecular profiling in identifying patients at risk. FGFR2 represents a potential therapeutic target, warranting further validation in larger cohorts to establish its clinical utility.

Aurora Kinase A and B inhibition abrogates 'Neosis', a non-mitotic cell division of GBM residual cells and prevents GBM recurrence

Glioblastoma (GBM) has a dismal median survival of 15 months owing to therapy resistance and inevitable recurrence. Using our cellular models of GBM radiation resistance, we had shown that GBM recurrence is due to survival and proliferation of residual disease cells enriched in multinucleated giant cells (MNGCs). However, MNGC division mechanism remained elusive. Here, using live-cell imaging we found daughter cells emerge from MNGCs by cytoplasmic pinching. Lack of DNA condensation, absence of spindle poles and acto-myosin contractile ring in dividing-MNGCs confirmed non-mitotic division of MNGCs. Furthermore, MNGCs harboured DNA damage, senescence phenotype, repeated atypical division after radiation exposure, characteristics of unconventional division called 'Neosis'. Molecularly, WGCNA co-expression network analysis of RNA-Sequencing from parent, non-dividing MNGCs and dividing-MNGCs identified significantly high expression of aurora kinases (AurA and AurB) specifically in dividing-MNGCs. Pharmacological and genetic inhibition of aurora kinases abrogated MNGC neosis, preventing GBM recurrence in vitro and in vivo in an orthotopic GBM mouse model. Together, this study demonstrates that MNGCs divide by neosis, an atypical division mediated by AurA and AurB and identify aurora kinases as a potential molecular target to inhibit neosis and prevent GBM recurrence.

GRHL3 specifically initiated by the TP63 transcription factor promotes the metastasis of squamous cell carcinogenesis

Metastasis is the primary cause of death in squamous cell carcinoma (SCC) patients; thus, identification of highly sensitive tumor biomarkers and therapeutic targets that can be exploited to prevent SCC metastasis and clarification of the underlying molecular mechanism is critically important. Reports have shown that Grainyhead-like 3 (GRHL3) plays a crucial role in tumorigenesis and cancer progression; nevertheless, its functions and molecular mechanism in the development of cancer remain controversial. In the present study, GRHL3 was found to be specifically overexpressed in SCCs, including lung squamous cell carcinoma (LUSC), esophageal squamous cell carcinoma (ESCC), and cervical squamous cell carcinoma (CSCC). In particular, the study revealed that high GRHL3 expression is correlated with poor overall survival (OS) and progression-free survival (PFS) in LUSC patients. Functionally, GRHL3 knockdown suppressed the invasion and migration of SCC cells in vitro and decreased their lung metastasis potential in vivo but had little effect on cell proliferation. Mechanistically, the specific overexpression of GRHL3 in SCCs is orchestrated by a well-known oncogenic transcription factor: tumor protein p63 (TP63). GRHL3 stimulates the expression of heparanase (HPSE), thereby activating the AKT-SRC signaling axis. Taken together, our work reveals a novel molecular pathway through which GRHL3 mediates the metastasis of SCCs, which has important implications for the diagnosis and targeted treatment of SCC.

Toward cancer detection by label-free microscopic imaging in oncological surgery: Techniques, instrumentation and applications

This review examines the clinical application of label-free microscopy and spectroscopy, which are based on optical signals emitted by tissue components. Over the past three decades, a variety of techniques have been investigated with the aim of developing an in situ histopathology method that can rapidly and accurately identify tumor margins during surgical procedures. These techniques can be divided into two groups. One group encompasses techniques exploiting linear optical signals, and includes infrared and Raman microspectroscopy, and autofluorescence microscopy. The second group includes techniques based on nonlinear optical signals, including harmonic generation, coherent Raman scattering, and multiphoton autofluorescence microscopy. Some of these methods provide comparable information, while others are complementary. However, all of them have distinct advantages and disadvantages due to their inherent nature. The first part of the review provides an explanation of the underlying physics of the excitation mechanisms and a description of the instrumentation. It also covers endomicroscopy and data analysis, which are important for understanding the current limitations in implementing label-free techniques in clinical settings. The second part of the review describes the application of label-free microscopy imaging to improve oncological surgery with focus on brain tumors and selected gastrointestinal cancers, and provides a critical assessment of the current state of translation of these methods into clinical practice. Finally, the potential of confocal laser endomicroscopy for the acquisition of autofluorescence is discussed in the context of immediate clinical applications.

