Systematic inference of enzyme activity in human tumors is key to understanding cancer progression and resistance to therapy. However, standard protein or transcript abundances are blind to the activity status of the measured enzymes, regulated, for example, by active-site amino acid mutations or post-translational protein modifications. Current methods for activity-based proteome profiling (ABPP), which combine mass spectrometry (MS) with chemical probes, quantify the fraction of enzymes that are catalytically active. Here, we describe depletion-dependent ABPP (dd-ABPP) combined with automated SWATH/DIA-MS, which simultaneously determines three molecular layers of studied enzymes: i) catalytically active enzyme fractions, ii) enzyme and background protein abundances, and iii) context-dependent enzyme-protein interactions. We demonstrate the utility of the method in advanced lung adenocarcinoma (LUAD) by monitoring nearly 4000 protein groups and 200 serine hydrolases (SHs) in tumor and adjacent tissue sections routinely collected for patient histopathology. The activity profiles of 23 SHs and the abundance of 59 proteins associated with these enzymes retrospectively classified aggressive LUAD. The molecular signature revealed accelerated lipoprotein depalmitoylation via palmitoyl(protein)hydrolase activities, further confirmed by excess palmitate and its metabolites. The approach is universal and applicable to other enzyme families with available chemical probes, providing clinicians with a biochemical rationale for tumor sample classification.

Pancreatic ductal adenocarcinoma (PDAC) is an age-associated malignancy closely linked to the extracellular matrix (ECM). However, the impact of age-related ECM changes in the normal pancreas on PDAC progression remains unclear. Here, we find that increased linear ECM alignment in normal pancreatic tissues from aged PDAC patients is associated with PDAC progression and worse outcomes. Furthermore, serum methylmalonic acid (MMA) levels are elevated in aged PDAC patients and associated with increased linear ECM alignment in normal pancreatic tissues of PDAC patients. Functionally, MMA promotes LOXL2 expression in pancreatic stellate cells (PSCs), increases linear ECM alignment in normal pancreatic tissues, and facilitates tumor progression. Mechanistically, MMA upregulates KLF10, which forms a transcriptional complex with SP1 to enhance LOXL2 expression in PSCs. Our study demonstrates the role of MMA-induced LOXL2+PSCs in ECM remodeling, thus serving as a potential therapeutic target to mitigate PDAC progression in aged patients. Schematic diagram showing the molecular mechanism by which MMA-induced LOXL+PSCs promote PDAC progression in the aging pancreas. In aged individuals, elevated levels of MMA in the blood induce the activation of the KLF10/SP1‒LOXL2 axis in PSCs to increase linear ECM alignment. Following the initiation of pancreatic cancer, this increased linear ECM alignment leads to increased tumor invasion into surrounding tissues, resulting in a greater proportion of stage T3/T4 tumors and a greater incidence of LVI and PNI in aged patients, ultimately leading to poorer outcomes (This schematic was created with www.figdraw.com ,export id: PRPRS4e268).

Evolutionary cancer therapy (ECT) delays or forestalls the progression of metastatic cancer by adjusting treatment based on individual patient and disease characteristics. Clinical implementation of ECT can improve patient outcomes but faces technical and cultural challenges. To address those, we propose a systems approach incorporating systems modeling, problem structuring, and stakeholder engagement. This approach identifies and addresses barriers to implementation, ensuring the feasibility of ECT in clinical practice and enabling better metastatic cancer care.

The lack of curative therapies for acute myeloid leukaemia (AML) remains an ongoing challenge despite recent advances in the understanding of the molecular basis of the disease. Here we identify the WNK1-OXSR1/STK39 pathway as a previously uncharacterised dependency in AML. We show that genetic depletion and pharmacological inhibition of WNK1 or its downstream phosphorylation targets OXSR1 and STK39 strongly reduce cell proliferation and induce apoptosis in leukaemia cells in vitro and in vivo. Furthermore, we show that the WNK1-OXSR1/STK39 pathway controls mTORC1 signalling via regulating amino acid uptake through a mechanism involving the phosphorylation of amino acid transporters, such as SLC38A2. Our findings underscore an important role of the WNK1-OXSR1/STK39 pathway in regulating amino acid uptake and driving AML progression.

The over-activation of oncogenes is a critical genetic event in the development and progression of solid malignancies. Gene amplification and specific mutations represent the prominent mechanisms that convert proto-oncogenes into their active, oncogenic forms. C-myc oncogene (gene locus: 8q24.21) regulates crucial cell and tissue functions, whereas its deregulation is implicated in carcinogenesis. Our research aimed to investigate the impact C-myc numerical imbalances on a series of laryngeal squamous cell carcinomas (LSCCs) characterized by different clinic-pathological features.

Disruptions in the circadian rhythm are linked to various diseases. The clock gene DEC1 is related to the progression and recurrence of various types of cancer; however, its role in colorectal cancer has not been determined. Therefore, we aimed to evaluate the significance of DEC1 expression level in colorectal cancer and its relationship with prognosis.

