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Abstract The analysis of the secretome provides important information on proteins defining intercellular communication and the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, secretome data can support decisions for diagnosis and therapy. The mass spectrometry–based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Metabolic labeling using azide-containing amino acid analogs in combination with click chemistry facilitates this type of analysis in the presence of serum, preventing serum starvation-induced effects. The modified amino acid analogs, however, are less efficiently incorporated into newly synthesized proteins and may perturb protein folding. Combining transcriptome and proteome analysis, we elucidate in detail the effects of metabolic labeling with the methionine analog azidohomoalanine (AHA) on gene and protein expression. Our data reveal that 15–39% of the proteins detected in the secretome displayed changes in transcript and protein expression induced by AHA labeling. Gene Ontology (GO) analyses indicate that metabolic labeling using AHA leads to induction of cellular stress and apoptosis-related pathways and provide first insights on how this affects the composition of the secretome on a global scale. Key messages Azide-containing amino acid analogs affect gene expression profiles. Azide-containing amino acid analogs influence cellular proteome. Azidohomoalanine labeling induces cellular stress and apoptotic pathways. Secretome consists of proteins with dysregulated expression profiles.

Background: The importance of styryl benzyl sulfones that induce G2/M cell cycle arrest and apoptosis in tumor cells has raised interest in cancer therapeutics. Rigosertib (ON 01910.Na) has been characterized as a disruptor of multiple signaling pathways including RAS-MAPK signaling through multiple mechanisms. The aim of our study was to further elucidate the mechanism of action and to identify potential novel targets engaged by rigosertib. Methods: Thermal shift, NanoBiT, in vitro tubulin polymerization and a variety of biochemical, molecular and cell biological assays were performed to characterize the binding of rigosertib to previously proposed targets and its effect on RAS-MAPK signaling and tumor cell survival. A mass spectrometry-based Cellular Thermal Shift Assay (CETSA-MS) that serves as a key tool to identify the targets in the entire proteome engaged by chemical ligands or small molecules of interest at physiological levels in cells, was conducted in multiple cell types to identify potential new protein targets of rigosertib. Results: Our data suggest that rigosertib exerts its inhibitory effect on RAS-MAPK signaling through ROS induced activation of JNK signaling. While we confirm that rigosertib might affect microtubules at higher concentrations, the main cellular target(s) responsible for the induction of stress and JNK-mediated inhibition of RAS-RAF-MEK signaling needs to be further characterized. By performing comparative CETSA profiling of rigosertib and colchicine, a classical anti mitotic drug that binds to soluble tubulin, we are able to identify unique targets of rigosertib in multiple tumor cell types. In particular, we identify two ROS-related proteins, ERO1A and NQO2 that potentially contribute to the induction of ROS-dependent JNK activation. NEK7, a relevant protein for microtubule organization and essential for NLRP3 inflammasome activation, is another potential target for rigosertib. Indeed, rigosertib activates NLRP3-dependent inflammatory responses via NEK7 and Caspase-1 to trigger IL-1β secretion. Conclusion: These results suggest that rigosertib may represent an effective compound for inhibition of RAS-MAPK signaling through ROS-mediated JNK activation. Our findings reveal a rigosertib-dependent mechanism for NLRP3 activation that might be the cause of rigosertib synergistic effect with immune checkpoint blockers to induce cell death in advanced KRAS-mutated non-small cell lung cancer patients. This MOA suggests rigosertib can modulate the mutated RAS pathway no matter the mutation present, now confirmed with clinical data. Further clinical trials in a number of RAS mutated cancers are continuing. Citation Format: Petros Kechagioglou, Camille Dupont, Hajime Yurugi, Alexey Chernobrovkin, Kristina Riegel, Stephen Cosenza, Steven M. Fruchtman, Krishnaraj Rajalingam. CETSA profiling unveils novel targets engaged by anti-tumor drug rigosertib to inhibit RAS-MAPK signaling and trigger NLRP3 inflammasome activation [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 A020.