Hiding in plain sight: NUT carcinoma is an unrecognized subtype of squamous cell carcinoma of the lungs and head and neck

In the past two decades, treatment for non-small-cell lung cancers (NSCLCs) and head and neck squamous cell carcinoma (HNSCC) has advanced considerably, owing largely to the characterization of distinct oncological subtypes, the development of targeted therapies for each subtype and the advent of immunotherapy. Data emerging over the past two decades suggest that NUT carcinoma, a highly aggressive malignancy driven by a NUT fusion oncoprotein and arising in the lungs, head and neck, and rarely in other sites, is a squamous cell carcinoma (SCC) based on transcriptional, histopathological, cell-of-origin and molecular characteristics. NUT carcinoma has an estimated incidence of 1,400 cases per year in the United States, surpassing that of some rare NSCLC and HNSCC subtypes. However, NUT carcinoma is currently not recognized as an SCC of the lungs or head and neck. The orphan classification of NUT carcinoma as a distinct entity leads to a lack of awareness of this malignancy among oncologists and surgeons, despite early diagnosis being crucial for this cancer type with a median survival of only ~6.5 months. Consequently, NUT carcinoma is underdiagnosed and often misdiagnosed, resulting in limited research and progress in developing effective treatments in one of the most aggressive forms of lung and head and neck cancer. With a growing number of targeted agents that can potentially be used to treat NUT carcinoma, improved recognition through reclassification and inclusion of NUT carcinoma as a squamous NSCLC or an HNSCC when arising in these locations will accelerate the development of effective therapies for this disease. Thus, in the Perspective, we propose such a reclassification of NUT carcinoma as an SCC and discuss the supporting evidence.

Comparing the Effectiveness and Safety of First-line Interventions in Patients With Advanced Epidermal Growth Factor Receptor-mutant Non-small Cell Lung Cancer, With Particular Focus on Brain Metastatic Status: A Systematic Review and Network Meta-analysis

AIMS

This network meta-analysis (NMA) aimed to identify the most effective first-line intervention (FLI) for advanced epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC), particularly in patients with varying brain metastasis (BM) status.

MATERIALS AND METHODS

Data were collected from randomized controlled trials (RCTs) evaluating first-line EGFR-tyrosine kinase inhibitors (EGFR-TKIs), either alone or in combination, for EGFR-mutated advanced NSCLC (EMAN) patients. The sources included EMBASE, Web of Science, Cochrane Library, PubMed, and relevant conference abstracts from inception until December 2023.

RESULTS

A total of 37 RCTs, encompassing 24 intervention options, were included in the NMA. Osimertinib combined with chemotherapy (CT) significantly improved progression-free survival (PFS) compared to aumolertinib (HR, 0.61; 95% CI, 0.40-0.93), furmonertinib (HR, 0.64; 95% CI, 0.41-0.98), lazertinib (HR, 0.64; 95% CI, 0.41-0.98), osimertinib alone (HR, 0.62; 95% CI, 0.48-0.80), osimertinib + bevacizumab (HR, 0.72; 95% CI, 0.51-1.00), befotertinib (HR, 0.57; 95% CI, 0.36-0.90), and zorifertinib (HR, 0.61; 95% CI, 0.39-0.93). Further, amivantamab + lazertinib showed slightly better PFS compared to aumolertinib, furmonertinib, zorifertinib, and osimertinib + bevacizumab (HR <1, but P >0.05). Regarding overall survival (OS), amivantamab + lazertinib demonstrated superior results relative to furmonertinib (HR, 0.54; 95% CI, 0.30-0.95) and befotertinib (HR, 0.43; 95% CI, 0.24-0.77). No significant OS differences were observed among osimertinib, osimertinib + bevacizumab, osimertinib + CT, lazertinib, and amivantamab + lazertinib. In BM patients, osimertinib + CT significantly enhanced PFS compared to osimertinib (HR, 0.47; 95% CI, 0.33-0.66), furmonertinib (HR, 0.44; 95% CI, 0.21-0.90), befotertinib (HR, 0.45; 95% CI, 0.21-1.00), and zorifertinib (HR, 0.47; 95% CI, 0.25-0.89). However, no noticeable PFS differences were observed between osimertinib + CT and amivantamab + lazertinib or aumolertinib. Lastly, osimertinib + CT and zorifertinib were associated with higher rates of all-grade adverse events (AEs) and grade ≥3 AEs, respectively.

