MAPK Pathway Genes Research Articles

Fine-Mapping of SMAD6 Sequence Data Identifies Additional Putative Risk Loci for Langerhans Cell Histiocytosis

Background: Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate. Sequencing studies have identified recurrent, mutually exclusive somatic activating mutations in MAPK pathway genes in ~85% of LCH lesions, including BRAF V600E in 50-65%. Despite advances to elucidate the somatic mutational landscape underlying LCH pathogenesis, germline risk factors remain largely unknown. We previously conducted a genome-wide association study of LCH and identified and validated a risk variant in SMAD6 (rs12438941, G->A) associated with a 3.7-fold increase in LCH risk. SMAD6 inhibits bone morphogenetic protein and transforming growth factor-beta (TGF-β)/activin signaling, which are determinants of physiologic myeloid dendritic cell differentiation, and is in close proximity to MAP2K1. Notably, this risk allele is more common in Hispanics, who are at the highest risk of developing LCH, and absent in those of African ancestry who experience the lowest risk of LCH. Our current objective is to further analyze risk of acquiring LCH associated with SMAD6 variations. Methods: Four-hundred and sixty-seven cases diagnosed with LCH were recruited at Texas Children's Hospital. Targeted sequencing of SMAD6 was conducted among cases with ~200x coverage at the Avera Institute of Human Genetics. We accessed aggregate-level SMAD6 sequence data at 940 overlapping loci in SMAD6 from a median of 15,694 non-cancer controls in gnomAD v2.1.1. Variants were pruned using SNPclip due to high linkage disequilibrium (LD; r2 > 0.8) (n = 216 removed), low minor allele frequency (MAF < 0.01) (n = 326 removed), absence from 1000Genomes (n = 240 removed), non-biallelic (n = 3 removed), and absence from dbSNP155 (GRCh37; n = 1 removed). The Fisher's exact test was applied to 154 SMAD6 variants with a Bonferroni critical P-value of 3.2 x 10-4 to assess any association between SMAD6 variation and case status. Sequence data were analyzed in SAS v9.2. Results: In this case-control analysis, 49 variants within SMAD6 were significantly associated with LCH risk (P-values ranging from 4.54 x 10-28 to 2.9 x 10-4), including our previously identified risk locus (P-value: 8.55 x 10-14). Most (48) of the hits were intronic, and one was in the 5' UTR (p = 2.88 x 10-5). The top 4 SNPs had low MAF globally (range 2-9%) but were enriched in the 1000 Genomes AMR (Admixed American superpopulation) population (range 15-23%). The top two SNPs are in high LD in some populations (r2: MXL (Mexican ancestry from Los Angeles) = 0.71, ASW (Americans of African Ancestry in the Southwest USA) = 1.0, PEL (Peruvian from Lima, Peru) = 0.92), but not globally. The third SNP was also in moderately high LD with the peak SNP in some populations (r2: MXL= 0.28, ASW = 0.83, PEL = 0.51). The fourth SNP, which was the variant that was previously identified in our LCH GWAS, has only moderate LD with the peak SNP in some populations (r2: MXL= 0.31, CLM (Colombian from Medellian, Colombia) = 0.3, PEL = 0.13), suggesting that these may be independent signals, and/or that specific SNPs contribute to LCH risk differentially based on ancestry. Conclusions: We identified additional support for associations of germline SMAD6 variants with LCH susceptibility. Our previous risk locus was again enriched among those who develop LCH, and a cluster of loci surrounding our risk locus was identified using this sequence-based approach. Next steps include functional annotation of top hits, analyses to assess whether top hits are associated with LCH patient or clinical characteristics (e.g., genomic ancestry, BRAF V600E mutation status, risk organ involvement), and burden analysis to investigate highly penetrant variants. Overall, this study suggests potential contributions of germline genomics in LCH pathogenesis that may identify a functional role for SMAD6 and account for different incidence rates according to race/ethnicity.

Myeloid Progenitors Define Extent of Disease in Mouse Models of Histiocytic Disorders: BRAFV600E Expression in Monocyte Lineage Recapitulates Erdheim-Chester Phenotype

Langerhans cell histiocytosis (LCH) is a myeloid neoplastic disorder characterized by granulomatous lesions with CD207+ dendritic cells associated with a wide spectrum of clinical presentations. Activating MAPK pathway genes (most frequently BRAFV600E) are identified in lesion DCs as well as in precursor cells in bone marrow and peripheral blood in some cases. LCH typically arises in children, but can also occur de novo in adults. Erdheim-Chester disease (ECD) is a related histiocytic disorder characterized by CD163+ histiocytic lesions with activating MAPK mutations (most frequently BRAFV600E) arising primarily in adults. Unlike LCH, ECD lesion distribution frequently includes kidneys and heart. In order to test the impact of cell of origin on disease phenotype, we developed Cre-inducible mouse models in which BRAFV600E expression is enforced at distinct stages of differentiation: BRAFV600ECD11c and BRAFV600EMSaA3. ITGAX/CD11c is expressed across a range of myeloid dendritic cell and monocyte lineages, where MS4a3 is expressed exclusively in GMPs and GMP-derived cells (e.g. monocytes). BRAFV600E expression was enforced through Cre-mediated recombination to create BRAFV600ECD11c and BRAFV600EMSaA3 mice. Mice were analyzed at weeks 5, 10, 25, and 52 for body and organ weights and histology. Tissues were characterized by immunohistochemistry, gene expression, Luminex, CYTOF and RNASeq. BRAFV600ECD11c mice exhibited a more aggressive phenotype than BRAFV600EMS4A3 counterparts, though both developed systemic histiocytic infiltration. Kinetics of organomegaly, histiocytic infiltration, and systemic inflammation was much slower in the BRAFV600EMS4a3 mice. Notably, BRAFV600EMS4a3 demonstrated increased enrichment of CD207-negative macrophages in spleen, liver and bone marrow. BRAFV600EMS4a3 mice readily survived past 52 weeks, while BRAFV600ECD11c had 100% mortality by 16 weeks. Bulk RNASeq and Ingenuity Pathway Analysis identified relative decrease in macrophage functionality in BRAFV600EMSaA3 mice. Additionally, macrophage infiltrate was observed in heart, major blood vessels and kidneys of BRAFV600EMS4a3 where these organs were not affected in BRAFV600ECD11c. The same mutation that creates an aggressive LCH-like phenotype in CD11c-derived cells creates an indolent ECD-like phenotype in monocyte-derived cells. This study demonstrates a critical role for ontogeny in pathogenesis of histiocytic disorders. Further, the BRAFV600EMS4a3 mouse provides an ECD model for pre-clinical testing of therapeutic strategies.

