E2F Target Research Articles

Investigation of the Synergistic Combination of a Novel Celmod (CC-99282) and BET Inhibitors in Preclinical DLBCL

Background: Golcadomide (GOLCA; CC-99282) is a novel cereblon E3 ligase modulator (CELMoD), which binds to cereblon (CRBN), a substrate receptor of CRL4 CRBN E3 ubiquitin ligase, and induces proteasome-dependent degradation of Ikaros and Aiolos, transcription factors essential for B cell malignancies. GOLCA was shown to exhibit promising cell of origin independent activity in pre-clinical DLBCL models and is currently being investigated in early clinical trials (NCT03930953) for relapsed/refractory non-Hodgkin lymphomas (R/R NHL). Ikaros and Aiolos have previously been shown to have occupancy on the promoter of the proto-oncogene MYC, which is subsequently downregulated by CELMoDs in DLBCL models. Given MYC is a well-studied downstream target of BET inhibitors and a driver of lymphoma disease, we investigated the mechanistic synergy of anti-proliferative and pro-apoptotic effects of GOLCA in combination with BMS-986158, a potent BET inhibitor. Results: Dose titration and analysis of the anti-proliferative effects of DLBCL cell lines (SU-DHL-4, WSU-DLCL2 and CARNAVAL) treated with either GOLCA or BMS-986158 suggests significant single agent activity of either agent. Bliss synergy score was determined and strong synergism of the two drugs was observed on day 5, with maximal bliss score (14.3-29.8) centered at low doses (1.25 and 2.5 nM) of BMS-986158 and sub-lethal doses of GOLCA (5-50 nM). Similar synergistic effects were found when combining GOLCA with JQ1, another tool compound BET inhibitor, confirming BET inhibition potentiates the anti-DLBCL effects of the CELMoD agent. Incucyte-based live cell image confirmed the enhanced anti-proliferative capacity of the combination compared to single agents. EdU (5-ethynyl-2′-deoxyuridine)-based cell cycle analysis revealed an increased proportion of G1-phase cells in combination treatment (67%) compared to GOLCA (38%), BMS-986158 (43%) and DMSO (35.4%) in the GOLCA resistant SU-DHL-4 cells. To identify key pathways responsible for the observed synergistic combination effect, we performed transcriptomic analyses of SU-DHL-4 and WSU-DLCL2 cells treated with GOLCA/BMS-986158 for 72 hrs. Compared to either single agents, the combination treatment downregulated significantly more genes (~1000 and 500 genes in SU-DHL-4 and WSU-DLCL2, respectively), which were enriched with cell cycle pathways. Gene set enrichment analysis (GSEA) showed the top downregulated gene sets in combination treatment were E2F targets such as CHEK1 and G2M checkpoint molecules including AURKA and CDC45. Given the critical role of CDKN1A (gene encodes p21) in cell cycle arrest, we examined its expression by real-time PCR. We found treatment of GOLCA induced CDKN1A mRNA expression (16.4 and 25.1-fold in SU-DHL-4 and WSU-DLCL2, respectively); remarkably, this induction was further enhanced by the combination with BMS-986158 (40.1 and 128.5-fold in SU-DHL-4 and WSU-DLCL2, respectively). Western blot confirmed the synergistic induction of p21 in combination compared to single agents, with a concomitant reduction of phosphorylated Rb, E2F target genes (Chk1, SKP2 and E2F1) and MYC. Since the main targets of GOLCA and BMS-986158 are transcription factors (Ikaros and Aiolos) and transcriptional regulator (Brd4), respectively, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) with antibodies targeting these three proteins along with various histone marks including H3K27ac and H3K4me3. Interestingly, the chromatin occupancies of Ikaros/Aiolos/Brd4 were highly overlapping in genes that are upregulated ( CDKN1A) and downregulated (e.g. CHEK1 and MYC) by the combination treatment. Further characterization of the interplay between Ikaros/Aiolos/Brd4 and their loci-specific interactomes may help elucidate the synergism at epigenetic levels. Conclusions: BET inhibition potentiates anti-proliferative effects of GOLCA in DLBCL cells through synergistic induction of p21 and inhibition of E2F signaling. The synergetic effects of BMS-986158 and GOLCA suggest potential clinical benefits of combining lower doses of single agents to achieve better efficacy with reduced risk of adverse effects.

