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1. A novel pH-dependent membrane peptide that binds to EphA2 and inhibits cell migration

   https://doi.org/10.7554/eLife.36645  

   Alves, Daiane S; Westerfield, Justin M; Shi, Xiaojun; Nguyen, Vanessa P; Stefanski, Katherine M; Booth, Kristen R; Kim, Soyeon; Morrell-Falvey, Jennifer; Wang, Bing-Cheng; Abel, Steven M; et al (September 2018, eLife)

   Misregulation of the signaling axis formed by the receptor tyrosine kinase (RTK) EphA2 and its ligand, ephrinA1, causes aberrant cell-cell contacts that contribute to metastasis. Solid tumors are characterized by an acidic extracellular medium. We intend to take advantage of this tumor feature to design new molecules that specifically target tumors. We created a novel pH-dependent transmembrane peptide, TYPE7, by altering the sequence of the transmembrane domain of EphA2. TYPE7 is highly soluble and interacts with the surface of lipid membranes at neutral pH, while acidity triggers transmembrane insertion. TYPE7 binds to endogenous EphA2 and reduces Akt phosphorylation and cell migration as effectively as ephrinA1. Interestingly, we found large differences in juxtamembrane tyrosine phosphorylation and the extent of EphA2 clustering when comparing TYPE7 with activation by ephrinA1. This work shows that it is possible to design new pH-triggered membrane peptides to activate RTK and gain insights on its activation mechanism. 

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2. Mapping Tyrosine Kinase Receptor Dimerization to Receptor Expression and Ligand Affinities

   https://doi.org/10.3390/pr7050288  

   Mamer, Spencer B.; Palasz, Alexandra A.; Imoukhuede, P. I. (May 2019, Processes)

   Tyrosine kinase receptor (RTK) ligation and dimerization is a key mechanism for translating external cell stimuli into internal signaling events. This process is critical to several key cell and physiological processes, such as in angiogenesis and embryogenesis, among others. While modulating RTK activation is a promising therapeutic target, RTK signaling axes have been shown to involve complicated interactions between ligands and receptors both within and across different protein families. In angiogenesis, for example, several signaling protein families, including vascular endothelial growth factors and platelet-derived growth factors, exhibit significant cross-family interactions that can influence pathway activation. Computational approaches can provide key insight to detangle these signaling pathways but have been limited by the sparse knowledge of these cross-family interactions. Here, we present a framework for studying known and potential non-canonical interactions. We constructed generalized models of RTK ligation and dimerization for systems of two, three and four receptor types and different degrees of cross-family ligation. Across each model, we developed parameter-space maps that fully determine relative pathway activation for any set of ligand-receptor binding constants, ligand concentrations and receptor concentrations. Therefore, our generalized models serve as a powerful reference tool for predicting not only known ligand: Receptor axes but also how unknown interactions could alter signaling dimerization patterns. Accordingly, it will drive the exploration of cross-family interactions and help guide therapeutic developments across processes like cancer and cardiovascular diseases, which depend on RTK-mediated signaling. 

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3. Mapping kinase-dependent tumor immune adaptation with multiplexed single-cell CRISPR screens

   https://doi.org/10.64898/2026.01.08.698516  

   Shi, Lingting; Giglio, Ross M; Cai, Qingyuan; Vaikunthan, Mathini; Hong, Justin; Naqvi, Abdullah; Milea, Marina; Khanshali, Hannah; Schoonen, Anna; Hou, Nicholas; et al (January 2026, bioRxiv)