MYC and TP53 Alterations but Not MAPK Pathway Mutations Are Common Oncogenic Mechanisms in Follicular Dendritic Cell Sarcomas.

Despite their stromal origin, follicular dendritic cells (FDCs) share many functions with hematopoietic system cells. FDC neoplasms are currently classified by the World Health Organization along with those of a histiocytic nature. However, the molecular alterations driving oncogenesis in FDC sarcomas (FDCSs) are beginning to be unveiled and do not seem to concur with those described in histiocytic neoplasms, namely MAPK pathway activation. To identify molecular alterations driving tumorigenesis in FDCS. We investigated the role of MYC and TP53 in FDC-derived tumor oncogenesis and assessed comprehensively the status of the MAPK pathway in 16 FDCSs, 6 inflammatory pseudotumor (IPT)-like FDCSs, and 8 IPTs. MYC structural alterations (both amplifications and rearrangements) were identified in 5 of 14 FDCSs (35.7%), all associated with MYC overexpression. TP53 mutations were identified in 4 of 14 FDCSs (28.6%), all of which displayed intense and diffuse p53 expression. None of these alterations were identified in any IPT-like FDCSs or in IPT cases. No MAPK pathway gene alterations were identified in any of the cases studied. The presence of MYC and TP53 alterations and the lack of association with Epstein-Barr virus segregate classical FDCS from IPT-like FDCS, pointing at different oncogenic mechanisms in both entities. Our results suggest a possible oncogenic role of MYC and TP53 alterations in FDCS. The absence of MAPK pathway alterations confirms the lack of a significant role of this pathway in the oncogenesis of FDC-derived neoplasms.

Identification of novel prognostic and predictive biomarkers in salivary duct carcinoma via comprehensive molecular profiling

Molecular targets and predictive biomarkers for prognosis in salivary duct carcinoma (SDC) have not been fully identified. We conducted comprehensive molecular profiling to discover novel biomarkers for SDC. A total of 67 SDC samples were examined with DNA sequencing of 464 genes and transcriptome analysis in combination with the clinicopathological characteristics of the individuals. Prognostic biomarkers associated with response to combined androgen blockade (CAB) treatment were explored using mRNA expression data from 27 cases. Oncogenic mutations in receptor tyrosine kinase (RTK) genes or genes in the MAPK pathway were identified in 55 cases (82.1%). Alterations in the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway were identified in 38 cases (56.7%). Interestingly, patient prognosis could be predicted using mRNA expression profiles, but not genetic mutation profiles. The risk score generated from the expression data of a four-gene set that includes the ADAMTS1, DSC1, RNF39, and IGLL5 genes was a significant prognostic marker for overall survival in the cohort (HR = 5.99, 95% confidence interval (CI) = 2.73–13.1, p = 7.8 × 10−6). Another risk score constructed from the expression of CD3E and LDB3 was a strong prognostic marker for progression-free survival for CAB treatment (p = 0.03). Mutations in RTK genes, MAPK pathway genes, and PI3K/AKT pathway genes likely represent key mutations in SDC tumorigenesis. The gene expression profiles identified in this study may be useful for stratifying patients who are good candidates for CAB treatment and may benefit from additional systemic therapies.

MM-356 Deep Coverage Targeted Next Generation Sequencing Approach to Determine Somatic Mutational Spectrum of Recurrently Mutated Genes in Newly Diagnosed Multiple Myeloma in a Large Indian Cohort