Prognostic and Therapeutic Implications of TP53 expression in Chronic Myelomonocytic Leukaemia: Results of a Multicentre Study

Thetumor suppressor TP53 is among the most mutated genes in cancer, including many hematological malignancies in which it usually imparts more aggressive, chemo-refractory, and poor prognosis diseases. TP53 mutations are, though, remarkably rare in chronic myelomonocytic leukemia (CMML): affecting 2.4% of cases in a recent study ( Gurney et al, Leukemia 2023). We found pathogenic TP53 mutations ( TP53MT) in only 1.1% of 640 genotyped UK CMML patients. As expected, TP53MT conferred worse leukemia-free (LFS: median 23 v 28 mo, p=0.031) and overall (OS: 26 v 29 mo, p=0.015) survival compared with TP53WTcases. The clinical relevance in CMML of TP53 expression, however, remains unexplored. To address this we studied 92 TP53WT CMML patients (discovery cohort) from the National Taiwan University Hospital (Taipei, Taiwan) with available RNA-seq on presentation bone marrow (BM), each with extensive longitudinal clinical, laboratory and outcome data. Validation cohorts comprised 33 RNA-sequenced patients from The Christie (Manchester, UK) and 24 from Hospital Morales Meseguer (Murcia, Spain). For all cohorts, RNA-seq data from healthy controls (HCs) were available. Patients in the discovery cohort were divided into low and high TP53 expression groups, determined by the maximally selected rank statistics. TP53low patients (n=15) displayed significantly lower expression than HCs, while TP53high (n=77) had expression levels comparable to HCs. Thus, although most CMML patients are TP53WT, a subset has down-regulated TP53 expression and potential for altered p53 (and downstream) functions. TP53low and TP53high patients did not differ in clinical features or concurrent genetic alterations, although in all cohorts TP53low patients showed a trend towards poorer response to hypomethylating agents (HMA). TP53 low patients displayed significantly worse outcomes than TP53high patients (LFS 7 v 19 mo, p=0.002; OS 11 v 26 mo, p=0.001). Moreover, TP53 expression further stratified prognosis within different CMML-specific prognostic scoring system (CPSS)-molecular risk groups (Fig 1) . Time-dependent ROC analysis indicated TP53 expression as complementary to current risk stratification systems. In multivariable analysis, low TP53 expression remained prognostically detrimental. Survival analyses were consistent in both validation cohorts. GSEA and IPA analyses revealed that compared with HCs or TP53high, TP53low cells exhibited depleted expression of p53-dependent pathways, including MYC targets, E2F targets, G2/M checkpoints, and DNA repair. Interestingly, these are all among the most upregulated pathways in TP53MT (v TP53WT) samples across multiple cancers in TCGA data ( Donehower et al, Cell Rep 2019), indicating distinct roles for p53 in regulating these pathways in a TP53WT context, and that the driving biology of TP53low CMML is distinct from (and not functionally equivalent to) that of oncogenic TP53 mutations. TP53low patients demonstrated significantly enhanced TNF-alpha and inflammatory response signals, highlighting other distinctive pathobiology of the TP53low subgroup. In line with our clinical observation, single-sample GSEA showed significant enrichment of HMA resistance signatures in TP53low patients, potentially contributing to the dismal prognosis in this group. We next investigated whether this could be exploited therapeutically. We treated primary CMML BM cells ex vivo with azacitidine and NSC-207895, an MDMX inhibitor with p53 activating properties, observing clear and substantial synergy for combination therapy in samples from 10 of 11 patients. There was a trend towards inverse correlation between TP53 expression and empirical synergy scores (r=-0.35), suggesting potential for p53 activation to enhance HMA sensitivity in CMML, with broad efficacy, perhaps preferentially in adverse risk TP53low cases. In summary, we have identified and validated, across three cohorts from three countries, that a subgroup of CMML patients display aberrantly low TP53 expression, associated with HMA resistance and worse survival. Transcriptomic analyses revealed distinctive biology driving this novel TP53low subgroup (Fig 2), mandating further mechanistic study. Importantly we report consistent and substantial synergy for combining pharmacological p53 activation with HMA, presenting a novel targeted approach to improve HMA response for this unmet clinical need.

Single-Cell RNA-Seq Reveals Intermediate Cell States and Identifies Features Defining Cellular Heterogeneity in Inv(16) Acute Myeloid Leukemia (AML)

