The P21 activated kinases (PAK) are frequently dysregulated in cancer and have central roles in oncogenic signalling, prompting the development of PAK inhibitors (PAKi) as anticancer agents. However, such compounds have not reached clinical use because, at least partially, there is a limited mechanistic understanding of their mode of action. Here, we aimed to characterize functional and molecular responses to PAKi (PF-3758309, FRAX-486 and IPA-3) in multiple acute myeloid leukaemia (AML) models to gain insights on the biochemical pathways affected by these inhibitors in this disease and identify determinants of response in patient samples.
We mined phosphoproteomic datasets of primary AML, and used proteomics and phosphoproteomics to profile PAKi impact in immortalized (P31/Fuj and MV4-11), and primary AML cells from 8 AML patients. These omics datasets were integrated with gene dependency data to identify which proteins targeted by PAKi are necessary for the proliferation of AML. We studied the effect PAKi on cell cycle progression, proliferation, differentiation and apoptosis. Finally, we used phosphoproteomics data as input for machine learning models that predicted ex vivo response in two independent datasets of primary AML cells (with 36 and 50 cases, respectively) to PF-3758309 and identify markers of response.
We found that PAK1 activation- measured from phosphoproteomics data- was predictive of poor prognosis in primary AML cases. PF-3758309 was the most effective PAKi in reducing proliferation and inducing apoptosis in AML cell lines. In cell lines and primary cells, PF-3758309 inhibited PAK, AMPK and PKCA activities, reduced c-MYC transcriptional activity and the expression of ribosomal proteins, and targeted the FLT3 pathway in FLT3-ITD mutated cells. In primary cells, PF-3758309 reduced STAT5 phosphorylation at Tyr699. Functionally, PF-3758309 reduced cell-growth, induced apoptosis, blocked cell cycle progression and promoted differentiation in a model-dependent manner. ML modelling accurately classified primary AML samples as sensitive or resistant to PF-3758309 ex vivo treatment, and highlighted PHF2 phosphorylation at Ser705 as a robust response biomarker.
In summary, our data define the proteomic, molecular and functional responses of primary and immortalised AML cells to PF-3758309 and suggest a route to personalise AML treatments based on PAK inhibitors.
© 2025. The Author(s).

Abstract Patients with GATA2 deficiency are predisposed to developing myelodysplastic syndrome (MDS), which can progress to acute myeloid leukemia (AML). This progression is often associated with the acquisition of additional cytogenetic and somatic alterations. Mutations in SETBP1 and ASXL1 genes are frequently observed in pediatric GATA2 patients, but their roles in disease progression remain poorly understood. Genome editing of induced pluripotent stem cells (iPSCs) enabled precise reconstruction of mutation combinations found in patients. Here we developed a human hiPSC-based model to study the impact of SETBP1 and ASXL1 mutations in context of GATA2 deficiency. We show that germline heterozygous GATA2 mutation alone showed no significant effect on myeloid development, while the addition of SETBP1 and ASXL1 mutations impaired myelopoiesis, resulting in monocytopenia. We identified a key role of the SETBP1 mutation in promoting chromatin remodeling near genes involved in myeloid neoplasms, which likely initiated the blockage of myeloid differentiation observed in vitro. Motif analysis of more accessible chromatin regions in the SETBP1 and SETBP1/ASXL1 mutant background highlighted an enrichment for MEIS1, PU.1, RUNX1, and HOXA9, implicating these factors in the disease progression. Our study establishes a novel humanized model system for studying GATA2 deficiency. We demonstrate that SETBP1 mutations act as a primary driver in hematopoietic impairment, providing insights that may inform future therapeutic strategies for patients progressing to MDS/AML

Genetic variants in Leucine-rich Repeat Kinase 2 ( LRRK2) gene have been linked to Parkinson’s disease (PD) and are also associated with inflammatory bowel diseases (IBD), specifically Crohn’s disease (CD), a transmural inflammation that can affect the entire length of the gastrointestinal tract and is commonly seen in the ileum 1 . In ileal CD, defects in specialized intestinal epithelial cells known as Paneth cells are believed to drive disease pathogenesis 2,3 . Paneth cells contribute to mucosal defense by secreting antimicrobial peptides including lysozyme and to the maintenance of intestinal stem cells by secreting growth factors. A previous article published by Zhang et al 4 in Nature Immunology identified a key role for LRRK2 in selective sorting and secretion of lysozyme in Paneth cells. However, after extended analyses, we find that LRRK2 is not required for lysozyme expression in the murine gut and is not expressed in either murine or human Paneth cells.

There are immunological consequences to the method by which neutrophils undergo cell death. Neutrophil apoptosis, called silent death, leads to the resolution of inflammation, while NETosis deepens and prolongs the inflammatory response and is associated with a worse prognosis of severe infections, e.g., sepsis. Besides nociceptive inhibition, local anaesthetics modulate leukocyte functions, even at low, clinically relevant concentrations. There is currently no data on ropivacaine NETosis, and this study aimed to evaluate the impact of clinical concentrations of ropivacaine (0.0007, 0.007 and 1.4 mmol/L) and lidocaine (0.002, 0.02 and 4 mmol/L) on apoptosis and NETosis of adult peripheral blood neutrophils after 2 h of incubation. Neutrophil identification, apoptosis and NETosis were evaluated by flow cytometry using forward and side scatter characteristics and fluorescent labelling: CD15 for neutrophils identification; Annexin V and propidium iodide for apoptosis and citrullinated histone H3 and myeloperoxidase for NETosis. Lidocaine (4 mmol/L) and ropivacaine (1.4 mmol/L) induced early apoptosis in resting but not in stimulated neutrophils. Low doses of ropivacaine (0.0007 and 0.007 mmol/L) decreased the number of late apoptotic neutrophils, and the lowest dose slightly increased their viability. None of the drugs induced NETosis in resting neutrophils but decreased NETosis at clinical concentrations compared to PMA-stimulated 4 mM lidocaine, PMA-stimulated control, and 1.4 mM ropivacaine. The effect of lidocaine and ropivacaine on apoptosis and NETosis depended on neutrophil stimulation and drug concentrations. Ropivacaine tends to be cytoprotective at concentrations observed in plasma under local anaesthesia. Lidocaine enhanced NETosis at high concentration only in stimulated neutrophils. Thus, both drugs have the ability to change the course of inflammation.
© 2023. The Author(s).

Metastasis is the principal cause of cancer treatment failure and an area of dire diagnostic needs. Colorectal cancer metastases to the liver (CRCLMs) are predominantly classified into desmoplastic and replacement based on their histological growth patterns (HGPs). Desmoplastic responds well to current treatments, while replacement HGP has a poor prognosis with low overall survival rates.
We hypothesised that complex cellular response underlying HGPs may be reflected in the proteome of circulating extracellular vesicles (EVs). EV proteomics data was generated through LC-MS/MS and analysed with Maxquant and Perseus. To validate the S100A9 signature, ELISA was performed, and IHC and IF were conducted on tissue for marker detection and colocalization study.
Plasma EV proteome signature distinguished desmoplastic from the replacement in patients with 22 differentially expressed proteins, including immune related markers. Unsupervised PCA analysis revealed clear separation of the two lesions. The marker with the highest confidence level to stratify the two HGPs was S100A9, which was traced in CRCLM lesions and found to colocalize with macrophages and neutrophils. EV-associated S100A9 in plasma may reflect the innate immunity status of metastatic lesions and their differential therapeutic responses.
Plasma EV-derived S100A9 could be useful in personalising therapy in patients with CRCLM.
© 2023. The Author(s).