To determine the mutational spectrum of recurrently mutated genes in a large cohort of Indian patients presenting with multiple myeloma (MM) in our center by performing deep coverage-targeted NGS. Samples of 151 multiple myeloma patients (149 NDMM and 6 follow-up) were sequenced. Patients were diagnosed with MM per IMWG criteria 2014. The study was initiated following approval from the institute's ethical committee, and written informed consent was obtained from all patients. BMA was subjected to plasma cell isolation using CD138+ MACS. DNA underwent automated extraction using the Maxwell System. Mutations were tested on a commercially available 47-gene custom panel (Illumina) specifically designed for MM. Libraries were prepared using a TruSeq Custom Amplicon Low Input Kit (Illumina). DNA (25 ng) was hybridized with oligos specific for targeted regions of interest. Libraries were pooled. Paired-end sequencing was carried out on Illumina's MiSeq sequencer using micro flow cell with V3 chemistry and MS600 V3 series reagent cartridge. Sequenced reads were mapped to GRCh37/Hg19 reference and data obtained as FASTQ files and processed with MiSeq Reporter. As output, .vcf files were generated. Genomic variants were annotated by ANNOVAR. Sequencing coverage of 4771 X (Range 2063X-10980X) revealed different types of variants (exonic, intronic, splice region, 3' and 5' UTR, and upstream gene). Pathogenicity was checked by COSMIC. At least one pathogenic mutation was found in 77% (116/151) of patients (median 1 mutation per patient, range 0-7) and 51% (24/47) of genes. Forty-five percent (68/151) of patients had mutations in more than one gene. The most frequently mutated genes were KRAS, NRAS, BRAF, TP53, DIS3, FAT4, FAT3, and DNAH5. Genomic aberrations found were compared with the frequency of mutations as per the MMRF and TCGA datasets and related literature; good concordance was found (especially in MAPK pathway genes). BRAF and RAS mutations were mutually exclusive. Few mutations were validated by Sanger sequencing. The high frequency of mutations in MAPK pathway genes (KRAS, NRAS, BRAF) suggested the importance of this pathway in myelomagenesis and therapeutics. Follow-up sample sequencing may help deduce clonal evolution during disease course. Identification of clinically relevant target driver mutations may aid in prognosis and therapy personification.

Effects of Lactobacillus kefiri fermentation supernatant on skin aging caused by oxidative stress

• • Lactobacillus kefiri fermentation components(LAF) shows excellent antioxidant effect in vitro. • •Achievements of Lactobacillus kefiri fermentation components providing more possibilities for their application as functional raw materials in cosmetics. • •LAF can regulate the expression of oxidative stress, autophagy, and aging-related genes in damaged cells treated with H 2 O 2 , thereby delaying cell senescence. Lactobacillus kefiri is a beneficial bacteria that is often used to make yogurt only, and is beneficial to human health when it is used in food fermentation. In this article, a fermentation supernatant (LAF) is prepared by culturing Lactobacillus kefiri , and the anti-aging effects of LAF are evaluated at the biochemical, cellular, and molecular biology levels. The antioxidant activity of LAF is comprehensively evaluated by three free radical scavenging tests and the total antioxidant capacity (ABTS method) test. The toxicity of LAF on human skin fibroblasts (HSF) is detected using the MTT method, and the effects of LAF on H 2 O 2 -induced oxidative stress in terms of intracellular reactive oxygen species (ROS), Malondialdehyde (MDA) content, antioxidant enzyme activity are evaluated. The gene expression levels of LC3 and Beclin-1 are detected using the real-time reverse transcription-polymerase chain reaction (qRT-PCR) method, and the protein expression levels of LC3 are detected using the Western blot method to evaluate the effects of LAF on HSF autophagy. The expression of type I collagen (COL-1), Matrix metalloproteinase-1(MMP-1), AKT pathway, MAPK pathway, and other genes are detected by qRT-PCR to study the anti-aging effects of LAF. From the experimental results, it is found that LAF can delay the aging of HSF at the biochemical, cellular, and molecular biology levels, and can be utilized as a functional food ingredient.

Optimizing component formula suppresses lung cancer by blocking DTL-mediated PDCD4 ubiquitination to regulate the MAPK/JNK pathway

Ethnopharmacological relevanceSalvia miltiorrhiza Bunge and Panax ginseng C. A. Meyer have special curative effect on cancer treatment. The optimizing component formula (OCF) extracted from those two herbs was in line with the anti-lung cancer treatment principle of activating blood and supplementing ‘Qi’. However, the study on the mechanism of component formula has always been an insurmountable challenge. Nowadays, the application of network pharmacology and artificial intelligence (AI) in the field of TCM provides new ideas for the study of new targets and mechanisms of TCM, which promotes the modernization of TCM. Aim of the studyThis study aims to further explore the anti-lung cancer mechanism of OCF by using an integrated strategy of network pharmacology and AI technology. Materials and methodsBioinformatic analysis was used to analyze the expression levels, prognosis and survival of DTL and PDCD4 in cancer patients. The binding strength of OCF and DTL was simulated by molecular docking, and the affinity between them was detected by Bio-layer interferometry. Network pharmacology was used to predict the active components, potential targets and pathways of OCF. The association between key targets and their corresponding components and DTL was analyzed by Ingenuity Pathway Analysis (IPA). MTT assay, colony formation assay, wound-healing assay and transwell assay were used to verify the inhibitory effects of OCF on lung cancer cells in vitro. qRT-PCR and Western blot assay were used to detect the effects of OCF on mRNA and protein expression of DTL, PDCD4 and key genes in MAPK/JNK pathways. ResultsBioinformatics analysis showed that DTL was significantly up-regulated in lung cancer, which was associated with high malignancy rate, high metastasis rate and poor prognosis of primary tumor. PDCD4 was down-regulated in lung cancer, and associated with high metastasis rate and poor prognosis. The good affinity between OCF and DTL was predicted and verified by molecular docking and Bio-layer interferometry. Based on the network pharmacological databases, 40 active components and 220 corresponding targets of OCF were screened out. KEGG analysis showed that OCF component targets were mainly enriched in MAPK signaling pathway. IPA results showed the interrelationship between DTL, PDCD4, MAPK pathway genes and their corresponding OCF components. In addition, in vitro experiments demonstrated anti-lung cancer activity of OCF, as validated, via impairing cell viability and cell proliferation, as well as inhibiting migration and invasion abilities in lung cancer cells. qRT-PCR showed that OCF down-regulated the mRNA expression of DTL, MAP4K1, JNK, c-Jun and c-Myc, and up-regulated the mRNA expression of PDCD4 and P53 genes in A549 lung cancer cells. Western blot suggested that OCF suppressed the protein level of DTL and blocked the ubiquitination of PDCD4 in A549 lung cancer cells, and down-regulated the protein levels of MAP4K1, p-JNK and p-c-Jun while up-regulated the proteins expression level of P53. ConclusionsOCF might elicit an anti-lung cancer effect by blocking DTL-mediated PDCD4 ubiquitination and suppression of the MAPK/JNK pathway. Meanwhile, our work revealed that network pharmacology and AI technology strategy are cogent means of studying the active components and mechanism of TCM.