Purpose Clinical studies have confirmed that the hair-growth-promoting effect of approved oral drug combinations is beneficial for the treatment of diffuse telogen effluvium, which is characterized by the excessive loss of telogen club hairs. Since data elucidating the mode of action of such combinations are limited, our study focused on the identification of cellular processes potentially supporting the treatment of hair loss. Materials and methods A minimal growth culture system (MGM) was used to mimic in vitro the reduced activity of human hair follicular keratinocytes (HHFKs). The effect of four core compounds (L-cystine, thiamine, calcium D-pantothenate, and folic acid) of a marketed oral combination (Panto[vi]gar®), which are approved for the treatment of diffuse hair loss, was examined by comparing HHFKs cultured either with or without the compounds. After determining their impact on metabolic activity and proliferation, we conducted a comparative whole-genome gene expression study with subsequent functional grouping of differentially expressed genes to identify cellular processes influenced by the tested compounds. Results The four core compounds of an oral hair-growth formulation enhanced proliferation and metabolic activity of HHFKs compared to HHFKs cultivated in MGM only. Functional grouping of differentially expressed genes confirmed the regulation of cell cycle-/proliferation-associated genes (cdk1, HJURP) and revealed regulation of cell death- and oxidative stress-associated gene groups. A supportive effect of the compounds on cell viability was demonstrated by lower sensitivity to solar-simulated UV-radiation and increased protection against oxidative stress. We established a central role for L-cystine, as changes in the expression of the anti-oxidative gene hmox1 were L-cystine-dependent. However, to reach a maximal stimulating effect on proliferation, the combination of all four compounds was necessary. Conclusion The tested compound combination had positive effects on metabolic activity, cell viability, and proliferation of keratinocytes. Furthermore, this study suggested that L-cystine primarily contributes to the observed protection against endogenous oxidative stress.

RAF kinases are highly conserved serine/threonine kinases, and among the three RAF isoforms (ARAF, BRAF, and CRAF), the pathophysiological relevance of ARAF is not well defined. Here, we show that patients with lung cancer exhibit low expression of ARAF, which is associated with lymph node metastasis and poor patient survival. We uncover that depletion of ARAF promotes anchorage-independent growth and metastasis through activation of AKT signaling in a subset of lung cancer cells. We identified that loss of ARAF was associated with an increase in ERBB3 expression in a kinase-independent manner. ARAF suppressed the promoter activity of ERBB3, and reconstitution of ARAF in ARAF-depleted cells led to the reversal of enhanced ERBB3-AKT signaling. Furthermore, ARAF inhibited neuregulin 1 (hNRG1)–mediated AKT activation through controlling ERBB3 expression via the transcription factor KLF5. Our results disclose a critical dual role for ARAF kinase in the negative regulation of ERBB3-AKT signaling, thereby suppressing tumor metastasis.

CDK4/6 inhibitors are clinically approved for the treatment of HR+, HER2- metastatic breast cancer by reinstating the G1/S checkpoint in tumor cells. Despite clinical benefit, safety concerns such as neutropenia and diarrhea, and disease progression, raises a critical need to identify novel therapeutic strategies. Narazaciclib (ON123300), novel CDK4/6i, designed to enhance efficacy and safety by its multi-targeted kinase inhibitor activity at low nM concentrations against CDK4/6, ARK5, CSF1R, and c-Kit. Narazaciclib is in Ph I trials; NCT04739293 and CXHL1900340; studying different administration regimens. Since several oncogenic signaling pathways are affected, we examined the efficacy of ON123300 in various breast cancer cell lines, and consolidate its mechanism of action by identifying the other targets engaged by ON123300. To identify direct and secondary targets engaged by narazaciclib and palbociclib, proteome wide Cellular Thermal Shift Assay (CETSA) was performed. To investigate narazaciclib’s effect on signaling pathways, Integrative Inferred Kinase Activity (INKA) was performed. Bioinformatics analysis explored the potential clinical effect of the identified targets. Molecular docking simulations investigated the potential interactions of narazaciclib to engage the new targets compared to other CDK4/6i. Both CETSA and INKA analysis revealed more potential targets engaged by narazaciclib compared to palbociclib in both MDA-MB-231 lysates and intact cells such as BUB1, CHEK1, AURKA, GSK3α and GSK3β. In TNBC patients with BUB1 overexpression bioinformatics analysis indicates a low survival correlation. Docking data showed a higher affinity of narazaciclib with BUB1 compared to palbociclib and abemaciclib. A stronger induction of apoptosis and senescence was detected in narazaciclib treated MMTV-PYMT cells, a murine mammary carcinoma model, compared to the other CDK4/6i, while narazaciclib enhanced CCL5 and CXCL10 mRNA levels. Reduction of PD-L1 protein levels and a promoting effect on the H2D1 and B2M mRNA levels was perceived in narazaciclib treated PYMT cells. Lastly, inhibition of autophagy, both at the early and late stages, may sensitize cancer cells to narazaciclib and induce irreversible cell proliferation inhibition, providing a novel therapeutic approach. Our data unveiled the differential targets engaged by narazaciclib in comparison to palbociblib. Narazaciclib treatment led to BUB1 protein degradation, overexpression of which is associated with poor prognosis in TNBC. Combination of narazaciclib with autophagy inhibitors sensitized several breast cancer cells to cell death. Narazaciclib treatment may promote antitumor immunity by influencing the expression of various immune modulators in the tumor cells which needs to be further validated in preclinical animal models; and ultimately in the clinic. Citation Format: Petros Kechagioglou, Camille Dupont, Hajime Yurugi, Ute Distler, Stefan Tenzer, Alexey Chernobrovkin, Kristina Riegel, Juliane Mooz, Mahil Lambert, Volker Dötsch, Stephen Cosenza, Steven M. Fruchtman, Krishnaraj Rajalingam. Differential targets engaged by narazaciclib in comparison to the approved CDK4/6 inhibitors contribute to enhanced inhibition of tumor cell growth. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5987.