AML is an aggressive hematological malignancy with heterogeneous genetic abnormalities. One recurrent chromosomal translocation common in AML is chromosome 16 inversion, inv(16)(p13.1q22), which results in the leukemogenic fusion gene CBFB- MYH11. Using a conditional Cbfb-MYH11 (CM) knock-in mouse model to mimic the somatic expression of the CM fusion gene, we demonstrated that CM expression leads to impaired hematopoietic differentiation as well as accumulation of phenotypic hematopoietic stem cells (HSC) and pre-megakaryocyte/erythrocyte (Pre-Meg/E) progenitors, which are predisposed to leukemic transformation. Flow cytometry-based phenotypic analysis revealed that the transformed leukemic blasts are predominantly characterized as pre-granulocyte-macrophage progenitor (pre-GM) (Lin −cKit +Sca1 −CD16/32 -/loCD150 −CD105 −). However, cell type characterization via conventional surface markers is limited by known cell markers and is incapable of resolving pathologic heterogeneities. We previously reported that modeling AML in a continuum of differentiation states using single-cell RNA-seq (scRNA-seq) data predicts intermediate states of differentiation in AML. Herein, we utilized scRNA-seq to characterize CM leukemic blasts, and identified transcriptomic alternations and features that defined the leukemic cell states and heterogeneities. CM expression was induced by poly (I:C) and mice (n=3) were monitored for leukemia progression. At the leukemic end-stage (detection of >50% of circulating cKit + cells), we collected unfractionated and ckit + sorted peripheral blood mononuclear cells (PBMC) and bone marrow (BM) cells. Similarly poly(I:C)More than 105,000 cells harvested from the WT and CM leukemic mice were analyzed by scRNA-seq. We applied uniform manifold approximation and projection (UMAP) for dimensionality reduction and performed cell type annotation by SingleR. First, we mapped mature hematopoietic cell types in the WT PB and hematopoietic stem/progenitor cell populations (HSPC) in the WT BM, and in contrast, leukemic PB and BM were highly similar and showed distinct cell clusters compared to WT. To characterize HSPC subpopulations, we focused on cKit+ sorted WT and leukemic BM cells, visualized them via UMAP, and performed clustering and cell type annotation. The leukemic cKit+ cells were mostly identified as megakaryocytic-erythroid progenitor (MEP)-like HSC, revealing a discrepancy between flow cytometry-based phenotypic characterization and transcriptome-based cell type assignment. These leukemic MEP-like HSCs showed up-regulation of erythroid differentiation genes, including Hba-a1, Hba-a2, Hbb-bs, Hbb-bt and Sox6, together with decreased expression of granulocytic markers such as Elane, Prtn3, S100a8, S100a9 and Mpo. Comparison of leukemic MEP-like HSCs vs WT MEP clusters via gene set enrichment analysis (GSEA) with a threshold of nominal p-value ≤ 0.05 and FDR ≤ 0.05 in 50 hallmark gene sets (MSigDB) indicated dysregulated pathways, including up-regulation of “TNFα signaling pathway via NFκB”, “inflammatory response”, and “UV responsive downregulated genes”; and down-regulation of “MYC target V1”, “MYC target V2”, “E2F targets”, “G2M checkpoint”, and “oxidative phosphorylation”. Similarly, GSEA in Gene Ontology (GO) showed downregulation of pathways relevant to mitochondrial protein translation and ribosomal biogenesis/assembly in leukemic MEP-like HSCs, compared to WT MEP. In addition, cKit+ BM cells can be separated into 31 clusters (C0-C30), of which 9 leukemic clusters were identified. Through gene expression-based cell cycle scoring, single sample gene set enrichment (ssGSEA), and marker identification, these 9 leukemic clusters can be defined by several features, including high heme-metabolism (C0, C1, and C2), high proliferation (C1, C8), S phase (C4, C10), low oxidative phosphorylation (C2, C5, C17), high Cd9 (C10), high Egfl7 (C7, C8). Altogether, these data reveal intermediate differentiation cell states in inv(16) leukemic cells which are highly heterogeneous populations with distinct cell cycle stages, metabolic activities, and marker expression.

Deconvoluting Clonal and Cellular Architecture in IDH-Mutant Acute Myeloid Leukemia