CONCLUSIONS

In EMAN patients, osimertinib + CT and amivantamab + lazertinib were associated with optimal PFS and OS, respectively. Among BM patients, osimertinib + CT offered the best PFS benefits. These findings may assist in clinical decision-making and personalized care for EMAN and BM patients. The study is registered on PROSPERO (CRD42024506995).

Can Knowledge From Treating Chronic Myeloid Leukemia Inform Therapy of EGFR-Mutant Lung Adenocarcinoma?

This Viewpoint discusses how therapy of chronic myeloid leukemia can inform therapy of lung cancer.

Transcriptional regulation by LKB1 in lung adenocarcinomas: Exploring oxidative stress, neuroglial and amino acid signatures

Lung adenocarcinoma (LUAD) is one of the most prevalent cancer types worldwide and has one of the poorest survival rates. Understanding its developpment is crucial for improving diagnosis, prognosis, and treatment. A key factor in LUAD is the frequent loss-of-function mutations in LKB1/STK11, a kinase that regulates metabolism. These mutations are linked to increased metastasis and worse clinical outcomes. In this study, we analyzed gene expression data from LUAD patients to explore how LKB1 mutations affect cancer behavior. We found that LKB1 mutations in KRAS-driven LUAD lead to widespread gene downregulation. By integrating avalaible protein interaction data, mass spectrometry analysis of LKB1 nuclear partners, and co-immunoprecipitations experiments, we identified BRG1, a chromatin activator and subunit of the BAF complex, as a nuclear partner of LKB1. Further analysis suggested that LKB1 mutations may impair BRG1 activity, disrupting chromatin regulation and gene expression. Notably, LUAD patients with mutated LKB1 showed gene expression patterns indicative of oxidative stress, defective neuronal-glial and neuroinflammation programs, and altered amino acid homeostasis. These changes resemble the roles LKB1 plays in neural crest stem cells, suggesting that LKB1 may reduce tumor aggressiveness in LUAD by maintaining a developmental gene expression program.

The impact of co-occurring tumor suppressor mutations with mEGFR as early indicators of relapse in lung cancer

BACKGROUND

Lung adenocarcinoma frequently presents with EGFR mutations, often progressing on EGFR tyrosine kinase inhibitors (TKIs) despite an initial response. Progression is frequently driven by additional genetic changes, including mutations in tumor suppressor genes (TSGs). Understanding the role of these concurrent TSG mutations can help elucidate resistance mechanisms and guide the development of more effective treatment approaches.

MATERIALS AND METHODS

We examined survival outcomes in 483 EGFR-mutant (mEGFR) patients from the GENIE BPC non-small-cell lung cancer (NSCLC) dataset. To understand the mutational landscape and clonal dynamics, whole exome sequencing (WES) was carried out on 48 tumor samples from 16 mEGFR patients at both baseline and post-relapse. A comprehensive gene panel was applied to 200 liquid biopsy samples obtained longitudinally from 25 patients to track clonal evolution.