Specialized surveillance mechanisms are essential to maintain the genetic integrity of germ cells, which are not only the source of all somatic cells but also of the germ cells of the next generation. DNA damage and chromosomal aberrations are, therefore, not only detrimental for the individual but affect the entire species. In oocytes, the surveillance of the structural integrity of the DNA is maintained by the p53 family member TAp63α. The TAp63α protein is highly expressed in a closed and inactive state and gets activated to the open conformation upon the detection of DNA damage, in particular DNA double-strand breaks. To understand the cellular response to DNA damage that leads to the TAp63α triggered oocyte death we have investigated the RNA transcriptome of oocytes following irradiation at different time points. The analysis shows enhanced expression of pro-apoptotic and typical p53 target genes such as CDKn1a or Mdm2, concomitant with the activation of TAp63α. While DNA repair genes are not upregulated, inflammation-related genes become transcribed when apoptosis is initiated by activation of STAT transcription factors. Furthermore, comparison with the transcriptional profile of the ΔNp63α isoform from other studies shows only a minimal overlap, suggesting distinct regulatory programs of different p63 isoforms.

e15096 Background: Despite clinical benefit of CDK4/6 inhibitors in HR+Her2-mBC, patients progress. Neutropenia and diarrhea are safety concerns. Narazaciclib (ON 123300) is a multi-targeted kinase inhibitor of CDK4/6, ARK5 (NUAK1), CSF1R, and c-Kit at low nM concentrations designed to enhance efficacy and safety. Narazaciclib is in Ph I trials; NCT04739293 and CXHL1900340; in different regimens. Treatment of tumor cell lines with narazaciclib induces G1; G2 arrest and apoptosis. Mouse models suggest narazaciclib causes less neutropenia than palbociclib (palbo). Since signaling pathways are affected, we explored the activity of narazaciclib in direct comparisons with abemaciclib (abe), palbo and ribociclib (ribo) using in vitro and cell based assays. Methods: Comparison of narazaciclib’s in vitro IC50 profile to abe, palbo and ribo was studied against a panel of 370 kinases (HotSpot). Kd values were determined by KINOMEscan. Intracellular IC50 kinase values were determined by NanoBret technology. Protein specific binding of narazaciclib and palbo was investigated by Cellular Thermal Shift Assay (CETSA). To investigate narazaciclib’s effect on signaling pathways, integrative Inferred Kinase Activity (INKA) analysis was performed. Results: Narazaciclib and abe were found to be the most promiscuous in vitro kinase inhibitors and ribo the most specific. Abe and narazaciclib had similar profiles against the CDK family members. Kd values of CDK4/cyclinD1 binding show similar trends; abe (0.08 nM), narazaciclib (0.18 nM), palbo (0.75 nM) and ribo (1.3 nM). Narazaciclib and abe displayed nM activity against CDK2/cyclinA. The IC50 values against GSK3β, whose inhibition putatively causes diarrhea, was 374 nM for narazaciclib and 13 nM for abe. Although narazaciclib displayed nM IC50 values in the in vitro assays against many CDKs, narazaciclib was very specific in cellular kinase assays with highest activity against CDK4/6, CSF1R and NUAK1. CETSA-MS revealed more potential targets engaged by narazaciclib compared to palbo in both lysates and intact cells such as CHEK1, AAK1, BMP2K, GSK3α and GSK3β, but did not identify binding to NUAK1 or CSF1R. INKA analysis demonstrated that narazaciclib induced unique deregulated phosphorylation compared to palbo, including BUB1 (highly expressed in TNBC), NUAK1, CAMK2D, CDK16 and ULK1. Inhibition of autophagy, both at early and late stages, may sensitize cancer cells to narazaciclib and induce irreversible cell proliferation inhibition, providing a novel therapeutic approach. Conclusions: These studies identify important differences generated from assay models studying kinase inhibition, binding and pathway engagement and will guide future studies with narazaciclib targeting specific kinase driven tumors with the potential for improved safety. These preclinical data await confirmation from current and future clinical trials.

