Intracellular Signaling Networks Research Articles

Septins: Structural Insights, Functional Dynamics, and Implications in Health and Disease.

Septins are a class of proteins with diverse and vital roles in cell biology. Structurally, they form hetero-oligomeric complexes and assemble into filaments, contributing to the organization of cells. These filaments act as scaffolds, aiding in processes like membrane remodeling, cytokinesis, and cell motility. Functionally, septins are essential to cell division, playing essential roles in cytokinetic furrow formation and maintaining the structural integrity of the contractile ring. They also regulate membrane trafficking and help organize intracellular organelles. In terms of physiology, septins facilitate cell migration, phagocytosis, and immune responses by maintaining membrane integrity and influencing cytoskeletal dynamics. Septin dysfunction is associated with pathophysiological conditions. Mutations in septin genes have been linked to neurodegenerative diseases, such as hereditary spastic paraplegias, underscoring their significance in neuronal function. Septins also play a role in cancer and infectious diseases, making them potential targets for therapeutic interventions. Septins serve as pivotal components of intracellular signaling networks, engaging with diverse proteins like kinases and phosphatases. By modulating the activity of these molecules, septins regulate vital cellular pathways. This integral role in signaling makes septins central to orchestrating cellular responses to environmental stimuli. This review mainly focuses on the human septins, their structural composition, regulatory functions, and implication in pathophysiological conditions underscores their importance in fundamental cellular biology. Moreover, their potential as therapeutic targets across various diseases further emphasizes their significance.

Navigating the landscape of the unfolded protein response in CD8+ T cells.

Endoplasmic reticulum stress occurs due to large amounts of misfolded proteins, hypoxia, nutrient deprivation, and more. The unfolded protein is a complex intracellular signaling network designed to operate under this stress. Composed of three individual arms, inositol-requiring enzyme 1, protein kinase RNA-like ER kinase, and activating transcription factor-6, the unfolded protein response looks to resolve stress and return to proteostasis. The CD8+ T cell is a critical cell type for the adaptive immune system. The unfolded protein response has been shown to have a wide-ranging spectrum of effects on CD8+ T cells. CD8+ T cells undergo cellular stress during activation and due to environmental insults. However, the magnitude of the effects this response has on CD8+ T cells is still understudied. Thus, studying these pathways is important to unraveling the inner machinations of these powerful cells. In this review, we will highlight the recent literature in this field, summarize the three pathways of the unfolded protein response, and discuss their roles in CD8+ T cell biology and functionality.

Synthetic strategy for the production of electrically polarized polyvinylidene fluoride-trifluoroethylene-co-polymer osseo-functionalized with hydroxyapatite scaffold.

The physiological mechanism of bone tissue regeneration is intricately organized and involves several cell types, intracellular, and extracellular molecular signaling networks. To overcome the drawbacks of autografts and allografts, a number of synthetically produced scaffolds have been manufactured by integrating ceramics, polymers, and their hybrid-composites. Considering the fact that natural bone is composed primarily of collagen and hydroxyapatite, ceramic-polymer composite materials seem to be the most viable alternative to bone implants. Here, in this experimental study, copolymer PVDF-TrFE has been amalgamated with HA ceramics to produce composite scaffolds as bone implants. In order to fabricate PVDF-TrFE-HA (polyvinylidene fluoride-trifluoroethylene-hydroxyapatite) composite scaffolds, solvent casting-particulate leaching technique was devised. Two scaffold specimens were produced, with different PVDF-TrFE and HA molar ratios (70:30 and 50:50), and then electrically polarized to observe the subsequent polarization impact on the tissue growth and the suppression of bacterial cell proliferation. Both the specimens underwent characterization to analyze their biocompatibility and bactericidal activities. The bacterial culture of Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus) bacteria on the composites was studied to understand the antibacterial characteristics. Moreover, MG63 cells cultured on these as-formed composites provided information about osteogenesis. Improved osteogenesis and antibacterial efficacy were observed on both the composites. However, the composite with 70 wt% PVDF-TrFE and 30 wt% HA showed a higher bactericidal effect as well as osteogenesis. It was found that PVDF-TrFE-HA-based biomaterials have the potential for bone tissue engineering applications.