Nasopharyngeal carcinoma (NPC) is a virally associated epithelial malignancy with a high prevalence in East Asia. While Epstein-Barr virus (EBV) infection is a well-established risk factor, the role of host immune-related genetic variants remains insufficiently understood. Interleukin-12 (IL-12), a key immunoregulatory cytokine, is essential for EBV-specific T-cell responses, however, the impact of IL-12A gene polymorphisms on NPC susceptibility remains unknown.

Colorectal cancer (CRC) is a leading cause of cancer-related deaths, often due to liver metastases. Neoantigen-based immunotherapy has shown promise in clinical trials of solid tumors, including CRC. However, the immunogenic factors of neoantigens and their optimal selection in metastatic tumors are not well understood. Therefore, this study aimed to identify the relationship between tumor mutation burden and immunogenicity of neoantigens in CRCs and metastatic CRCs and evaluate the changes in immunogenic neoantigens between the primary and metastatic lesions in metastatic CRCs.

Triple-negative breast cancer (TNBC) is an aggressive malignancy with few available targeted therapies. In this study, we examined the predictive power of several biomarkers, comprising the IMmunotherapy Against GastrIc Cancer (IMAGiC) model, PD-L1 combined positive score (CPS), intra-tumoral tumor-infiltrating lymphocytes (iTILs), and stromal TILs (sTILs), in an Asian population of patients with metastatic TNBC treated with immunotherapy.

To investigate the effects of acyclic retinoid (ACR) on v-raf murine sarcoma viral oncogene homolog BV600E (BRAFV600E)-mutant melanoma cells and its potential to overcome vemurafenib resistance by targeting the mitogen-activated protein kinase (MAPK)/phosphoinositide 3-kinase (PI3K)/AKT serine/threonine kinase 1 (AKT)/mammalian target of rapamycin (mTOR) pathways.

The poor prognosis of triple-negative breast cancer (TNBC) is largely due to the lack of targeted therapies, as a result of the absence of estrogen, progesterone, and HER2 receptors. Our previous studies highlighted Del-1 as a potential therapeutic target and biomarker for TNBC. This study further explores molecules regulated by Del-1 through transcriptomic analysis.

Our study was designed to assess whether paired normal-tumour testing increased access to targeted therapy, clinical trials and influenced cancer screening recommendations given to patients and their families.

Chimeric antigen receptor T (CAR-T) cell therapy is under clinical investigation in patients with metastatic triple-negative breast cancer (TNBC). However, the identification of targetable antigens remains a high priority to avoid toxicity and prevent tumor escape.

Liquid biopsies using circulating tumour DNA (ctDNA) have emerged as an alternative to conventional biopsies. They can be used to aid in diagnosing and selecting an agent for treatment and can possibly be used to monitor disease response to treatment. In this report, we present a patient who initially presented with lower abdominal pain. Imaging showed extensive retroperitoneal lymphadenopathy and lymph node biopsy demonstrated poorly differentiated carcinoma. Further workup did not reveal a primary lesion, but his genetic analysis revealed a BRAF V600E mutation and CD274 amplification which was used to guide treatment of the adenocarcinoma as a melanoma of unknown primary. He was initiated on ipilimumab and nivolumab and his ctDNA levels showed rapid improvement. After treatment was stopped due to adverse events, he was monitored via ctDNA, with an increase prompting repeat imaging that demonstrated enlargement of his lesions prompting a resumption of treatment.

The long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1) and microRNA-145-5p (miR-145) axis play a pivotal role in regulating drug resistance, apoptosis and senescence in non-small cell lung cancer (NSCLC). MALAT1 drives drug resistance by suppressing miR-145 and activating MUC1, thereby inhibiting ferroptosis; however, its precise role in regulating ferroptosis in NSCLC remains unclear. Therefore, we propose a computational modelling approach to unravel the impact of the MALAT1/miR-145 axis on ferroptosis and drug resistance, to identify potential therapeutic strategies that promote ferroptosis. Using Boolean logic and a stochastic updating scheme, we developed and validated a robust regulatory model that encompasses ferroptosis, apoptosis, senescence and drug resistance pathways. The model, based on extensive literature and validated through gain- and loss-of-function perturbations, demonstrated strong alignment with observed clinical data that were not included in its construction. Our analysis identified three previously unreported feedback loops, miR-145/Wip1/p53, miR-145/Myc/MALAT1 and miR-145/MUC1/BMI1, establishing miR-145 as a central regulator in NSCLC. Perturbations targeting MALAT1 and wild-type p53-induced phosphatase 1 (Wip1) revealed potential therapeutic opportunities, with miR-145 activation emerging as a promising strategy to induce ferroptosis and overcome drug resistance. These findings highlight the MALAT1/miR-145 axis as a transformative therapeutic target, presenting a computational foundation to advance NSCLC treatment strategies.

NR2F6 is an orphan nuclear receptor with dual tumorigenic activity in the immune system and tumor cells, playing an essential role in tumor differentiation and immunity. This study aimed to investigate the expression level of NR2F6 in various tumors and its effect on neuroblastoma (NB).