Introduction Mutations in Isocitrate dehydrogenase 1/2 ( IDH) occur in 20% of acute myeloid leukemias (AML) and frequently co-occur with DNMT3A, NPM1, SRSF2, and NRAS. In clonal hematopoiesis (CH), IDH mutations confer high risk of AML transformation. Recently developed methods linking single cell genotype to single cell transcriptomic profiles and cell lineage offer the opportunity to define the transcriptomic consequences of each mutation across leukemic cell lineages and clonal phylogenies. Here, we develop an integrative single cell laboratory and analytical framework to study the genetic, clonal and cellular heterogeneity of IDH mutated CH and AML, across disease stages (diagnosis and relapse) and deliver a high-resolution map of IDH-mutant AML. Methods Bone marrow or peripheral blood mononuclear samples from 15 AML patients, 2 CH individuals, and 12 unaffected age-matched donors were profiled by single cell RNA-sequencing. For the AML cases, a median of 3 samples per patient were profiled under treatment with IDH inhibitor (IDHi) monotherapy (n=5 patients), IDHi in combination with intensive chemotherapy (NCT02632708, n=6) or in combination with hypomethylating agent (n=2). This dataset comprised 259,610 cells across AML (n=190,133), CH (n=16,705) and normal controls (n=52,772). Genotyping of Transcriptomes (Nam et al., 2019) (for IDH1/2, NPM1, SRSF2, and NRAS mutations) across 6 AML patients enabled genotyping 23% of cells at diagnosis for at least one clone-defining mutation. Results Through meta-analysis of 3,653 diagnostic AML samples profiled by a targeted DNA panel (Papaemmanuil et al., 2016; Tazi et al., 2022), we identified DNMT3A, SRSF2 and NPM1 as critical co-operative mutations in IDH-mutant AML. Amongst the 15 AML patients, 6 had IDH1 mutation, 8 had IDH2 mutations, and 1 had both IDH1 and IDH2. The co-occurring mutations in DNMT3A (n=11 patients), NPM1 (n=5), SRSF2 (n=5) reflected the genomic landscape of IDH-mutant AML. At diagnosis, IDH-mutant AML was enriched in immature hematopoietic stem and progenitor-like blasts. Compared to normal hematopoiesis, IDH-mutant AML blasts upregulated inflammatory response markers including TNFɑ/NFκB-signaling and downregulated proliferation-associated pathways including G2M Checkpoint, and MYC and E2F Targets, and DNA damage response. To investigate how co-mutations modify the IDH-mutant phenotype, we established an integrative single-cell profiling approach to assign single cells to distinct phylogenetic subclones and extract clone-specific transcriptional programs. SRSF2 and NPM1 co-mutations modulated the AML blast phenotype, towards erythroid ( SRSF2) or granulomonocytic lineage ( NPM1). NRAS- or SRSF2-mutant subclones defined distinct gene expression-derived clusters and upregulated proliferation and metabolic pathways. Furthermore, NPM1 co-mutated blasts upregulated KMT2A-target genes. Next, we tracked clonal responses to combination IDHi and chemotherapy using GoT and targeted DNA sequencing. In 4 cases, the ancestral clone, defined by IDH and DNMT3A mutations, retained clonal dominance in both mature and immature myeloid compartments at complete response (median 4 weeks). Conversely, subclones defined by mutations in NPM1, NRAS, or SRSF2, were either reduced or not detectable (limit of detection 2%). In two cases, mutations were not detected after therapy. In patients who relapsed after IDHi monotherapy treatment, blasts upregulated stemness, fatty acid metabolism, OxPHOS, and inflammation at relapse compared to diagnosis. Furthermore, MHC Class II was downregulated at relapse, pointing to immune evasion of AML as a potential relapse mechanism. Finally, we investigated the role of IDH2 mutations at CH. IDH-mutant CH-derived monocytes upregulated inflammation-associated pathways, mirroring the phenotypes observed in IDH-mutant AML at diagnosis. Conclusion We defined how IDH mutations and their frequent co-mutations dysregulated hematopoiesis. We leveraged state-of-the-art single cell techniques to assign leukemic cells to phylogenetic subclones and delineated the role of serially acquired co-mutations in shaping lineage bias and transcriptional programs. Furthermore, we defined genetic, clonal and transcriptional changes at three stages of the AML disease process: diagnosis, remission, and relapse under IDH inhibitor therapy.

Truncating SPEN Mutations Highlight BN2-Subtype DLBCL with Aggressive Biology and Features of Immune Evasion