Abstract 6212: A differential ligand-receptor network inference method to identify alterations in communication between myeloid cells and CD8 T cells in response to PancVAX neo-epitope peptide vaccine, anti-CTLA-4 and anti-PD-1 antibodies in a murine model of pancreatic ductal adenocarcinoma

Abstract Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly cancer with a low tumor mutational burden that leads to the generation of few neo-epitopes derived from mutated genes that can be recognized by cytotoxic T cells. The immunosuppressive microenvironment of PDAC comprises suppressive cell populations that include myeloid cells, cancer associated fibroblast subpopulations, and regulatory T cells that reduce T cell infiltration and cytotoxic function. We have developed a murine personalized cancer vaccine to enhance cytotoxic T cell function against PDAC, PancVAX (Kinkead et al, JCI Insight 2018). Survival benefit with PancVAX was dependent on the addition of immune checkpoint inhibitor (ICI) therapy to increase the number of cytotoxic CD8 T cells infiltrating tumors and maintain their cytotoxic function (Huff et al, JCI Insight 2023). Yet, the impact of cell-cell communication on effector T cell function arising from the immunosuppressive microenvironment of PDAC remains unknown. We previously developed a ligand-receptor inference method called Domino that infers inter- and intra-cellular signaling networks in single-cell RNA-seq data (Cherry et al, Nat Biomed Eng 2021). However, this technique is limited to data from single conditions. Understanding how this combination immunotherapy alters cellular signaling networks requires new computational tools that identify changes in regulatory networks between treatment conditions. We developed capabilities for assessment of differential signaling with Domino founded on a basis of differential signal receipt. Active receptors are identified by receptor expression in recipient cells that is correlated with downstream transcription factors in the intracellular signaling cascade. Identification of causative ligands for receptor activation is assessed by a probability of interaction for ligand-receptor interactions between cell types. This probability metric considers mean expression of ligand and receptor genes as well as the number of sender cells for comparison across treatment groups. Comparing communication networks in PancVAX alone to PancVAX with ICI, PancVAX with ICI enhances cell-cell adhesion and interferon gamma signaling in cytotoxic CD8 T cells towards exhausted CD8 T cells. Macrophages in PancVAX with ICI enhance expression of immune checkpoint ligands towards CD8 T cells, despite the presence of blocking ICI antibodies. Intracellular signaling downstream of PD-1 in exhausted T cells shows diminished numbers of transcription factors linked to PD-1 signaling. This software informs prioritization of inhibitory signals for modulation in future immunotherapy regimens and can be applied generally to other tumor subtypes and treatment contexts. Citation Format: Jacob T. Mitchell, Atul Deshpande, Amanda L. Huff, Chris Cherry, Sushma Nagaraj, Kavita Krishnan, Dmitrijs Lvovs, Jennifer H. Elisseeff, Elizabeth M. Jaffee, Neeha Zaidi, Elana J. Fertig. A differential ligand-receptor network inference method to identify alterations in communication between myeloid cells and CD8 T cells in response to PancVAX neo-epitope peptide vaccine, anti-CTLA-4 and anti-PD-1 antibodies in a murine model of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6212.

Abstract 3026: STK11 negatively regulates NFKB signaling in KRAS-driven lung adenocarcinoma