RESULTS

mEGFR patients with co-occurring TSG mutations exhibited significantly worse outcomes. In the GENIE dataset, overall survival (OS) was shorter [51.11 versus 99.3 months; hazard ratio (HR) 1.8, confidence interval (CI) 1.22-2.75, P = 0.003] and progression-free survival (PFS) was reduced (9.83 versus 11.48 months; HR 1.4, CI 1.03-1.91, P = 0.026). WES analysis revealed 17 TSG mutations that were retained and showed clonal enrichment, particularly in early relapse (progression within 10 months of TKI initiation) or intermediate-stage relapse (relapse occurred between 10 and 20 months), indicated by increased variant allele frequency and their presence was strongly linked to early relapse. Longitudinal clonal studies further confirmed that TSG mutations co-occurring with mEGFR were often truncal, predominantly in early relapsers. Survival analysis using this subset of 17 TSGs showed significantly shorter OS (55.26 versus 99.3 months; HR 1.7, CI 1.12-2.65, P = 0.011) and PFS (9.67 versus 13.12 months; HR 1.5, CI 1.08-2.10, P = 0.013).

CONCLUSIONS

A set of 17 co-occurring TSG mutations has been identified as key biomarkers for early relapse in mEGFR lung adenocarcinoma. Longitudinal genomic monitoring, with a focus on clonal evolution, offers valuable insights that can inform personalized treatment strategies and potentially improve patient outcomes.

Intratumoral Fusobacterium nucleatum is associated with better cancer-specific survival in head and neck cancer patients

Background

The oral microbiome, particularly Fusobacterium nucleatum (Fn), has been implicated in head and neck cancers (HNC), influencing local immunity and Human Papillomavirus (HPV) status. Here, we evaluated the presence of Fn and its association with HPV infection, TERT promoter (TERTp) mutations, and patient outcomes.

Materials and Methods

We analyzed 94 formalin-fixed paraffin-embedded (FFPE) tumor tissues from HNC patients previously evaluated for TERTp mutations. Fn DNA was detected using droplet digital PCR (ddPCR), and HPV status was determined via p16 immunohistochemistry in pre-treatment samples. Associations between Fn presence, clinicopathological features, HPV, and TERTp mutation status were assessed.

Results

Tumors primarily originated from the oropharynx (70.2%) and oral cavity (29.8%). Tobacco and alcohol use were reported in 87.2% and 79.8% of cases, respectively. Fn was present in 59.6% of cases, with higher prevalence in oropharyngeal (62.1%) than oral cavity (53.6%) tumors. No significant associations were found between Fn and clinicopathological features, TERTp, or HPV status. However, patients with Fn positivity showed significantly improved cancer-specific survival (61.5% vs. 39.1%, p = 0.013), similar to HPV-positive patients (72.7% vs. 42.7%, p = 0.014).

Conclusion

The presence of Fusobacterium nucleatum in HNC correlates with longer survival, highlighting its potential as a prognostic marker.

Non-coding RNAs, a double-edged sword in breast cancer prognosis

Cancer is a rising issue worldwide, and numerous studies have focused on understanding the underlying reasons for its occurrence and finding proper ways to defeat it. By applying technological advances, researchers are continuously uncovering and updating treatments in cancer therapy. Their vast functions in the regulation of cell growth and proliferation and their significant role in the progression of diseases, including cancer. This review provides a comprehensive analysis of ncRNAs in breast cancer, focusing on long non-coding RNAs such as HOTAIR, MALAT1, and NEAT1, as well as microRNAs such as miR-21, miR-221/222, and miR-155. These ncRNAs are pivotal in regulating cell proliferation, metastasis, drug resistance, and apoptosis. Additionally, we discuss experimental approaches that are useful for studying them and highlight the advantages and challenges of each method. We then explain the results of these clinical trials and offer insights for future studies by discussing major existing gaps. On the basis of an extensive number of studies, this review provides valuable insights into the potential of ncRNAs in cancer therapy. Key findings show that even though the functions of ncRNAs are vast and undeniable in cancer, there are still complications associated with their therapeutic use. Moreover, there is an absence of sufficient experiments regarding their application in mouse models, which is an area to work on. By emphasizing the crucial role of ncRNAs, this review underscores the need for innovative approaches and further studies to explore their potential in cancer therapy.