   Abstract Immune dysfunction in cancer is enacted by multiple programs, including tumor cell-intrinsic responses to distinct immune subpopulations. A subset of these immune evasion programs can be systematically recapitulated through direct tumor-immune interactionsin vitro. Here, we present an integrated, high-throughput single-cell CRISPR screening framework focused on the protein kinome for mapping the tumor-intrinsic regulation of T cell-driven immune pressure in glioblastoma (GBM). We combine pooled CRISPR interference and activation (CRISPRi/a) with immune-matched NY-ESO-1 antigen-specific allogeneic GBM-T cell co-culture and massively multiplexed single-cell transcriptomics to systematically quantify how genetic perturbation reshapes baseline tumor state and adaptive responses across graded effector-to-target ratios. We further leverage deep generative models for analyzing pooled CRISPR screens to decipher the effects of genetic perturbations on the mechanisms of tumor resistance. This framework resolves distinct modules of immune evasion and survival, including the regulation of the antigen-presentation machinery, interferon/NF-κB signaling, oxidative stress resilience, and checkpoint/cytokine programs, while identifying perturbations that reroute the continuous tumor transcriptional trajectory induced by T cell engagement. A secondary chemical screen in patient-derived GBM cultures identified putative kinase targets of immune evasion phenotypes (e.g., EPHA2 and PDGFRA), whose inhibition leads to the blockade of evasive programs and enhances T cell-mediated GBM killing. Together, this workflow provides a scalable blueprint for comprehensive charting of the genetic control of tumor-immune interactions. 

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4. Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization

   https://doi.org/10.1038/s41467-021-25248-5  

   Agnew, Christopher; Ayaz, Pelin; Kashima, Risa; Loving, Hanna S.; Ghatpande, Prajakta; Kung, Jennifer E.; Underbakke, Eric S.; Shan, Yibing; Shaw, David E.; Hata, Akiko; et al (December 2021, Nature Communications)

   Abstract Upon ligand binding, bone morphogenetic protein (BMP) receptors form active tetrameric complexes, comprised of two type I and two type II receptors, which then transmit signals to SMAD proteins. The link between receptor tetramerization and the mechanism of kinase activation, however, has not been elucidated. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS), small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations, combined with analysis of SMAD signaling, we show that the kinase domain of the type I receptor ALK2 and type II receptor BMPR2 form a heterodimeric complex via their C-terminal lobes. Formation of this dimer is essential for ligand-induced receptor signaling and is targeted by mutations in BMPR2 in patients with pulmonary arterial hypertension (PAH). We further show that the type I/type II kinase domain heterodimer serves as the scaffold for assembly of the active tetrameric receptor complexes to enable phosphorylation of the GS domain and activation of SMADs. 

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5. Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer

   https://doi.org/10.1073/pnas.2206588119  

   Brown, Benjamin P.; Zhang, Yun-Kai; Kim, Soyeon; Finneran, Patrick; Yan, Yingjun; Du, Zhenfang; Kim, Jiyoon; Hartzler, Abigail Leigh; LeNoue-Newton, Michele L.; Smith, Adam W.; et al (July 2022, Proceedings of the National Academy of Sciences)

   Oncogenic mutations within the epidermal growth factor receptor (EGFR) are found in 15 to 30% of all non–small-cell lung carcinomas. The term exon 19 deletion (ex19del) is collectively used to refer to more than 20 distinct genomic alterations within exon 19 that comprise the most common EGFR mutation subtype in lung cancer. Despite this heterogeneity, clinical treatment decisions are made irrespective of which EGFR ex19del variant is present within the tumor, and there is a paucity of information regarding how individual ex19del variants influence protein structure and function. Herein, we identified allele-specific functional differences among ex19del variants attributable to recurring sequence and structure motifs. We built all-atom structural models of 60 ex19del variants identified in patients and combined molecular dynamics simulations with biochemical and biophysical experiments to analyze three ex19del mutations (E746_A750, E746_S752 > V, and L747_A750 > P). We demonstrate that sequence variation in ex19del alters oncogenic cell growth, dimerization propensity, enzyme kinetics, and tyrosine kinase inhibitor (TKI) sensitivity. We show that in contrast to E746_A750 and E746_S752 > V, the L747_A750 > P variant forms highly active ligand-independent dimers. Enzyme kinetic analysis and TKI inhibition experiments suggest that E746_S752 > V and L747_A750 > P display reduced TKI sensitivity due to decreased adenosine 5′-triphosphate K m . Through these analyses, we propose an expanded framework for interpreting ex19del variants and considerations for therapeutic intervention. 

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