Abstract In the US, more people die each year from lung cancer than breast, colorectal, and prostate cancers combined. Despite advances in lung cancer detection and treatment, the overall prognosis for patients remains poor. Patients whose lung tumors harbor druggable mutations often experience initial responses with targeted therapies, but acquisition of therapy resistance results in 5-year survival rates that have remained near ~20%. Immune check-point inhibitors (ICI) promise to improve outcomes in patients with lung cancer by targeting mechanisms of immune evasion. Drugs that disrupt PD-L1-mediated immune evasion, including pembrolizumab and nivolumab, have revolutionized treatment for some cancers. Unfortunately, only ~30% of lung adenocarcinomas (LUADs) respond to anti-PD-1 therapy and we cannot reliably identify this group prior to treatment. This underscores the need to discriminate which patients will respond to ICI therapies, while simultaneously highlighting the ~70% non-responder rate. To that end, recent clinical studies have linked anti-PD-1 therapy resistance with Serine/Threonine Kinase 11 (STK11) loss of function (LoF). STK11 operates in a heterotrimeric complex with the pseudo-kinase STRADα and the scaffolding protein MO25 where it regulates numerous intracellular signaling networks impacting metabolism, proliferation, transcription, and cell morphology. Why STK11 LoF correlates with anti-PD-1 resistance in the context of KRAS-driven LUAD remains unknown and represents a critical question in lung oncology. As an initial approach to understand this phenomenon, we knocked-out STK11 in multiple KRAS-driven, STK11-competent human LUAD cell lines and performed whole transcriptome analyses to identify STK11-loss-dependent differential gene expression profiles. We assert the transcriptional mediators downstream of STK11 governing the changes we report represent therapeutic targets whose antagonism may restore anti-PD-1 efficacy. Supporting this rationale, our data has identified STK11-loss-dependent activation of the NFκ-B transcriptional network. NFκB is a master transcription factor that regulates numerous cytokines, but whether and/or how STK11 directs NFκB activity remains largely unaddressed. We highlight NFκB activation as a potential mechanistic link between STK11 loss and tumor-intrinsic cytokine upregulation. We speculate that STK11 normally acts as a key player in the negative feedback loop limiting NFκB activity. When STK11 is lost, that activity continues unabated. In summary, we propose STK11 loss drives anti-PD-1 therapy resistance by generating an altered tumor immune microenvironment via constitutive activation of NFκB-mediated cytokine production. In future we intend to assess strategies for reversing anti-PD-1 therapy resistance via disruption of the NFκB transcriptional axis in KRAS-driven LUAD lacking STK11. Citation Format: David Joseph Seward, Sean Lenahan, Allison Racela, Israel Odekunle. STK11 negatively regulates NFKB signaling in KRAS-driven lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3026.

Abstract 1233: Novel inhibitor targeting triple integrated stress response kinase HRI, PERK, and GCN2 provides new insights into overcoming resistance to proteasome inhibitors in multiple myeloma

Abstract The introduction of novel treatments for Multiple myeloma (MM), particularly proteasome inhibitors (PI) such as bortezomib (BTZ), has greatly improved outcomes. However, many patients eventually experience relapse. Therefore, new approaches for managing patients with resistance to PI should be explored. The integrated stress response (ISR) is an evolutionarily conserved intracellular signaling network that is activated in response to both intrinsic and extrinsic stresses. Stresses are sensed by four specialized kinases: HRI, PERK, PKR, and GCN2, which converge on the phosphorylation of eIF2α. This phosphorylation triggers the translation of ATF4, thus promoting cell survival and homeostasis. Recent studies investigating the contribution of the four ISR kinases in overcoming resistance to PI treatment, have revealed the potential of a selective GCN2 inhibitor to overcome this resistance. Here, we observed that PI simultaneously induced mitochondrial stress, ER stress, and amino acid starvation, leading to the activation of HRI, PERK, and GCN2, respectively. However, the contribution of crosstalk among ISR kinases has not been considered thus far. To gain a comprehensive understanding of ISR kinases in BTZ resistance, we generated single or combination patterns of double and triple KO of the four ISR kinases and reevaluated their contribution to BTZ treatment. Sensitivity screening using the HAP1 single, double, and triple KO cell library showed that HRI primarily, and to a lesser extent, PERK and GCN2, contribute to BTZ resistance. Consistent with the HAP1 KO screening, MM cell line-derived KO cells revealed a similar dependency on these three kinases. Building upon our observation of the significance of the HRI/PERK/GCN2 triple kinase, we developed a novel and orally available small molecule, CRD-1367799, which inhibits these triple kinases in cells. CRD-1367799 effectively dampened the activity of these ISR kinases, leading to a complete inhibition of eIF2α phosphorylation and ATF4 activation. Additionally, we observed a distinct anti-growth effect when combined with BTZ in vitro and in vivo, which was not replicated by the GCN2 or PERK-selective inhibitor. Furthermore, we uncovered the mechanism of cell death induction in combination with proteasome inhibitors. Notably, the apoptosis inducers NOXA and CHOP were upregulated, but the mechanism did not seem to rely on previously known processes such as ATF4-mediated transcriptional induction. In summary, our novel findings on the contribution of the triple ISR kinase provides us with new insights for overcoming resistance to proteasome inhibitors with HRI/PERK/GCN2 inhibitor. To the best of our knowledge, the use of a triple kinase inhibitor in this context has not been reported thus far, making CRD-1367799 a new therapeutic strategy for MM with PI. Citation Format: Yasumichi Inoue, Koki Hikami, Shunsuke Ebara, Midori Sugiyama, Robert Oda, Akio Mizutani, Misaki Yoshida, Hiroko Yamakawa, Shigehiro Yagishita, Akinobu Hamada, Hidetoshi Hayashi, Masaki Ri, Shinsuke Iida, Daisuke Morishita. Novel inhibitor targeting triple integrated stress response kinase HRI, PERK, and GCN2 provides new insights into overcoming resistance to proteasome inhibitors in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1233.