Therapeutic innovations: targeting ROS production in AML with natural and synthetic compounds

Reactive oxygen species (ROS) play a dual role in the pathophysiology of acute myeloid leukemia (AML), functioning as both signaling molecules and agents of cellular damage. This review offers an in-depth analysis of ROS production in AML, highlighting their impact on essential cellular pathways that govern cell survival, proliferation, and apoptosis. It explores both natural and synthetic pharmacological agents that modulate ROS generation and enhance oxidative stress, assessing their therapeutic potential and the challenges they present in clinical practice. Additionally, the review identifies ROS-associated prognostic biomarkers that could enhance patient stratification and improve treatment outcomes in AML. Despite the promising potential of ROS-targeted therapies, significant challenges remain, such as the complexity of ROS dynamics, resistance mechanisms, and the influence of the tumor microenvironment. This review aims to shed light on current advancements and emphasize the need for further research to refine therapeutic strategies that leverage the ROS pathway in AML.

Molecular and immunohistochemical characterization of ERBB2 activating mutations in low-grade serous ovarian carcinoma

AIMS

Low-grade serous carcinoma (LGSC) of the ovary presents unique therapeutic challenges due to its resistance to platinum-based chemotherapies and a tendency to present at an advanced stage. Approximately 50% of LGSC possess activating mutations in KRAS, NRAS, and BRAF, a finding associated with better overall survival. However, many tumours lack obvious driver alterations against which to direct targeted treatment strategies, necessitating further investigation into molecular drivers of LGSC and their impact on clinical outcomes.

METHODS AND RESULTS

We conducted a retrospective analysis of 84 LGSC patients who underwent tumour-only targeted next-generation sequencing at our institution. Molecular data were correlated with clinical outcomes, HER2 immunohistochemistry, and supplemented with additional tumour sequencing data from the AACR GENIE cohort v15.1 (n = 295). Approximately 5% of LGSC cases across the combined cohort harboured activating alterations in ERBB2 (n = 17/369), which encodes the HER2 receptor tyrosine kinase. These alterations were mutually exclusive of other MAP kinase pathway mutations and included exon 20 insertions (n = 6), extracellular domain/transmembrane domain missense alterations (n = 4), and exon 16 skipping mutations (n = 7). ERBB2 exon 16 emerged as a mutational hotspot in LGSC when compared to other tumour types. Immunohistochemistry revealed variable HER2 expression patterns that were independent of ERBB2 mutational status. In our institutional cohort, patients with RAS/RAF mutant tumours (n = 38) showed better overall survival compared to RAS/RAF wildtype tumours (n = 35). No tumours in our internal cohort (n = 84) harboured ERBB2 amplifications.

CONCLUSION

As the landscape of HER2-directed therapies continues to evolve, these findings suggest that ERBB2 alterations and HER2 expression may represent a potential therapeutic target in LGSC.

Increased amounts of cell-free DNA released from a culture with a high content of cancer stem cells

Background

The study and characterization of cell-free DNA (cfDNA) has gained significant importance due to its clinical applications as a diagnostic and prognostic marker. However, it remains unclear whether all cell populations within a tumor or culture contribute equally to its release. This pioneering research analyzes the contribution of cancer stem cells (CSCs) in colon cancer cell lines to the amount of cfDNA released and its role in cellular transformation.

Methods

The CSC population derived from the SW480 colon cancer cell line was enriched using a non-adhesive culture system to assess the quantity and electrophoretic profile of the released cfDNA. Subsequently, in vitro transformation assays were conducted to compare the transforming capacity of the cfDNA obtained from enriched cultures with that from non-enriched cultures. Group differences were analyzed using analysis of variance (ANOVA), followed by post hoc interpretation with Tukey's test.

Results

Our study revealed that cultures with CSCs released greater amounts of cfDNA, displaying a distinct fragment profile. Additionally, cfDNA from different cellular origins influenced the transformation characteristics of NIH3T3 cells. This is the first demonstration of a link between CSC proportions and cfDNA release, suggesting that CSCs and microenvironmental conditions can affect cfDNA quantity and its potential to induce transformation.