Abstract 2618: Convergent MAPK pathway alterations mediate acquired resistance to FGFR inhibitors in cholangiocarcinoma with FGFR fusions/rearrangements

Abstract Purpose: Genomic aberrations in fibroblast growth factor receptor (FGFR) are oncogenic drivers in several cancers. FGFR inhibitors (FGFRi) have demonstrated antitumor activity in cholangiocarcinoma (CCA) with FGFR2 fusions/rearrangements, though acquired resistance remains a therapeutic challenge and has been linked to FGFR2 mutations other than fusions/rearrangements. We sought to investigate mechanisms of acquired resistance to FGFRi and approaches to overcome resistance. Methods: Longitudinal plasma samples were collected from patients with FGFR pathway alterations enrolled in the futibatinib phase I trial (NCT02052778) and sequenced using a targeted, 73-gene panel. A separate retrospective analysis was conducted to evaluate possible evolution of genomic aberrations in CCA patients with FGFR2 fusion/rearrangement who had additional tumor and/or plasma next-generation sequencing (NGS) following FGFRi therapy. To assess the efficacy of futibatinib in cells with FGFR2 fusions in vitro, a FGFR2-BICC1 fusion H69 cholangiocyte cell line was developed. MAPK pathway alterations (BRAF_V600E or KRAS_G12D) were introduced to determine the impact of these co-alterations on FGFRi sensitivity, and combinations were tested to determine if efficacy could be enhanced. Cell viability assays, colony formation assays, and western blots were utilized to determine the effects of these agents in engineered cells. Results: A total of 58 plasma samples were collected from 17 patients with FGFR pathway alterations who were enrolled in the futibatinib phase I trial, including 13 (76.5%) of which had CCA. One patient with a FGFR2-CTNNA3 fusion who had NRAS G12D and BRAF A694T at baseline which were undetected during treatment had a dramatic increase in their variant allele frequency (VAF) upon progression (4.2%-0.0%-100% and 2.8%-0.0%-50.9%, respectively). Further, additional MAPK alterations were detected at time of progression, including BRAF V600E, NRAS Q61K, NRAS G12C, NRAS G13D and KRAS G12K mutations. In our separate retrospective series, of 17 patients who underwent repeat tumor and/or plasma NGS following treatment with one or more FGFRi, 10 (58.8%) had newly detectable alterations in MAPK pathway genes, 10 (58.8%) had new FGFR2 alterations, and 7 (41.2%) developed new alterations in both FGFR2 and MAPK pathway genes. In vitro studies demonstrated that in isogenic H69 biliary cell lines, introduction of FGFR2-BICC1 robustly sensitized to FGFRi when compared to a parental cell line, which was blunted by the introduction of secondary KRAS_G12D or BRAF_V600E mutations. Conclusions: Convergent genomic evolution in the MAPK pathway may be a potential mechanism of acquired resistance to FGFRi therapy. Work is ongoing to determine if targeting co-alterations may enhance the efficacy of FGFRi in FGFR2-fusion driven malignancies. Citation Format: TImothy P. DiPeri, Ming Zhao, Tyler Moss, Michael Kahle, Payal Rauli, Sunyoung S. Lee, Abdel Halim, Hiroshi Hirai, Volker Wacheck, Karim Benhadji, Jordi Rodon, Milind Javle, Funda Meric-Bernstam. Convergent MAPK pathway alterations mediate acquired resistance to FGFR inhibitors in cholangiocarcinoma with FGFR fusions/rearrangements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2618.

Abstract 4022: ERK1/2 inhibitor ulixertinib demonstrates activity in atypical (non-V600) BRAF mutant models

Abstract Atypical BRAF (non-V600) alterations comprise approximately half of all BRAF mutations in cancer and can be categorized according to characteristics of molecular signaling (either Class II or III). Atypical BRAF alterations are rare (approximately 3% across all human cancers) and there are currently no approved therapies for this indication. As next-generation sequencing becomes standard clinical practice, oncologists are frequently identifying atypical BRAF alterations in their patients’ tumors. The efficacy of the first-in-class ERK1/2 inhibitor, ulixertinib (BVD-523), was assessed across 10 patient-derived xenograft (PDX) models, which harbored class II or III BRAF alterations (5 models with type II alterations, 4 models with class III, and 1 model with both class II and III). Responses ranging from robust regression to moderate tumor growth delay were observed in 9/10 models. RNA sequencing was performed on tumors from the vehicle-treated and ulixertinib-treated groups with three replicates per PDX model. The samples were collected 2 hours after the last dose of treatment. Expression of the mutant BRAF alleles was readily confirmed from RNA-seq data in all PDX models. In addition, gene expression analysis showed differential expression of MAPK pathway genes in responders compared to the non-responders. In summary, ulixertinib has exhibited strong pre-clinical activity in a variety of patient-derived xenograft models with atypical BRAF alterations. Ulixertinib has FDA fast-track designation for patients with solid tumors, other than CRC, harboring specific BRAF mutations (G469A, L485W, or L597Q) and is currently under clinical evaluation in patients with tumors harboring any atypical BRAF alteration (NCT04488003). Citation Format: Deborah Knoerzer, Anupama Reddy, Adnan Derti, Caroline M. Emery. ERK1/2 inhibitor ulixertinib demonstrates activity in atypical (non-V600) BRAF mutant models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4022.