Introduction: Molecular classifications have been developed to characterize the heterogeneity of diffuse large B cell lymphoma (DLBCL), with activation of BCL6 and Notch signaling pathways acting as driving pathogenic features in C1/BN2 subtype tumors. Among C1/BN2 defining variants are truncating/inactivating SPEN mutations. SPEN regulates the Notch signaling pathway by initiating formation of a repressive complex that facilitates transcriptional repression of Notch target genes. Our group has identified SPEN mutations enriched in DLBCL cases failing to achieve event-free status at 24 months (EFS24). This contrasted with generally favorable outcomes in C1/BN2 tumors, suggesting a potential high-risk molecular feature with unexplored significance. Presenting an opportunity to expand underlying mechanisms and risk stratification in C1/BN2 tumors, we aimed to use a functional genomic approach, combined with clinical data, to characterize the alternative biology stemming from SPEN truncating mutations. Methods: FFPE tumor biopsies from newly diagnosed DLBCL cases (N=444) enrolled in the Mayo Clinic/Iowa Lymphoma Molecular Epidemiology Resource (MER) program were analyzed by WES (n=404) and RNA-seq (n=321). Biologic and clinical variables were annotated for all cases. CRISPR/Cas9 introduced truncating mutations to the endogenous SPEN locus in OCI-LY3 & SU-DHL-2 ABC-type human cell lines to establish models of SPEN depletion. Functional in vitro analysis utilized standard methods for RNA-seq, cell proliferation, western blot, and flow cytometry. Results: WES identified 29/404 ndDLBCL (7.2%) harboring SPEN mutations; n=17 missense and n=12 nonsense or frameshift insertions/deletions (truncating variants - [trunc]), the later considered as the focal point of our study. Against all cases, SPEN trunc cases displayed enrichment for high-risk factors including non-GCB COO (p=0.06, OR=3.7, 95% CI [0.9, 22.2]) and primary refractory disease (PTR; p=0.02, OR=5.0, 95% CI [1.05, 19.9]), and demonstrated inferior OS (p=0.06, HR=2.2), where a majority of clinical progression events occurred within 12 months of diagnosis. Leveraging RNA-seq, we observed 11 of 11 SPEN trunc cases exhibiting a double-hit negative gene expression signature, 9/11 cases with inflammatory or depleted microenvironment (LME), and 8/11 with a signature associating with intermediate/high risk of EFS24 failure. Applying the LymphGen algorithm, 5/12 SPEN trunc cases received the BN2 classification, observing co-occurring mutations with CD70 (p<0.01, OR=9.68), BRCA2 (p=0.03, OR=5.84), TET2 (p=0.02, OR=4.91), IRF4 (p=0.02, OR=7.27), and PTPRD (p<0.01, OR=8.31) genes, and were mutually exclusive with ARID1A, BCL2, EZH2, FAS, HLA-B, IRF8, and TMEM30A mutations ( Figure 1A). Isolating SPEN trunc against BN2 cases without SPEN variants (n=14), despite similar clustering of non-GCB COO (p=0.7), PTR was exclusively observed in SPEN trunc cases, accompanied again by inferior OS (p=0.07, HR=4.2; Figure 1B). In the OCI-LY3 SPEN depletion model, GSEA analysis from RNA-seq revealed activation of E2F (NES=2.7; p=9.4E-20) and MYC target genes (NES=2.3; p=4.1E-6), while both OCI-LY3 and SU-DHL-2 models featured depletion of antigen presentation genes (NES= -1.8, p=5.7E-4; NES= -2.2, p=3.8E-7, respectively). A decrease of MHC class II proteins (HLA-DR, HLA-DP) was confirmed by flow cytometry in both models (p<0.01). Hypothesizing loss of SPEN enhances reliance on the BCL6-HDAC3 axis featured in BN2 tumors, we treated both SPEN depletion models with a class-I HDAC inhibitor highly selective for HDAC3, BRD-3308, and indeed observed a 1.4 and 2.4-fold increase in sensitivity compared to WT cells (p=0.07, p<0.01, respectively). Significance: We find SPEN trunc mutations in poor acting DLBCL cases with clinical and biologic characteristics that diverge from C1/BN2 biology. The enhanced rate of clinical progression highlights urgency to better characterize these tumors. Our data suggests loss of SPEN regulatory mechanisms may act cooperatively with C1/BN2 biology to facilitate tumor immune evasion and drive progression through Notch-mediated pathways. Importantly, in vitro evidence shows SPEN deficient lymphoma cells are susceptible to targeted therapeutics against dependent pathways, providing rationale for advancing individualized care strategies for affected patients.

Comparative Transcriptome Analyses in Mantle Cell Lymphoma (MCL): Evidence of E2F1 As a Major Target in Aggressive Blastoid MCL Model