Abstract 2136: Genetic ancestry dependent variability in stromal cells: An unexplored player in breast cancer disparity

Abstract Genetic ancestry dependent variability in cancer incidence, mutation patterns, response to chemotherapy, and outcome has been documented. While an association between social determinants of health and breast cancer disparity has already been established, there is emerging evidence for genetic ancestry dependent variability in normal breast biology impacting breast cancer biology and potentially outcome. Tumor biology studies in the context of genetic ancestry and disparity have often focused on intrinsic properties of tumor cells or tumor infiltrating immune cells. However, other stromal cell types have received very little attention. Through immunohistochemistry of breast tissues from healthy women of African and European ancestry and primary cell culturing system, we had previously demonstrated enrichment of a stromal cell population called PZP cells (PROCR+/ZEB1+/PDGFRA+) with mesenchymal stem-like and fibroadipogenic properties in the normal breast tissues of women of African ancestry. In this study, we used single nuclei ATAC-seq and/or RNA-seq to further characterize stromal fibroblasts in the breast tissues of women of Ashkenazi Jewish-European, European, Indigenous American, Hispanic-European, African, and Asian ancestry. Among eight fibroblast cell clusters generated from women of African and European ancestry, only three cell clusters overlapped between two groups. While Complement Factor D (CFD, also called adipsin) expression was observed in unique fibroblast clusters of African ancestry, the expression of Insulin-like Growth Factor 1 (IGF1) was enriched in clusters unique to European ancestry. Interestingly, previous studies have demonstrated African ancestry-specific genomic variants for CFD linked to cardiometabolic disorders. Additional genes that showed genetic ancestry dependent variability in expression within fibroblasts include ABCA10, ABCA9, ABCA8, NEGR1 (enriched in African ancestry), MMP16, MAGI1, KIAA1217, PTPRK and SEMA5A (enriched in European ancestry). NEGR1 (Neuronal Growth Regulator 1) is a trans-neural growth promoting factor, whereas PTPRK (Protein Tyrosine Phosphatase Receptor Type K) is a negative regulator of EGFR signaling. These results suggest genetic ancestry dependent variability in stromal-epithelial cell communications under normal and cancerous conditions. These genetic ancestry dependent differences could impact intracellular signaling networks in epithelial cells with consequential effects on cancer incidence, mutation patterns, drug sensitivity, and outcome. Citation Format: Poornima Bhat-Nakshatri, Hongyu Gao, Cihat Erdogan, Yunlong Liu, Harikrishna Nakshatri. Genetic ancestry dependent variability in stromal cells: An unexplored player in breast cancer disparity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2136.

Charting cellular differentiation trajectories with Ricci flow

Complex biological processes, such as cellular differentiation, require intricate rewiring of intra-cellular signalling networks. Previous characterisations revealed a raised network entropy underlies less differentiated and malignant cell states. A connection between entropy and Ricci curvature led to applications of discrete curvatures to biological networks. However, predicting dynamic biological network rewiring remains an open problem. Here we apply Ricci curvature and Ricci flow to biological network rewiring. By investigating the relationship between network entropy and Forman-Ricci curvature, theoretically and empirically on single-cell RNA-sequencing data, we demonstrate that the two measures do not always positively correlate, as previously suggested, and provide complementary rather than interchangeable information. We next employ Ricci flow to derive network rewiring trajectories from stem cells to differentiated cells, accurately predicting true intermediate time points in gene expression time courses. In summary, we present a differential geometry toolkit for understanding dynamic network rewiring during cellular differentiation and cancer.

Spontaneous signal generation by an excitable system for cell migration.