Kinases form the major part of the druggable genome and their selective inhibition in human cancers has had reasonable clinical success. In contrast to tumorigenesis, the role of kinases in mediating immune responses is poorly understood. However, synergistic therapeutic regimens combining targeted therapy and immune therapy have been found to increase the median survival of tumor patients. In this context, we uncovered that RAF and MEK1/2 kinases, which are the integral parts of the classical MAPK cascade, have unique roles in driving DC differentiation and activation. RAF kinases are stabilized in their protein levels during DC differentiation and are obligatory for normal functioning of DCs. But, the targeting of MEK1/2 kinases with specific inhibitors did not phenocopy the effects observed with RAF inhibitors suggesting that RAF and MEK1/2 kinases may have specific and unique roles in driving immune responses, which deserves further studies to successfully administer these inhibitors in clinics.

Purpose Clinical studies have confirmed that the hair-growth-promoting effect of approved oral drug combinations is beneficial for the treatment of diffuse telogen effluvium, which is characterized by the excessive loss of telogen club hairs. Since data elucidating the mode of action of such combinations are limited, our study focused on the identification of cellular processes potentially supporting the treatment of hair loss. Materials and Methods A minimal growth culture system (MGM) was used to mimic in vitro the reduced activity of human hair follicular keratinocytes (HHFKs). The effect of four core compounds (L-cystine, thiamine, calcium D-pantothenate, and folic acid) of a marketed oral combination (Panto[vi]gar®), which are approved for the treatment of diffuse hair loss, was examined by comparing HHFKs cultured either with or without the compounds. After determining their impact on metabolic activity and proliferation, we conducted a comparative whole-genome gene expression study with subsequent functional grouping of differentially expressed genes to identify cellular processes influenced by the tested compounds. Results The four core compounds of an oral hair-growth formulation enhanced proliferation and metabolic activity of HHFKs compared to HHFKs cultivated in MGM only. Functional grouping of differentially expressed genes confirmed the regulation of cell cycle-/proliferation-associated genes (cdk1, HJURP) and revealed regulation of cell death- and oxidative stress-associated gene groups. A supportive effect of the compounds on cell viability was demonstrated by lower sensitivity to solar-simulated UV-radiation and increased protection against oxidative stress. We established a central role for L-cystine, as changes in the expression of the anti-oxidative gene hmox1 were L-cystine-dependent. However, to reach a maximal stimulating effect on proliferation, the combination of all four compounds was necessary. Conclusion The tested compound combination had positive effects on metabolic activity, cell viability, and proliferation of keratinocytes. Furthermore, this study suggested that L-cystine primarily contributes to the observed protection against endogenous oxidative stress.

RAF kinases (ARAF, BRAF, and CRAF) are highly conserved enzymes that trigger the RAF-MEK1/2-ERK1/2 (MAPK) pathway upon activation of RAS. Despite enormous clinical interest, relatively little is known on the role of RAFs in mediating immune responses. Here, we investigated the role of RAF kinases and MEK1/2 in dendritic cells (DCs), the central regulators of T cell-mediated antitumor immune responses and the adaptive immune system. We demonstrate that RAF kinases are active and stabilized at their protein levels during DC differentiation. Inhibition of RAF kinases but not MEK1/2 impaired the activation of DCs in both mice and human. As expected, DCs treated with RAF inhibitors show defects in activating T cells. Further, RAF and MEK1/2 kinases are directly required for the activation and proliferation of CD4+T cells. Our observations suggest that RAF and MEK1/2 have independent roles in regulating DC function that has important implications for administering RAF–MAPK inhibitors in the clinics.