Background Mantle cell lymphoma (MCL) is a highly aggressive B-cell lymphoma characterized by the translocation t(11;14)(q13;q32) which triggers the dysregulation of the cyclin D1 by placing its coding gene CC1ND1 under the control of an immunoglobulin promoter. One of the major consequences of this molecular event is the disturbance of the cyclin D/Rb pathway leading to Rb inactivation and activation the elongation factor E2F1 mainly implicated in cell cycle progression. The mainstay of MCL therapies remains the chemo-immunotherapy followed by autologous transplantation but recently several novel therapies have been developed such as BTK inhibitors, Venetoclax, CDK4/6 inhibitors and more recently CAR-T therapies. However, patients with aggressive forms of MCL exhibit low response rates, requiring the identification of novel therapeutic targets. Materials and Methods We have previously generated an MCL cell line (UPN-1) from a patient with a blastoid variant of MCL presenting unique morphological and cytogenetics characteristics (M'kacher et al, Oncogene 2003). This cell line has been shown to harbor a TP53 mutation and a highly increased sensitivity to radiation despite the absence of functional p53. The molecular basis of this phenomenon has not been explored. In this work, we further characterized UPN-1 cell line using the Clarium S human microarray which has been compared to the gene expression profile of other existing MCL cell lines (GRANTA-519, JEKO-1, JVM-2, MAVEK-1, MINO, REC-1, SP-49, SP-53, Z-138). After mathematical correction, a supervised analysis was performed between triplicate samples of UPN-1 and a group constituted with all other MCL cell lines. We have then set up in vitro assays to determine the effect of a direct E2F1 inhibitor on the proliferative potential of UPN-1. Results The comparative transcriptome analyses revealed a list of 47 genes specifically upregulated in UPN-1. Unsupervised classification allowed to discriminate UPN-1 samples from other MCL cell lines based on the expression of these 47 genes. These data suggested a specific expression profile of UPN-1 as compared to other cell lines. Among the upregulated genes, E2F1 elongation factor was found to be highly upregulated in UPN-1 as compared to other MCL cell lines along with positive enrichment of E2F targets which are mainly implicated in cell cycle progression (Figure 1). Interestingly, UPN-1 has a low level of BCL-2 as compared to other MCL lines that could explain its radio sensitivity. However, other signaling pathways involved in the inhibition of apoptosis were found to be present in UPN-1 by geneset enrichment analysis. The expression of CDKN1A (p21), major cell cycle regulator and known as a marker of aggressive MCL, was found to be low in UPN-1. A repression of immune response pathway such as NFKB with low expression of NFKBIA was identified. Finally, the expression of PIK3CD which encodes for a therapeutic target in MCL (such as PI3KDelta inhibitor Idelalisib) was also significantly repressed in UPN-1 as compared to nine other MCL cell lines. To evaluate the effect of the direct inhibition of E2F1, we treated UPN-1 cells with a targeted E2F1 inhibitor 5‘-Deoxy-5‘-(methylthio)adenosine (MTA) which is a protein methylation inhibitor. MTT assays revealed a 50% reduction of proliferation at + 4 hours in comparison to the vehicle-treated conditions (P<0.0001).Annexin assays showed an increase in early apoptosis (36.6 %) at + 8 hours with subsequent rise in late apoptotic cells (64.5 %) observed after 24 hours of treatment. Interestingly, qRT-PCR analyses of MTA-treated cells exhibited a decrease in the expression of downstream factors associated with E2F1, such as RAD51, BRCA1, CDK2, CCNB2, RANBP1. Conclusions We report here for the first time the comparative transcriptome analysis of the unique aggressive blastoid MCL line UPN-1 as compared to other MCL lines described. This cell line exhibited a major upregulation of E2F1 expression and a down regulation of the cell cycle inhibitor CDKN1A(p21). The potential effects of the direct inhibition of E2F1 using the targeted inhibitor MTA demonstrated a reduction in cell proliferation and induction of apoptosis, suggesting the possibility of associating clinically acceptable E2F1 inhibition strategies to other current therapies.

A PTP1B-Cdk3 Signaling Axis Promotes Cell Cycle Progression of Human Glioblastoma Cells through an Rb-E2F Dependent Pathway.

PTP1B plays a key role in developing different types of cancer. However, the molecular mechanism underlying this effect is unclear. To identify molecular targets of PTP1B that mediate its role in tumorigenesis, we undertook a SILAC-based phosphoproteomic approach, which allowed us to identify Cdk3 as a novel PTP1B substrate. Substrate trapping experiments and docking studies revealed stable interactions between the PTP1B catalytic domain and Cdk3. In addition, we observed that PTP1B dephosphorylates Cdk3 at tyrosine residue 15 invitro and interacts with it in human glioblastoma cells. Next, we found that pharmacological inhibition of PTP1B or its depletion with siRNA leads to cell cycle arrest with diminished activity of Cdk3, hypophosphorylation of Rb, and the downregulation of E2F target genes Cdk1, Cyclin A, and Cyclin E1. Finally, we observed that the expression of a constitutively active Cdk3 mutant bypasses the requirement of PTP1B for cell cycle progression and expression of E2F target genes. These data delineate a novel signaling pathway from PTP1B to Cdk3 required for efficient cell cycle progression in an Rb-E2F dependent manner in human GB cells.