Eukaryotic cells exhibit random migration in the absence of extracellular directional cues. This random migration acts as basal motility for various migratory responses such as chemotaxis. The self-organization of random motility requires the internal signals that determine the anterior side of the migrating cell be generated spontaneously from the intrinsic activities of intracellular signaling networks. Recent studies have identified an excitable system as the mechanism of the spontaneous signal generation. Here, we discuss how the excitable system of Ras, a small G protein, regulates signaling networks in Dictyostelium discoideum as a model organism. The excitability produces a domain where an active form of Ras is enriched on the cell membrane without extracellular directional cues, such that Ras serves as the anterior signal. The typical spatiotemporal characteristics are mathematically explained by reaction-diffusion models. These models further enable a quantitative analysis of the dynamics that depends on the internal cellular states and surrounding environments. Downstream of the Ras excitable system, a phosphoinositide metabolic network composed of PI3K, PTEN, PI(3,4,5)P3 and PI(4,5)P2 exhibits bistability to discretize the anterior and posterior regions of the cell membrane. Upstream, a local excitation and global inhibition local excitation global inhibition network, which works for gradient sensing in the presence of chemoattractant gradients, spatiotemporally biases the excitability of Ras for chemotaxis. In parallel with the Ras excitable system, the cGMP signaling pathway constitutes another excitable system of its own periodicity to ensure flexible migratory dynamics. In addition to these intracellular signaling networks, an intercellular signaling network activated by secreted cAMP is coupled with the Ras excitable system for collective cell migration. Finally, we discuss how the excitable system of Ras operates as a platform of information integration by receiving multiple intrinsic and extrinsic signals to ensure spontaneous cellular activity and robust responses in eukaryotic cell migration under natural complex environments.

GPCRs as targets for flavonoids in cancer cells: new options for intervention.

For a long time, the family of receptor tyrosine kinases, including epidermal growth factor receptor and insulin-like growth factor 1 receptor, was regarded as the main players stimulating cell proliferative signaling. Today, it is increasingly clear that many G protein-coupled receptors (GPCRs) are also involved in controlling the hallmarks of cancer by activating diverse intracellular signaling networks. GPCRs can therefore be considered as promising drug targets for fighting against diverse types of human malignancies. Although plant polyphenols, flavonoids, are well known for their diverse anticancer effects inhibiting the growth, proliferation, migration, and invasion of malignant cells, involvement of GPCRs in these activities has still remained largely unelucidated. Therefore, in this review article, the current knowledge about the role of GPCRs in anticancer action of structurally varied flavonoids is compiled, highlighting the ability of these natural polyphenols to modulate the expression levels of GPCRs but also suppress the action of endogenous ligands and downstream tumor-promoting events. These data show that targeting the respective GPCRs by specific flavonoids may open new perspectives in the therapeutic intervention in human malignancies.

Activity of Protein Kinase A in the Frontal Cortex in Schizophrenia.

Schizophrenia is a serious cognitive disorder characterized by disruptions in neurotransmission, a process requiring the coordination of multiple kinase-mediated signaling events. Evidence suggests that the observed deficits in schizophrenia may be due to imbalances in kinase activity that propagate through an intracellular signaling network. Specifically, 3'-5'-cyclic adenosine monophosphate (cAMP)-associated signaling pathways are coupled to the activation of neurotransmitter receptors and modulate cellular functions through the activation of protein kinase A (PKA), an enzyme whose function is altered in the frontal cortex in schizophrenia. In this study, we measured the activity of PKA in human postmortem anterior cingulate cortex (ACC) and dorsolateral prefrontal cortex (DLPFC) tissue from schizophrenia and age- and sex-matched control subjects. No significant differences in PKA activity were observed in male and female individuals in either brain region; however, correlation analyses indicated that PKA activity in the ACC may be influenced by tissue pH in all subjects and by age and tissue pH in females. Our data provide novel insights into the function of PKA in the ACC and DLPFC in schizophrenia.

Anthracycline cardiotoxicity is exacerbated by global p38b genetic ablation in a sexually dimorphic manner but unaltered by cardiomyocyte-specific p38a loss.

