ITK degradation to block T cell receptor signaling and overcome therapeutic resistance in T cell lymphomas

Interleukin-2-inducible T-cell kinase inhibition to block NF-κB signaling exerts anti-tumor effects and enhances chemotherapy in NK/T-cell lymphoma

Natural killer/T-cell lymphoma (NKTCL) is a highly aggressive non-Hodgkin lymphoma. Relapsed/refractory (R/R) NKTCL patients have dismal prognosis and lack effective treatments, novel therapeutics are urgently needed. Here we found interleukin-2-inducible T-cell kinase (ITK) expression was elevated in NKTCL cells and patient tumors. And higher ITK expression was associated with worse clinical outcomes. In vitro ITK knockdown inhibited NKTCL cell growth, induced apoptosis, cell cycle arrest and impaired its colony-forming ability while ITK overexpression accelerated cell proliferation. In vivo ITK knockdown greatly impeded lymphoma growth in mouse model, indicating it as a potential therapeutic target. Mechanistically, ITK knockdown inhibited NKTCL cell growth by attenuating oncogenic NF-κB signaling, which is revealed by transcriptomic profiling and further validated by in vitro assays and in vivo NKTCL models. Additionally, we showed that ITK inhibitors could inhibit NKTCL cell proliferation, promote apoptosis and suppressed tumor progression in NKTCL cell line-derived xenograft (CDX) model. Furthermore, we established a patient-derived xenograft (PDX) model from a NKTCL patient refractory to prior anti-PD-1 and asparaginase containing therapy. The primary cells from this patient highly expressed ITK and were responsive to ITK inhibitor. And ITK inhibitor effectively repressed tumor progression in PDX model. Finally, we found ITK inhibition improved the response of NKTCL cell lines to chemotherapy and overcome chemotherapy resistance in primary cells. Collectively, our results demonstrated that ITK served as an oncogene in NKTCL and represented a novel therapeutic vulnerability to be targeted or in combination with chemotherapy drugs for this disease.

Workflow for E3 Ligase Ligand Validation for PROTAC Development

Proteolysis targeting chimeras (PROTACs) have gained considerable attention as a new modality in drug discovery. The development of PROTACs has been mainly focused on using CRBN (Cereblon) and VHL (Von Hippel-Lindau ligase) E3 ligase ligands. However, the considerable size of the human E3 ligase family, newly developed E3 ligase ligands, and the favorable druggability of some E3 ligase families hold the promise that novel degraders with unique pharmacological properties will be designed in the future using this large E3 ligase space. Here, we developed a workflow aiming to improve and streamline the evaluation of E3 ligase ligand efficiency for PROTAC development and the assessment of the corresponding "degradable" target space using broad-spectrum kinase inhibitors and the well-established VHL ligand VH032 as a validation system. Our study revealed VH032 linker attachment points that are highly efficient for kinase degradation as well as some of the pitfalls when using protein degradation as a readout. For instance, cytotoxicity was identified as a major mechanism leading to PROTAC- and VHL-independent kinase degradation. The combination of E3 ligase ligand negative controls, competition by kinase parent compounds, and neddylation and proteasome inhibitors was essential to distinguish between VHL-dependent and -independent kinase degradation events. We share here the findings and limitations of our study and hope that this study will provide guidance for future evaluations of new E3 ligase ligand systems for degrader development.

Covalent targeting of splicing in T cells

Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and extensive ITK mRNA alternative splicing. We further introduce the most comprehensive list to date of proteins involved in splicing and leverage cysteine- and protein-directed activity-based protein profiling with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.

The application of PROTACs in immune-inflammation diseases

Immune-inflammatory diseases are a class of conditions with high prevalence that severely impact the quality of life. Current treatment strategies include immunosuppressants, glucocorticoids, and monoclonal antibodies. However, these approaches have certain limitations, such as poor membrane permeability, immunogenicity, and the requirement for injection in large molecule drugs. Small molecule compounds, on the other hand, suffer from issues like poor selectivity, inability to inhibit non-enzymatic functions, and biological compensation. These factors constrain the effectiveness of current therapeutic strategies in immune-inflammatory diseases. As a novel small molecule drug development technology, proteolysis-targeting chimeras (PROTACs) regulate protein levels by inducing interactions between target proteins and E3 ubiquitin ligases, leading to the selective degradation of target proteins. This technology has already shown promising therapeutic effects in the treatment of immune-inflammatory diseases. This review aims to comprehensively summarize the application of PROTAC technology in the field of immune inflammation and provide insights into its potential in treating immune-inflammatory diseases.

Recent insights of PROTAC developments in inflammation-mediated and autoimmune targets: a critical review

According to the mounting evidence in the literature, pro-inflammatory mediators/targets activate multiple signalling pathways to trigger illnesses that are ultimately responsible for acute pain, chronic inflammatory diseases, and several auto-immune disorders. Conventional drugs have been ruled out since proteolysis-targeting chimeras (PROTACs) are poised to overcome the limitations of traditional therapies. These heterobifunctional molecules help to degrade the targeted proteins of interest through ubiquitination. This review encompasses current and future aspects of PROTACs in inflammation-mediated and autoimmune targets. Different key points are highlighted and discussed, such as why PROTACs are preferred in this disease area, drawbacks and lessons learnt from the past, the role of linkers in establishing crucial degradation, in vitro findings, pharmacokinetics, in silico parameters, limitations of PROTACs in clinical settings, and future outcomes.

Comprehensive analysis of single cell and bulk RNA sequencing reveals the heterogeneity of melanoma tumor microenvironment and predicts the response of immunotherapy

BACKGROUND

Tumor microenvironment (TME) heterogeneity is an important factor affecting the treatment response of immune checkpoint inhibitors (ICI). However, the TME heterogeneity of melanoma is still widely characterized.

METHODS

We downloaded the single-cell sequencing data sets of two melanoma patients from the GEO database, and used the "Scissor" algorithm and the "BayesPrism" algorithm to comprehensively analyze the characteristics of microenvironment cells based on single-cell and bulk RNA-seq data. The prediction model of immunotherapy response was constructed by machine learning and verified in three cohorts of GEO database.

RESULTS

We identified seven cell types. In the Scissor+ subtype cell population, the top three were T cells, B cells and melanoma cells. In the Scissor- subtype, there are more macrophages. By quantifying the characteristics of TME, significant differences in B cells between responders and non-responders were observed. The higher the proportion of B cells, the better the prognosis. At the same time, macrophages in the non-responsive group increased significantly. Finally, nine gene features for predicting ICI response were constructed, and their predictive performance was superior in three external validation groups.

CONCLUSION

Our study revealed the heterogeneity of melanoma TME and found a new predictive biomarker, which provided theoretical support and new insights for precise immunotherapy of melanoma patients.

Covalent Targeting of Splicing in T Cells

Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide chemical probe EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and availability of functional mRNA pools that can be depleted due to extensive alternative splicing. We further introduce a comprehensive list of proteins involved in splicing and leverage both cysteine- and protein-directed activity-based protein profiling (ABPP) data with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in primary human T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.