Conclusion

These findings highlight the importance of cfDNA in carcinogenesis and its potential as a biomarker and therapeutic target, especially given the role of CSCs in drug resistance and tumor aggressiveness.

Long-term survival was achieved through multidisciplinary treatment of a patient with gallbladder carcinosarcoma accompanied by KRAS mutation: a case report and literature review

Carcinosarcoma of the gallbladder (CSGB) is an extremely rare subtype of primary gallbladder malignancy, which with a high rate of preoperative misdiagnosis due to its nonspecific clinical symptoms and imaging findings, as well as a high rate of recurrence within a short period of time after surgery, resulting in a very poor prognosis. Through a search of the medical literature, we found that there are few reports of CSGB receiving comprehensive treatments and achieving relatively good outcomes. Here, we report a rare case of CSGB with KRAS G12V mutation that achieved survival time of 32 months after receiving a combination of treatments including surgery, chemotherapy, radiotherapy, and immunotherapy, and we conducted a literature review for the disease with the aim of raising awareness of the disease.

Primary ocular, adnexal, and orbital rhabdomyosarcoma: A review

We review the primary orbital, ocular, and adnexal rhabdomyosarcoma (RMS) spectrum of tumors and describe its clinicoradiological and histopathological features, molecular updates, management protocols, outcomes, and challenges. Despite being a favorable site, the prognosis remains dismal for cases of relapsing, refractory, and metastatic orbital RMS. A wide heterogeneity of data exists in terms of survival rates and treatment regimens spread across various geographic locations and age groups. Molecular cytogenetics is a crucial factor in both the diagnosis and effective management of RMS. Novel targeted therapy may play an integral role in avoiding treatment-related morbidity and mortality. Large-scale studies are warranted to formulate standardized regimens and uniformity, especially for advanced and metastatic cases.

CAR T cells re-directed by a rationally designed human peptide tag demonstrate efficacy in preclinical models

Currently, only a few chimeric antigen receptor (CAR) T cell therapies have been approved by the Food and Drug Administration and European Medicines Agency for the treatment of B-cell malignancies. To enable broader application of the CAR T cell technology in other indications, improved control and flexible targeting of multiple tumor antigens are required. Here, we developed a novel adapter CAR (AdCAR) T cell platform for flexible targeting of multiple tumor antigens. This platform is based on a short peptide tag derived from an interdomain region of fibroblast growth factor receptor 2 (FGFR2), commonly mutated in cancer. To select AdCARs specific for mutated FGFR2-derived peptide tags, a multistep pooled screening approach in primary T cells was employed, incorporating MACS separation and next-generation sequencing. The resulting AdCAR was highly specific for the FGFR2-derived peptide tag. Using different in vitro and in vivo model systems, the activity of AdCAR T cells was shown to be strictly dependent on the presence of the adapter and corresponding target antigen. Moreover, AdCAR T cells could be redirected to different target antigens by the addition of respective adapter molecules (AM). Finally, in situ expression of functional AM in primary T cells under control of a drug-inducible promoter system was demonstrated, highlighting the potential for controlling the activity of AdCAR T cells by cellular micropharmacies.

Computational molecular insights into ibrutinib as a potent inhibitor of HER2-L755S mutant in breast cancer: gene expression studies, virtual screening, docking, and molecular dynamics analysis

Background

The proposed study integrates several advanced computational techniques to unravel the molecular mechanisms underlying breast cancer progression and drug resistance.

Methods

We investigated HER2-L755S mutation through a multi-step approach, including gene expression analysis, molecular docking, and molecular dynamics simulations.