Severe cardiotoxic effects limit the efficacy of doxorubicin (DOX) as a chemotherapeutic agent. Activation of intracellular stress signaling networks, including p38 mitogen-activated protein kinase (MAPK), have been implicated in DOX-induced cardiotoxicity (DIC). However, the roles of the individual p38 isoforms in DIC remain incompletely elucidated. We recently reported that global p38d deletion protected female but not male mice from DIC, while global p38g deletion did not significantly modulate it. Here we studied the in vivo roles of p38a and p38b in acute DIC. Male and female mice with cardiomyocyte-specific deletion of p38a or global deletion of p38b and their wild-type counterparts were injected with DOX. Survival and health were tracked for 10 days post-injection. Cardiac function was assessed by echocardiography and electrocardiography, and fibrosis by Picro Sirius Red staining. Expression and activation of signaling proteins and inflammatory markers were measured by western blot, phosphorylation array and chemokine/cytokine array, respectively. Global p38b deletion significantly aggravated DIC and worsened cardiac electrical and mechanical function deterioration in female mice. Mechanistically, DIC in p38b-null female mice correlated with increased autophagy, sustained hyperactivation of pro-apoptotic JNK signaling, as well as remodeling of myocardial inflammatory environment. In contrast, cardiomyocyte-specific deletion of p38a improved survival of DOX30-treated male mice 5 days post-treatment but did not influence cardiac function in DOX-treated male or female mice. Our data highlight the sex- and isoform-specific roles of p38a and p38b MAPKs in DOX-induced cardiac injury and suggest a novel in vivo function of p38b in protecting female mice from DIC.

A novel DOCK7 variant as a rare reason for epileptic encephalopathy, cortical blindness, dysmorphic features: A case report and brief review of the literature

Early infantile epileptic encephalopathy 23 (EIEE23; OMIM #615859) is a rare autosomal recessive disorder. It is characterized by refractory seizures, multifocal epileptic activity on electroencephalography, psychomotor development delay, dysmorphic facial features and cortical blindness/visual impairment. DOCK7 is involved in intracellular signaling networks and plays a role in axon formation and neuronal polarization. Function loss of this gene has previously been described in the molecular etiology of EIEE23. Here, we report a boy with a pathogenic novel variant in the DOCK7 gene presenting with, infantile-onset epileptic encephalopathy, severe neurodevelopmental delay, dysmorphic facial features, cortical blindness as well as previously unreported minor dental and extremity anomalies. Few cases with DOCK7 mutations have been reported in the literature. Due to its high genetic heterogeneity and scarcity, it is extremely important to report a novel and specific mutations and their associated clinical phenotypes. Whole exome sequencing revealed a novel pathogenic homozygous frameshift variant which has not been reported (c.5669dup (p.Cys1891ValfsTer2) mutation in the exon 44 of DOCK7).

Nucleotide Messenger Signaling of Staphylococci in Responding to Nitric Oxide - Releasing Biomaterials.

Nitric oxide (NO) releasing biomaterials are a promising approach against medical device associated microbial infection. In contrast to the bacteria-killing effects of NO at high concentrations, NO at low concentrations serves as an important signaling molecule to inhibit biofilm formation or disperse mature biofilms by regulating the intracellular nucleotide second messenger signaling network such as cyclic dimeric guanosine monophosphate (c-di-GMP) for many Gram-negative bacterial strains. However, Gram-positive staphylococcal bacteria are the most commonly diagnosed microbial infections on indwelling devices, but much less is known about the nucleotide messengers and their response to NO as well as the mechanism by which NO inhibits biofilm formation. This study investigated the cyclic nucleotide second messengers c-di-GMP, cyclic dimeric adenosine monophosphate (c-di-AMP), and cyclic adenosine monophosphate (cAMP) in both Staphylococcus aureus (S. aureus) Newman D2C and Staphylococcus epidermidis (S. epidermidis) RP62A after incubating with S-nitroso-N-acetylpenicillamine (SNAP, NO donor) impregnated polyurethane (PU) films. Results demonstrated that NO release from the polymer films significantly reduced the c-di-GMP levels in S. aureus planktonic and sessile cells, and these bacteria showed inhibited biofilm formation. However, the effect of NO release on c-di-GMP in S. epidermidis was weak, but rather, S. epidermidis showed significant reduction in c-di-AMP levels in response to NO release and also showed reduced biofilm formation. Results strongly suggest that NO regulates the nucleotide second messenger signaling network in different ways for these two bacteria, but for both bacteria, these changes in signaling affect the formations of biofilms. These findings provide cues to understand the mechanism of Staphylococcus biofilm inhibition by NO and suggest novel targets for antibiofilm interventions.