Treatment of a TP53 isogenic AML Cell Line Model with Decitabine and All Trans-Retinoic Acid (ATRA) Targets MYC for Antileukemic Activity in a p53-Independent Fashion

Background The DECIDER randomized phase II trial showed that the addition of ATRA to decitabine (DAC) significantly improves survival and overall response rate (ORR) in newly diagnosed elderly AML patients (Lübbert et. al., J Clin Oncol. 2020), with a higher ORR in TP53-mutated (mostly heterozygous) compared to TP53 wildtype. Mechanisms of this in vivo synergism are under study, involving changes in global transcriptome and chromatin accessibility in both TP53wt and TP53mut AML cell lines (Meier et. al., Blood Cancer J. 2022). To further unravel the mechanism of action of DAC+ATRA (D+A) in AML, these studies are now extended to an isogenic TP53 model representing wt vs knock-out. Methods TP53 isogenic MOLM13 cells ( TP53+/+, TP53-/-, Boettcher et al., Science 2019) were treated with 100nM DAC by 3 daily pulses, 250nM ATRA on day 4, and studied for proliferation (EdU), by RNA-sequencing (RNA-seq) and immunofluorescence (IF) at 24, 48 and 72h post ATRA addition. RNA-seq data were analyzed after pre-processing (Cutadapt) and annotation (RNA star) by DEseq2 (adj p-value <0.05, fold change >2), functional enrichment analysis by pyGSEA on ‘50 Hallmark pathways’ using T-statistics on differentially expressed genes (DEGs). Results D+A reduced cell proliferation and increased apoptosis by 88% and 44% in TP53 +/+ cells, by 50% and 15% in TP53 -/- cells relative to control at 48h. By RNA-seq, the global transcriptomic profile of D+A was distinct from single-agent treatment at all 3 timepoints, as the majority of the DEGs were unique to the combination. D+A had 2250 unique DEGs (uDEGs) in TP53 +/+ cells (compared to 192 uDEGs for DAC, 249 uDEGs for ATRA); D+A had 1209 uDEGs in TP53 -/- cells (compared to 328 uDEGs with DAC and 197 uDEGs with ATRA) at 72h. By functional enrichment analysis, we found that D+A requires TP53 for antileukemic activity, as most proliferative pathways (e.g. hallmark G2M checkpoint, hallmark E2F targets) were depleted exclusively in a p53-dependent manner. Interestingly, D+A was able to induce an interferon response and deplete MYC target genes and mTOR signalling independent of p53. As MYC is a known target depleted by D+A, we investigated MYC (by IF) as an additional target for antileukemic activity. We found that global MYC levels were significantly depleted upon ATRA addition to DAC. ATRA depleted MYC levels independent of the TP53 status, while DAC depleted MYC in a p53-dependent manner (Fig. 1A). DAC was able to induce MYC T58 phosphorylation in both TP53 +/+ and TP53 -/- cells (Fig. 1B) but was only able to reduce MYC global levels in TP53+/+ cells, pointing towards a possible p53-dependent perturbation of proteasomal activity. FBXW7 (SCF complex), responsible for ubiquitinating pMYC T58, and USP28 (deubiquitinase) expression levels analysis revealed that USP28 is depleted upon DAC treatment, suggesting that FBXW7 should be able to mark pMYC T58 for ubiquitination and degradation, and further investigation is ongoing to determine proteasomal perturbation and how p53 loss is associated with it. Conclusions Our results represent a mechanistic exploration of how the addition of ATRA was able to enhance DAC's antileukemic activity in two polar opposite TP53 states (intact vs. null). D+A treatment induces a unique molecular signature compared to either drug and targets p53 for an antileukemic effect, but not exclusively, as MYC depletion as well as interferon induction is independent of p53. We also identified p53-dependent perturbation of proteasomal activity, as high amounts of pMYC T58 accumulate in TP53-/- cells upon D+A treatment, and hypothesize that pMYC T58 accumulation results in development of resistance to D+A. These studies will be extended to the most clinically relevant heterozygous TP53 hotspot mutations.

High Comorbidity of Pediatric Cancers in Patients with Birth Defects: Insights from Whole Genome Sequencing Analysis of Copy Number Variations

BackgroundPatients with birth defects (BD) exhibit an elevated risk of cancer. We aimed to investigate the potential link between pediatric cancers and BDs, exploring the hypothesis of shared genetic defects contributing to the coexistence of these conditions. MethodsThis study included 1454 probands with BDs (704 females and 750 males), including 619 (42.3%) with and 845 (57.7%) without co-occurrence of pediatric onset cancers. Whole genome sequencing (WGS) was done at 30X coverage through the Kids First/Gabriella Miller X01 Program. Results8211 CNV loci were called from the 1454 unrelated individuals. 191 CNV loci classified as pathogenic/likely pathogenic (P/LP) were identified in 309 (21.3%) patients, with 124 (40.1%) of these patients having pediatric onset cancers. The most common group of CNVs are pathogenic deletions covering the region ChrX:52,863,011-55,652,521, seen in 162 patients including 17 males. Large recurrent P/LP duplications >5MB were detected in 33 patients. ConclusionsThis study revealed that P/LP CNVs were common in a large cohort of BD patients with high rate of pediatric cancers. We present a comprehensive spectrum of P/LP CNVs in patients with BDs and various cancers. Notably, deletions involving E2F target genes and genes implicated in mitotic spindle assembly and G2/M checkpoint were identified, potentially disrupting cell-cycle progression and providing mechanistic insights into the concurrent occurrence of BDs and cancers.