Abstract 3325: ERK inhibitor increases cancer stem cell population in NSCLC through Slug-Mediated epithelial-to-mesenchymal transition

Abstract The aberrant activation of the Mitogen-activated protein kinase pathway (MAPK/ERK pathway) has been found to play an important role in many cancers including non-small-cell lung cancer (NSCLC). Multiple inhibitors targeting this pathway have been developed to treat cancer patients harboring the aberrant MAPK pathway genes. ERK inhibitors (ERKi) have been shown to be effective in a variety of solid-tumor malignancies, but like other MAPK inhibitors, they rarely confer complete and durable responses. Therefore, it is important to define the mechanism underlying potential tumor relapse following ERKi treatment. In this study, we found that ERKi treatment expanded the cancer stem cell (CSC) population in various NSCLC cell lines and a NSCLC patient-derived xenograft (PDX) harboring aberrant MAPK signaling. Such expansion of the CSC population is mainly caused by enhanced epithelial-to-mesenchymal transition (EMT)-mediated cancer cell dedifferentiation. Mechanistically, we revealed that ERK inhibition induces EMT via pSTAT3-mediated upregulation of EMT-transcription factor Slug. Specifically, we found that ERK inhibition increased phosphorylation of STAT3 at Y705, which further increased the expression of miR-204. Increased miR-204 then downregulated expression of SPDEF, a transcriptional repressor of Slug, thereby derepressing Slug expression. Moreover, we found that a low expression of Slug is necessary for maintaining stemness properties of CSCs. Thus, ERKi treatment-increased Slug must be downregulated to allow these cells to fully acquire stemness, and this process is mediated by a Slug-miR-200c negative feedback loop. Finally, we demonstrated that the JAK/STAT pathway inhibitor Ruxolitinib can block the ERK inhibitor-induced EMT and CSCs expansion, providing a feasible combination inhibitor approach for treating NSCLC patients. Overall, these studies provide a better understanding of the tumor relapse following ERKi treatment, and define the role of Slug in de novo production of CSCs and their maintenance. Citation Format: Shurui Cai, Na Li, Xuetao Bai, Ananya Banerjee, Lavudi Kousalya, Qi-en Wang. ERK inhibitor increases cancer stem cell population in NSCLC through Slug-Mediated epithelial-to-mesenchymal transition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3325.

RARE-08. Profiling of recurrent adamantinomatous cranionpharyngioma confirms the activation of the MAPK pathway and identifies copy number aberrations in relapsed tumours

Craniopharyngiomas are rare challenging tumours, with around 25% of cases recurring despite surgery and/or radiotherapy. Whilst transcriptomic and proteomic profiling of adamantinomatous craniopharyngioma (ACP) have revealed activation of the MAPK pathway and IL-6 mediated inflammation, relatively little is known about the biological processes involved in tumour recurrence. To address this, we have analysed a cohort of primary and relapsed ACP tumour accessed from tissue banks, local pathology departments and international collaborators. Serial samples of recurrent ACP (n=11), recurrent papillary craniopharyngioma (PCP) (n=4) and 3 non-recurrent ACP were analysed using β-catenin, pERK1/2 immunostaining, DNA methylation array and RNA sequencing. Differential expression and methylation analyses confirmed differences between ACP and PCP, with over representation of WNT pathway genes in ACP and the MAPK pathway genes in PCP. All of the primary and all except for one of the relapsed ACP tumours showed a pERK1/2 expression. Differences in the immune environment were also identified between ACP and PCP, with higher levels of some inflammatory mediators and CD14+ cell signatures in PCP compared with ACP. Whilst differential methylation and expression analysis revealed relatively stable methylomes and transcriptomes between serial samples of cases, segmental chromosomal alterations were identified in recurrence samples from five ACP cases (5/11,45%). One relapsed case showed histological and molecular signs of malignant transformation, including high ki67 and deletion of TP53. Surprisingly, this malignant tumour showed nuclear beta-catenin in all neoplastic epithelial cells and absence of pERK1/2 staining, despite the primary tumour showing the typical beta-catenin and pERK1/2 expression patterns. These results suggest that the molecular landscape of craniopharyngioma remains stable between recurrences in most cases, but, there is evidence of molecular evolution in a subset of cases. Activation of the MAPK pathway in the vast majority of ACP tumours supports the clinical evaluation of MAPK pathway inhibitors in ACP patients.

Transcriptomic Analysis of Resistant and Wild-Type Isolates Revealed Fludioxonil as a Candidate for Controlling the Emerging Isoprothiolane Resistant Populations of Magnaporthe oryzae.