Nanobody Loop Mimetics Enhance Son of Sevenless 1-Catalyzed Nucleotide Exchange on RAS.

RAS proteins control various intracellular signaling networks. Mutations at specific locations were shown to stabilize their active guanosine triphosphate (GTP)-bound state, which is associated with the development of multiple cancers. An attractive approach to modulate RAS signaling is through its regulatory guanine nucleotide exchange factor (GEF) son of sevenless 1 (SOS1). With the recent discovery of Nanobody14 (Nb14), which potently enhances SOS1-catalyzed nucleotide exchange on RAS, we explored the feasibility of developing peptide mimetics by structurally mimicking the complementarity-determining region 3 (CDR3). Guided by a biochemical GEF assay and X-ray co-crystal structures, successive rounds of optimization and gradual conformational rigidification led to CDR3 mimetics showing half of the maximal activation potential of Nb14 with an EC50 value of 29 μM. Altogether, this study demonstrated that peptides able to modulate a protein-protein interaction can be obtained by structural mimicry of a Nb paratope.

Nanobody Loop Mimetics Enhance Son of Sevenless 1‐Catalyzed Nucleotide Exchange on RAS**

AbstractRAS proteins control various intracellular signaling networks. Mutations at specific locations were shown to stabilize their active guanosine triphosphate (GTP)‐bound state, which is associated with the development of multiple cancers. An attractive approach to modulate RAS signaling is through its regulatory guanine nucleotide exchange factor (GEF) son of sevenless 1 (SOS1). With the recent discovery of Nanobody14 (Nb14), which potently enhances SOS1‐catalyzed nucleotide exchange on RAS, we explored the feasibility of developing peptide mimetics by structurally mimicking the complementarity‐determining region 3 (CDR3). Guided by a biochemical GEF assay and X‐ray co‐crystal structures, successive rounds of optimization and gradual conformational rigidification led to CDR3 mimetics showing half of the maximal activation potential of Nb14 with an EC50 value of 29 μM. Altogether, this study demonstrated that peptides able to modulate a protein‐protein interaction can be obtained by structural mimicry of a Nb paratope.

Abstract IA16: RASopathies: the other face of RAS signaling upregulation

Abstract RAS proteins control a major intracellular signaling network that, depending on the cellular context, mediates response to external stimuli to control diverse biological functions. Within this network, signal flow through the RAF-MEK-ERK (MAPK, hereafter) pathway, modulates a wide array of cellular processes as well as early and late developmental programs. Signaling through the RAS-MAPK cascade is tightly controlled, and its enhanced activation has been known for decades to represent a major event in oncogenesis. Unexpectedly, discoveries derived from a massive disease gene hunting effort have more recently established a picture in which the upregulation of this signaling cascade underlies a group of clinically related developmental disorders collectively known as “RASopathies”, which share cardiac defects, reduced postnatal growth, variable cognitive deficits, facial dysmorphism, ectodermal and musculoskeletal anomalies, and variably increased risk for certain malignancies as major features. Based on the relatively high prevalence of some of these disorders (i.e., Noonan syndrome and neurofibromatosis type 1), the dysregulation of this signaling pathway represents one of the most common events affecting development. RASopathies are caused by mutations in genes encoding RAS proteins and structurally/functionally related GTPases, regulators of RAS function, modulators of RAS interaction with effectors or downstream signal transducers of the MAPK backbone. A subset of these genes have previously been implicated in cancer. Many of these RASopathy-causing alleles encode proteins with upregulated functional behavior, but with less activating strength compared to those contributing to oncogenesis. In these genes, a largely non-overlapping spectrum of germline and somatic mutations is generally observed. On the other hand, a few disorders result from a protein with defective function. In these, the implicated proteins negatively control signal flow, and the pathogenic event contributing to oncogenesis is generally represented by a second somatic hit involving the retained wild-type allele. The understanding of the molecular mechanisms involved in the pathogenesis of RASopathies has provided novel and relevant insights in cancer research. The identification of PTPN11 as major disease gene underlying Noonan syndrome represented the basis for the discovery that SHP2, the protein encoded by PTPN11, functions as an oncoprotein in childhood hematologic malignancies when mutated. More recently, genomic sequencing of RASopathies has allowed to identify circuits and players with previously unrecognized regulatory role on RAS function and signaling through the MAPK cascade. Here is provided an overview on the genes implicated in this group of developmental disorders, the molecular basis underlying the differential impact of germline and somatic mutations in development and cancer, the unanticipated molecular mechanisms converging toward the dysregulation of this signaling cascade, and major clinically relevant genotype-phenotype correlations. Citation Format: Marco Tartaglia. RASopathies: the other face of RAS signaling upregulation [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr IA16.