Results and Discussion

By conducting a network-based analysis of gene expression data from breast cancer samples, key hub genes such as MYC, EGFR, CDKN2A, ERBB2, CDK1, E2F1, TOP2A, MDM2, TGFB1, and FOXM1 were identified, all of which are critical in tumor growth and metastasis. The study mainly focuses on the ERBB2 gene, which encodes the HER2 protein, and its common mutation HER2-L755S, associated with breast cancer and resistance to the drug lapatinib. The HER2-L755S mutation contributes to both tumorigenesis and therapeutic failure. To address this, alternative therapeutic strategies were investigated using combinatorial computational approaches. The stability and flexibility of the HER2-L755S mutation were evaluated through comparative molecular dynamics simulations over 1000 ns using Gromacs in the unbound (Apo) state. Virtual screening with Schrodinger Glide identified ibrutinib as a promising alternative to lapatinib for targeting the HER2-L755S mutant. Detailed docking and molecular dynamics simulations in the bound (Holo) state demonstrated that the HER2-L755S-ibrutinib complex exhibited higher binding affinity and lower binding energy, indicating more stable interactions compared to other complexes. MM-PBSA analysis revealed that the HER2-L755S-ibrutinib complex had more negative binding energy than the HER2-L755S-afatinib, HER2-L755S-lapatinib, and HER2-L755S-neratinib complexes, suggesting that ibrutinib forms the most stable complex with favorable binding interactions.

Conclusion

These results provide in-depth atomic-level insights into the binding mechanisms of these inhibitors, highlighting ibrutinib as a potentially effective inhibitor for the clinical treatment of breast cancer.

DriverMEDS: Cancer driver gene identification using mutual exclusivity from embeded features and driver mutation scoring

Efficiently identifying cancer driver genes plays a key role in the cancer development, diagnosis and treatment. Current unsupervised driver gene identification methods typically integrate multi-omics data into gene function networks and employ network embedding algorithms to learn gene features. Additionally, they consider mutual exclusivity and mutation frequency as crucial concepts in identifying driver genes. However, existing approaches neglect the possible important implications of mutual exclusivity in the embedding space. Furthermore, they simply assume that all driver genes exhibit high mutation frequencies. Fortunately, we explored the mutual exclusivity implanted in the learned features and have verified that the Euclidean distances between learned features are strongly related to the mutual exclusivity and they can reveal more information for the mutual exclusivity. Thus, we designed an unsupervised driver gene predicting framework DriverMEDS based on the above idea and a novel driver mutation scoring strategy. First, we design a feature clustering algorithm to generate gene modules. In each module, the Euclidean distances of learned features are used to calculate a module importance score for each gene based on the related mutual exclusivity. Then, following the fact that most of driver genes have intermediate mutation frequencies, a driver mutation scoring function is designed for each gene to optimize the existing mutation frequency scoring strategy. Finally, the weighted sum of the module importance score and the driver mutation score is used to prioritize the genes. The experiment results and analysis show that DriverMEDS could detect novel cancer driver genes and relevant function modules, and outperforms other five state-of-the-art methods for cancer driver identification.

Saikosaponin A Mediates the Anti-Acute Myeloid Leukemia Effect via the P-JNK Signaling Pathway Induced by Endoplasmic Reticulum Stress

Objective

This study aims to investigate the antitumor effects of saikosaponin A (SSA) on acute myeloid leukemia (AML) and elucidate its underlying mechanisms, particularly focusing on the endoplasmic reticulum stress (ERS)-mediated MAPK-p-JNK signaling pathway.

Methods

The inhibitory effects of SSA on the proliferation of AML cell lines K562 and HL60 were evaluated using CCK8 and EdU assays. Apoptotic effects induced by SSA were analyzed via flow cytometry. RNA sequencing was performed to identify differentially expressed genes and enriched signaling pathways. Western blot analysis was utilized to confirm the involvement of ERS and activation of the MAPK-p-JNK signaling pathway. Further validation of the potential mechanism of SSA-induced apoptosis was conducted using SP600125 and 4PBA. The in vivo anti-AML efficacy of SSA was assessed using a xenograft model.