The point mutation R343W in MoIRR, a putative Zn2Cys6 transcription factor, introduces isoprothiolane (IPT) resistance in Magnaporthe oryzae. However, the function of MoIRR has not been characterized. In this study, the function of MoIRR was investigated by subcellular localization observation, transcriptional autoactivation test, and transcriptomic analysis. As expected, GFP-tagged MoIRR was translocated in the nucleus, and its C-terminal could autonomously activate the expression of reporter genes HIS3 and α-galactosidase in absence of any prey proteins in Y2HGold, suggesting that MoIRR was a typical transcription factor. Transcriptomic analysis was then performed for resistant mutant 1a_mut (R343W), knockout transformant ΔMoIRR-1, and their parental wild-type isolate H08-1a. Upregulated genes in both 1a_mut and ΔMoIRR-1 were involved in fungicide resistance-related KEGG pathways, including the glycerophospholipid metabolism and Hog1 MAPK pathways. All MoIRR deficiency-related IPT-resistant strains exhibited increased susceptibility to fludioxonil (FLU) that was due to the upregulation of Hog1 MAPK pathway genes. The results indicated a correlation between FLU susceptibility and MoIRR deficiency-related IPT resistance in M. oryzae. Thus, using a mixture of IPT and FLU could be a strategy to manage the IPT-resistant populations of M. oryzae in rice fields.

BRAF V600E and previously unidentified KRAS G12C mutations in odontogenic tumors may affect MAPK activation differently depending on tumor type.

Although several types of odontogenic tumors share the same mutations in MAPK pathway genes, their effects on MAPK activation remain unclarified. This study aimed to evaluate the associations between these mutations and ERK phosphorylation in ameloblastoma and mixed odontogenic tumors (MOTs) and to analyze the expression pattern of phosphorylated ERK (p-ERK) for determining the involvement of MAPK activation in the development and progression of odontogenic tumors. Forty-three odontogenic tumors consisting of 18 ameloblastomas and 25 MOTs were analyzed for BRAF, KRAS, and NRAS mutations by Sanger sequencing. The expressions of BRAFV600E protein and p-ERK were detected by immunohistochemistry. The associations between mutation status and p-ERK expression were statistically analyzed. The effect of BRAFV600E inhibition on MAPK activation was investigated in ameloblastoma cells. In benign MOTs, BRAFV600E mutations were neither expressed at the protein level nor associated with p-ERK expression. In contrast, BRAFV600E -mutant ameloblastic fibrosarcoma showed co-expression of BRAF V600E protein and p-ERK, especially in the sarcomatous component. In ameloblastoma, p-ERK was predominantly expressed in the tumor periphery showing a significant correlation with BRAFV600E mutations, and in vitro BRAFV600E inhibition decreased ERK phosphorylation. KRASG12C mutations, previously unidentified in odontogenic tumors, were detected in one case each of benign MOT and ameloblastoma; only the latter was high-p-ERK. In conclusion, unlike in benign MOTs, BRAFV600E and KRASG12C mutations lead to MAPK activation in ameloblastoma, suggesting their role as therapeutic targets. p-ERK intratumoral heterogeneity indicates that MAPK pathway activation may be associated with sarcomatous proliferation of ameloblastic fibrosarcoma and infiltrative behavior of ameloblastoma.

The antagonistic effect of selenium on lead-induced apoptosis and necroptosis via P38/JNK/ERK pathway in chicken kidney

Lead (Pb), as a toxic heavy metal pollutant, has been paid much attention. Pb is often discharged into the environment through the soot, wastewater and waste residue in industrial production, which poses a great threat to animal health. Selenium (Se) is a trace element known to antagonize the toxicity caused by heavy metals. However, the interaction between Se and Pb in chicken kidney and its specific biological mechanism are still unclear. So, we constructed chicken models of Pb exposure and Pb, Se co-exposure. Therefore, we used western blot and qRT-PCR to detect the expression of related genes. The results showed that Pb activated the MAPK signaling pathway by up-regulating the expression of MARK pathway genes to induce the expression of pro-apoptotic genes and necroptosis-related genes. Se can regulate the MARK signaling pathway and attenuated the expression of MAPK pathway genes altered by Pb to reduce apoptosis and necroptosis of chicken kidney cells. Our study gives new ideas for the specific mechanism of Pb nephrotoxicity and provides a reference for comparative medicine and clinical medication.