Cytoplasmic Kinase Network Mediates Defense Response to Spodoptera litura in Arabidopsis.

Plants defend against folivores by responding to folivore-derived elicitors following activation of signaling cascade networks. In Arabidopsis, HAK1, a receptor-like kinase, responds to polysaccharide elicitors (Frα) that are present in oral secretions of Spodoptera litura larvae to upregulate defense genes (e.g., PDF1.2) mediated through downstream cytoplasmic kinase PBL27. Here, we explored whether other protein kinases, including CPKs and CRKs, function with PBL27 in the intracellular signaling network for anti-herbivore responses. We showed that CRK2 and CRK3 were found to interact with PBL27, but CPKs did not. Although transcripts of PDF1.2 were upregulated in leaves of wild-type Arabidopsis plants in response to mechanical damage with Frα, this failed in CRK2- and PBL27-deficient mutant plants, indicating that the CRK2/PBL27 system is predominantly responsible for the Frα-responsive transcription of PDF1.2 in S. litura-damaged plants. In addition to CRK2-phosphorylated ERF13, as shown previously, ethylene signaling in connection to CRK2-phosphorylated PBL27 was predicted to be responsible for transcriptional regulation of a gene for ethylene response factor 13 (ERF13). Taken together, these findings show that CRK2 regulates not only ERF13 phosphorylation but also PBL27-dependent de novo synthesis of ERF13, thus determining active defense traits against S. litura larvae via transcriptional regulation of PDF1.2.

Computational Docking Studies of MAPK1 Target Protein Responsible for Heart Failure Using Catechin as Natural Inhibitor

Mitogen-activated protein kinases (MAPKs) are major thespians that have been the subject of in-depth research over the last few decades among the several intracellular signaling networks that regulate the pathophysiology and development of the heart. Heart failure is one of the most common reasons for hospitalization and is a serious public health issue. Heart failure mostly affects the elderly, and as life expectancy increases and chronic medical conditions are better managed, more people are expected to develop the condition. The thrust to investigate alternative traditional medicine has attracted much attention as there are many negative effects of the current pharmacological treatments that are being used to control the problem of heart failure. The protein's original configuration and the ligand combination both had binding energies of -5.62 kcal/mol, which may pave the way for future use of the knowledge about the responsible protein and optimization of their lead molecule for an alternative treatment for the cases of heart failure. But further research is needed, for the validation of the data in wet labs, larger trials and in-vitro studies, to establish its drug-likeliness and their applications.

Luteolin protects DYT-PRKRA cells from apoptosis by suppressing PKR activation.

DYT-PRKRA is a movement disorder caused by mutations in the PRKRA gene, which encodes for PACT, the protein activator of interferon-induced, double-stranded RNA (dsRNA)-activated protein kinase PKR. PACT brings about PKR's catalytic activation by a direct binding in response to stress signals and activated PKR phosphorylates the translation initiation factor eIF2α. Phosphorylation of eIF2α is the central regulatory event that is part of the integrated stress response (ISR), an evolutionarily conserved intracellular signaling network essential for adapting to environmental stresses to maintain healthy cells. A dysregulation of either the level or the duration of eIF2α phosphorylation in response to stress signals causes the normally pro-survival ISR to become pro-apoptotic. Our research has established that the PRKRA mutations reported to cause DYT-PRKRA lead to enhanced PACT-PKR interactions causing a dysregulation of ISR and an increased sensitivity to apoptosis. We have previously identified luteolin, a plant flavonoid, as an inhibitor of the PACT-PKR interaction using high-throughput screening of chemical libraries. Our results presented in this study indicate that luteolin is markedly effective in disrupting the pathological PACT-PKR interactions to protect DYT-PRKRA cells against apoptosis, thus suggesting a therapeutic option for using luteolin to treat DYT-PRKRA and possibly other diseases resulting from enhanced PACT-PKR interactions.