Results

SSA exhibited significant inhibitory effects on the proliferation of AML cell lines K562 and HL60, with IC50 values at 12, 24, and 48 hours demonstrating time- and dose-dependency (19.84 μM, 17.86 μM, and 15.38 μM for K562; 22.73 μM, 17.02 μM, and 15.25 μM for HL60, respectively). Western blot analysis demonstrated that SSA induces apoptosis in AML cells through the mitochondrial apoptotic pathway. Transcriptomic profiling and Western blot analyses confirmed that SSA activates the ERS-mediated p-JNK signaling pathway to induce apoptosis in AML, a process that can be reversed by the addition of 4PBA or SP600125. Furthermore, SSA significantly reduced tumor volume and weight in a NOD-SCID mouse xenograft model without causing notable toxicity to the liver, kidneys, lungs, or heart, while also activating the ERS and p-JNK signaling pathways in vivo.

Conclusion

SSA induces apoptosis in AML cells by activating the ERS-mediated p-JNK signaling pathway, exhibiting significant anti-AML effects both in vitro and in vivo, accompanied by a favorable safety profile.

Prognostic factors influencing overall survival in stage IV EGFR-mutant NSCLC patients treated with EGFR-TKIs

BACKGROUND

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are the established first-line treatment for non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations, but survival advantages in advanced-stage cases remain modest and show interpatient variability. This study seeks to delineate real-world survival outcomes in stage IV EGFR-mutant NSCLC patients undergoing treatment with EGFR-TKIs and to identify independent prognostic factors impacting overall survival (OS). The findings are expected to be a reference for clinicians in managing advanced lung cancer patients.

METHODS

Clinical characteristics from advanced EGFR-mutant NSCLC patients who received EGFR-TKIs were retrospectively analyzed to investigate the association between clinical factors and overall survival.

RESULTS

The median OS was 40.60 months (95% confidence interval: 34.72-46.48 months), with expected 1-, 3-, and 5-year OS of 87.2%, 57.8%, and 34.0%, respectively. Patients exhibiting specific characteristics, such as being under 60 years old, having stage IVA disease, adenocarcinoma histology, no liver or brain metastases, negative for neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), cytokeratin fragment 19 (CYFRA 21 - 1), progastrin-releasing peptide (ProGRP), and those who received chemotherapy and radiotherapy exhibited significantly longer survival times compared to patients with the opposite characteristics (being 60 years or older, having stage IVB or IVC disease, non-adenocarcinoma histology, presence of liver or brain metastases, positive for CEA, NSE, ProGRP, CYFRA 21 - 1, and not receiving chemotherapy or radiotherapy) (P < 0.05). Cox univariate and multivariate analyses identified pathological type, liver metastasis, brain metastasis, NSE, CYFRA 21 - 1, EGFR-TKIs type, radiotherapy, and chemotherapy as independent prognostic factors for patients with stage IV NSCLC treated with EGFR-TKIs.

CONCLUSIONS

Pathological type, liver metastasis, brain metastasis, NSE, and CYFRA 21 - 1 were identified as independent risk factors for stage IV NSCLC patients treated with EGFR-TKIs, while chemotherapy and radiotherapy were determined to be independent protective factors. Taking icotinib or gefitinib, as opposed to osimertinib, was an independent risk factor for advanced NSCLC patients.

The epigenetic mechanisms involved in the treatment resistance of glioblastoma

Glioblastoma (GBM) is an aggressive malignant brain tumor with almost inevitable recurrence despite multimodal management with surgical resection and radio-chemotherapy. While several genetic, proteomic, cellular, and anatomic factors interplay to drive recurrence and promote treatment resistance, the epigenetic component remains among the most versatile and heterogeneous of these factors. Herein, the epigenetic landscape of GBM refers to a myriad of modifications and processes that can alter gene expression without altering the genetic code of cancer cells. These processes encompass DNA methylation, histone modification, chromatin remodeling, and non-coding RNA molecules, all of which have been found to be implicated in augmenting the tumor's aggressive behavior and driving its resistance to therapeutics. This review aims to delve into the underlying interactions that mediate this role for each of these epigenetic components. Further, it discusses the two-way relationship between epigenetic modifications and tumor heterogeneity and plasticity, which are crucial to effectively treat GBM. Finally, we build on the previous characterization of epigenetic modifications and interactions to explore specific targets that have been investigated for the development of promising therapeutic agents.