Abstract P146: Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC

Abstract Activating mutations in the KRAS oncogene occur in approximately 30% of non-small cell lung cancers (NSCLC). Hence, multiple therapeutic strategies have been explored to block RAS including inhibition of downstream effector molecules in the MAPK pathway and direct pharmacological inhibition of the KRAS G12C mutant protein. However, inhibition of the RAS-RAF-MEK-ERK cascade with MEK inhibitor monotherapy has been insufficient to induce robust clinical responses. To identify novel drug targets that are synthetic lethal with MEK inhibition, CRISPR screens were conducted in multiple KRAS mutant NSCLC cell lines with or without trametinib treatment. Consistent with previous reports, several known MAPK-pathway genes, including KRAS, MEK, ERK, and FGFR1, were identified as top sensitizers validating our functional genomics approach. Interestingly, several novel targets were ranked among these top hits, including several members of the heparan sulfate biosynthesis pathway, such as the heparan sulfate 2-O-sulfotransferase (HS2ST1). In cells, HS2ST1 is responsible for transferring a sulfate from PAPS (3-phosphoadenosine-5’-phosphosulfate) to the 2-O position of a growing heparan sulfate chain. These chains partner with receptor tyrosine kinases at the cell surface to facilitate their interactions with growth factors. In this case, the interaction of FGF2 and FGFR1 has been shown to require HS2ST1-mediated 2-O sulfation, making HS2ST1 a novel druggable target in a well-validated FGFR-MAPK adaptive signaling axis. Here, we report that HS2ST1 is required for the feedback activation of the MAPK pathway that occurs downstream and in response to MEK or KRAS G12C inhibition via genetic validations studies. Knockout of HS2ST1 results in reduced feedback activation via FGFR1 and reduced MAPK pathway signaling. This reduced signaling leads to a reduction in cell growth in the presence of a MEK inhibitor, such as trametinib or selumetinib, or a KRAS G12C inhibitor like sotorasib. Our screen results reiterate the findings of others which indicate that effective MAPK suppression is key to inhibiting KRAS-mutant NSCLC cell growth. We find that HS2ST1 blockade would aid in maintaining the suppression of MAPK pathway signaling in KRAS-mutant NSCLC, leading to reduced cell viability and growth suppression. While others have described pairing receptor tyrosine kinase inhibitors with MAPK pathway inhibitors, this would be a novel approach to reducing upstream MAPK pathway feedback that may lead to reduced toxicity in patients. Citation Format: Leanne G. Ahronian, Silvia Fenoglio, Nikitha Das, Daniel Aird, David Guerin, Douglas Whittington, Haris Jahic, Erin Brophy, Patrick McCarren, Brian McMillan, James Tepper, Michaela Mentzer, Fang Li, Hongxiang Zhang, Xuewen Pan, John Maxwell, Jannik Andersen, Alan Huang, Robert Tjin Tham Sjin. Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P146.

ROS1 rearrangements in non-small cell lung cancer: screening by immunohistochemistry using proportion of cells staining without intensity and excluding cases with MAPK pathway drivers improves test performance

Therapeutically actionable ROS1 rearrangements have been described in 1-3% of non-small cell lung cancer (NSCLC). Screening for ROS1 rearrangements is recommended to be by immunohistochemistry (IHC), followed by confirmation with fluorescence in situ hybridisation (FISH) or sequencing. However, in practise ROS1 IHC presents difficulties due to conflicting scoring systems, multiple clones and expression in tumours that are wild-type for ROS1. We assessed ROS1 IHC in 285 consecutive cases of NSCLC with non-squamous histology over a nearly 2-year period. IHC was scored with ROS1 clone D4D6 (n=270), clone SP384 (n=275) or both clones (n=260). Results were correlated with ROS1 break-apart FISH (n=67), ALK status (n=194), and sequence data of EGFR (n=178) and other drivers, where possible. ROS1 expression was detected in 161/285 cases (56.5%), including 13/14 ROS1 FISH-positive cases. There was no ROS1 expression in one ROS1 FISH-positive case in which sequencing detected an ALK-EML4 fusion, but not a ROS1 fusion. The other 13 ROS1 FISH-positive cases showed moderate to strong staining with both IHC clones. However, one case with a TPM3-ROS1 fusion would have been scored as negative with SP384 and D4D6 clones by some previous criteria. ROS1 expression was also detected in 58/285 cases (20.4%) that had driver mutations in genes other than ROS1. A sensitivity of 100% for detecting a ROS1 rearrangement by FISH was achieved by omitting intensity from the IHC scoring criteria and expression in >0% cells with D4D6 or in ≥50% cells with SP384. Excluding cases with driver events in any MAPK pathway gene (e.g., in ALK, EGFR, KRAS, BRAF, ERBB2 and MET) substantially reduced the number of cases proceeding to ROS1 FISH. Only 15.9% of MAPK-negative NSCLC would proceed to FISH for an IHC threshold of >0% cells with D4D6, with a specificity of 42.4%. For a threshold of ≥50% cells with SP384, only 18.5% of MAPK-negative cases would proceed to FISH, with a specificity of 31.4%. Based on our data we suggest an algorithm for screening for ROS1 rearrangements in NSCLC in which ROS1 FISH is only performed in cases that have been demonstrated to lack activating mutations in any MAPK pathway gene by comprehensive sequencing and ALK IHC, and show staining at any intensity in ≥50% of cells with clone SP384, or >0% cells with D4D6.

Histiocytic disorders.

The historic term 'histiocytosis' meaning 'tissue cell' is used as a unifying concept for diseases characterized by pathogenic myeloid cells that share histological features with macrophages or dendritic cells. These cells may arise from the embryonic yolk sac, fetal liver or postnatal bone marrow. Prior classification schemes align disease designation with terminal phenotype: for example, Langerhans cell histiocytosis (LCH) shares CD207+ antigen with physiological epidermal Langerhans cells. LCH, Erdheim-Chester disease (ECD), juvenile xanthogranuloma (JXG) and Rosai-Dorfman disease (RDD) are all characterized by pathological ERK activation driven by activating somatic mutations in MAPK pathway genes. The title of this Primer (Histiocytic disorders) was chosen to differentiate the above diseases from Langerhans cell sarcoma and malignant histiocytosis, which are hyperproliferative lesions typical of cancer. By comparison LCH, ECD, RDD and JXG share some features of malignant cells including activating MAPK pathway mutations, but are not hyperproliferative. 'Inflammatory myeloproliferative neoplasm' may be a more precise nomenclature. By contrast, haemophagocytic lymphohistiocytosis is associated with macrophage activation and extreme inflammation, and represents a syndrome of immune dysregulation. These diseases affect children and adults in varying proportions depending on which of the entities is involved.

Molecular genetic evaluation of pediatric renovascular hypertension due to renal artery stenosis and abdominal aortic coarctation in neurofibromatosis type 1.