Combined hepatocellular carcinoma-cholangiocarcinoma (HCC-CCA) is a rare liver tumor comprising histologic features of both HCC and CCA. Due to its heterogeneous nature, treatment of combined HCC-CCA is a significant clinical challenge and prognosis remains poor. Therefore, further understanding of the tumor biology underlying the individual subtypes of this mixed tumor is required to improve treatment stratification and optimize treatment strategies. This study sought to identify altered epigenetic regulation and gene expression patterns in the individual components of combined HCC-CCA. Formalin fixed paraffin embedded (FFPE) tumor specimens from 9 patients diagnosed with combined HCC-CCA were utilized in this study. Hematoxylin and eosin (H&E) staining was performed for each sample, and regions representative of the individual HCC and CCA components were delineated. Adjacent unstained slides were cut and dissected to separate HCC and CCA components. DNA and RNA extraction was performed for each sample for DNA methylation (n = 7 HCC and 7 CCA) and gene expression (n = 7 HCC and 8 CCA) profiling via reduced representation bisulfite sequencing (RRBS) and RNA-seq, respectively. Samples did not cluster by tumor type when comparing genome-wide DNA methylation or gene expression patterns. Of the 5 patients with DNA methylation data available for both subtypes, 4 clustered by patient as opposed to cancer subtype, suggesting similar epigenetic regulatory patterns arising from development in the same microenvironment and genetic background. Differential analysis resulted in the identification of 57 differentially expressed genes (DEGs) and 808 differentially methylated regions (DMRs) between the HCC and CCA subtypes. Genes associated with DMRs were associated with Wnt signaling, voltage-gated channels, metal binding, and cellular regulation. Finally, increased expression of several genes previously implicated in tumor aggressiveness, prognosis, and treatment responses were identified. These results highlight the potential importance of accounting for underlying HCC and CCA tumor biology when determining the optimal course of treatment for this deadly disease.

Delineating the mechanisms that control the movement of cells is central to understanding diverse physiological and pathophysiological processes. The transcriptional coactivator YAP is important during development and associated with cancer metastasis. Here, we found that YAP promoted cell migration by modulating a Rho family guanosine triphosphatase (GTPase) switch involving Rac1 and RhoA, which are key regulators of cytoskeletal dynamics. YAP transcriptionally transactivated the gene encoding the Rac1 guanine nucleotide exchange factor TRIO by directly binding to its intronic enhancer. This led to the activation of Rac1 and inhibition of RhoA, which increased cell migration and invasion in vitro and in vivo. This YAP-dependent program was observed across many cell types, including human breast epithelial cells and astrocytes, but it was particularly enhanced in a patient-specific manner in glioblastoma (GBM), the most common malignant brain tumor. Additionally, YAP-TRIO signaling activated STAT3, a transcription factor implicated in invasive growth in cancer, suggesting potential for cross-talk with this pathway to exacerbate invasive behavior. Clinically, hyperactivation of YAP, TRIO, and STAT3 gene signatures in GBM were associated with poor survival outcomes in patients. Our findings suggest that the YAP-TRIO-Rho-GTPase signaling network regulates invasive cell spread in both physiological and pathological contexts.

This study aims to evaluate the efficacy of chemotherapy and optimize treatment strategies for patients with advanced ovarian cancer.

This study aims to investigate metabolic reprogramming heterogeneity in hepatocellular carcinoma (HCC) cells and identify novel therapeutic targets for HCC treatment. Single-cell RNA sequencing data from public databases were used to analyze the TME of HCC and reveal the characteristics of different cell subsets, including mononuclear phagocytes, epithelial cells, endothelial cells, NK/T cells, B cells, and unknown cells. The analysis revealed that these cell subsets play their own unique roles in tumor progression and immune escape. Analysis of copy number variations (CNVs) was performed on tumor-derived epithelial cells, with the epithelial cells in Cluster 3 subgroup showing the highest CNV levels. Gene Ontology (GO) enrichment analysis revealed that these cell subsets were involved in a variety of biological processes such as immune response, cell communication, and metabolic pathways, which were consistent with their functional roles. Pseudotemporal analysis further delineated the malignant trajectory of HCC cells, with Cluster 3 exhibiting enhanced phosphatidylinositol metabolism, suggesting a critical role for metabolic reprogramming in tumor invasion and proliferation. Furthermore, a diagnostic model incorporating metabolic reprogramming-associated gene signatures was established, which effectively distinguished HCC from normal tissues. Among these signatures, splicing factor 3a subunit 3 (SF3A3) was identified as both diagnostic and independent prognostic biomarker. Mechanistically, SF3A3 knockdown in HCC cell lines significantly suppressed proliferation, migration, PI3K/AKT signaling, and EMT marker expression, thereby demonstrating its role in driving HCC aggressiveness. In conclusion, these findings elucidate novel molecular characteristics of HCC based on metabolic reprogramming, while establishing SF3A3 as a promising multi-faceted target for HCC diagnosis, prognostic assessment, and therapeutic intervention.