The etiology of renal artery stenosis (RAS) and abdominal aortic coarctation (AAC) causing the midaortic syndrome (MAS), often resulting in renovascular hypertension (RVH), remains ill-defined. Neurofibromatosis type 1 (NF-1) is frequently observed in children with RVH. Consecutive pediatric patients (N = 102) presenting with RVH secondary to RAS with and without concurrent AAC were prospectively enrolled in a clinical data base, and blood, saliva and operative tissue, when available, were collected. Among the 102 children, 13 were having a concurrent clinical diagnosis of NF-1 (12.5%). Whole exome sequencing was performed for germline variant detection, and RNA-Seq analysis of NF1, MAPK pathway genes and MCP1 levels were undertaken in five NF-1 stenotic renal arteries, as well as control renal and mesenteric arteries from children with no known vasculopathy or NF-1. In 11 unrelated children with sequencing data, 11 NF1 genetic variants were identified, of which 10 had not been reported in gnomAD. Histologic analysis of NF-1 RAS specimens consistently revealed intimal thickening, disruption of the internal elastic lamina and medial thinning. Analysis of transcript expression in arterial lesions documented an approximately 5-fold reduction in NF1 expression, confirming heterozygosity, MAPK pathway activation and increased MCP1 expression. In summary, NF-1-related RVH in children is rare but often severe and progressive and, as such, important to recognize. It is associated with histologic and molecular features consistent with an aggressive adverse vascular remodeling process. Further research is necessary to define the mechanisms underlying these findings.

CLL-358: Adaptation of Chronic Lymphocytic Leukemia to Ibrutinib Is Mediated by Epigenetic Plasticity of Residual Disease and Bypass Signaling via the MAPK Pathway

Context: Ibrutinib inhibits BTK with the most typical response in CLL being partial remission (PR) with measurable minimal residual disease (MRD) in blood. Remission is usually maintained until development of genetically-driven resistance. Objective: Mechanism of adaptation and survival in MRD. Patients and Methods: Pre-treatment CLL cells and under-treatment MRD were systematically collected from 33 high-risk CLL patients. Samples were characterized by high-dimensional, single-cell flow cytometry; bulk genomic, transcriptomic, and chromatin accessibility profiling; and single-cell RNA-seq profiling. Results: The genetic composition of MRD remained constant across timepoints, indicating that ibrutinib did not have any impact in shaping its genomic diversity. Ibrutinib induced chromatin dynamics in MRD resulting in a predominantly closed state. Chromatin regions that became more accessible under ibrutinib were enriched of binding sites for transcription factor that lay downstream ERK signaling. Regions that turned into a less accessible state were enriched for the binding sites of TF emanating from the BCR. At the transcriptomic level, most of the differentially expressed genes between pre- and post-treatment samples were downregulated in MRD, while only a fraction was upregulated. IL4, NF-kB, and metabolism and proliferation signatures were downregulated in MRD, while MAPK and RAS signatures were upregulated. CLL spleen samples from TCL1 mice under ibrutinib treatment showed an upregulation of MAPK pathway genes compared to untreated mice. Single-cell transcriptomes revealed a distinct post-treatment cell population driven by MAPK activity that functionally pre-existed in a fraction of CLL cells of baseline samples before ibrutinib start. At the signaling level, ibrutinib had no effect on the integrity of RAS-BRAF-MAPK-ERK pathway protein expression upon crosslinking of the BCR with anti-IgM but not after stimulation of TLR9 or CD40. Functional validation on primary samples by western blotting shows that RAS/ERK can be activated by BCR stimulation, irrespective of ibrutinib treatment in ex vivo experiments. Pharmacological inhibition of MEK (trametinib) and ERK (ulixertinib) synergized with ibrutinib, leading to decreased cell viability. Conclusions: MRD under ibrutinib adapts its phenotype in an epigenetic way to maintain functional competence of BCR signaling via the MAPK pathway, which turned to be a vulnerability of MRD persisting under ibrutinib.

Profile of Podocyte Translatome During Development of Type 2 and Type 1 Diabetic Nephropathy Using Podocyte-Specific TRAP mRNA RNA-seq.

Podocyte injury is important in development of diabetic nephropathy (DN). Although several studies have reported single-cell-based RNA sequencing (RNA-seq) of podocytes in type 1 DN (T1DN), the podocyte translating mRNA profile in type 2 DN (T2DN) has not previously been compared with that of T1DN. We analyzed the podocyte translatome in T2DN in podocin-Cre; Rosa26fsTRAP; eNOS-/-; db/db mice and compared it with that of streptozotocin-induced T1DN in podocin-Cre; Rosa26fsTRAP; eNOS-/- mice using translating ribosome affinity purification (TRAP) and RNA-seq. More than 125 genes were highly enriched in the podocyte ribosome. More podocyte TRAP genes were differentially expressed in T2DN than in T1DN. TGF-β signaling pathway genes were upregulated, while MAPK pathway genes were downregulated only in T2DN, while ATP binding and cAMP-mediated signaling genes were downregulated only in T1DN. Genes regulating actin filament organization and apoptosis increased, while genes regulating VEGFR signaling and glomerular basement membrane components decreased in both type 1 and type 2 diabetic podocytes. A number of diabetes-induced genes not previously linked to podocyte injury were confirmed in both mouse and human DN. On the basis of differences and similarities in the podocyte translatome in T2DN and T1DN, investigators can identify factors underlying the pathophysiology of DN and novel therapeutic targets to treat diabetes-induced podocyte injury.