Comprehensive transcriptomic analyses identify the immunosuppressive effects of LLDT-8 in ART-treated SIV-infected rhesus macaques

BackgroundChronic immune activation plays a significant role in the pathogenesis and disease progression of human immunodeficiency virus (HIV), and the existing interventions to address this issue are limited. In a phase II clinical trial, (5R)-5-hydroxytriptolide (LLDT-8) demonstrated promising potential in enhancing CD4+ T cell recovery. However, the therapeutical effects of LLDT-8 remained to be systemic explored. MethodsTo assess the treatment effects of LLDT-8, we conducted flow cytometry and RNA-seq analyses on eight Chinese rhesus monkeys infected with simian immunodeficiency virus (SIV). Additionally, we performed comprehensive transcriptomic analyses, including cross-sectional and longitudinal differentially expressed gene (DEG) analysis, gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), and deconvolution analysis using peripheral blood mononuclear cell (PBMC) samples from 14-time points. These findings were further validated with RNA-seq analysis on patients who received LLDT-8 treatment, along with in vitro cellular experiments using human PBMCs. ResultsFlow cytometry analysis revealed that LLDT-8 treatment significantly reduced the percentage of HLA-DR+CD38+CD8+ T cells in SIV-infected rhesus monkeys (P < 0.001). The cross-sectional and longitudinal analysis identified 2531 and 1809 DEGs, respectively. GSEA analysis indicated that LLDT-8 treatment led to significant downregulation of proliferation-related pathways, such as E2F targets, G2M checkpoint, and mitotic spindle pathways. WGCNA analysis identified two modules and 202 hub genes associated with CD8 activation levels. Deconvolution analysis showed a significant decrease in the proportion of CD8+ T cells and activated CD4+ T cells during LLDT-8 treatment. Gene ontology results demonstrated that the common DEGs between LLDT-8-treated patients and rhesus monkeys were primarily enriched in cell activation and cell cycle progression. Furthermore, in vitro cellular experiments validated the consistent impact of LLDT-8 in inhibiting proliferation, activation (HLA-DR and CD38 expression), exhaustion (PD-1 expression), and IFN-γ production in human CD4+ and CD8+ T cells. ConclusionLLDT-8 exhibited notable efficacy in alleviating immune activation in both an in vivo animal model and in vitro human cell experiments. These findings suggest that LLDT-8 may hold potential as a drug for managing systemic immune activation associated with SIV/HIV infection, warranting further prospective clinical exploration.

Molecular portraits of colorectal cancer morphological regions.

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole-tumor molecular descriptors depend on the morphological heterogeneity with significant impact on current molecular predictors. We investigated intra-tumor heterogeneity by morphology-guided transcriptomics to better understand the links between gene expression and tumor morphology represented by six morphological patterns (morphotypes): complex tubular, desmoplastic, mucinous, papillary, serrated, and solid/trabecular. Whole-transcriptome profiling by microarrays of 202 tumor regions (morphotypes, tumor-adjacent normal tissue, supportive stroma, and matched whole tumors) from 111 stage II-IV CRCs identified morphotype-specific gene expression profiles and molecular programs and differences in their cellular buildup. The proportion of cell types (fibroblasts, epithelial and immune cells) and differentiation of epithelial cells were the main drivers of the observed disparities with activation of EMT and TNF-α signaling in contrast to MYC and E2F targets signaling, defining major gradients of changes at molecular level. Several gene expression-based (including single-cell) classifiers, prognostic and predictive signatures were examined to study their behavior across morphotypes. Most exhibited important morphotype-dependent variability within same tumor sections, with regional predictions often contradicting the whole-tumor classification. The results show that morphotype-based tumor sampling allows the detection of molecular features that would otherwise be distilled in whole tumor profile, while maintaining histopathology context for their interpretation. This represents a practical approach at improving the reproducibility of expression profiling and, by consequence, of gene-based classifiers.

Molecular portraits of colorectal cancer morphological regions

Heterogeneity of colorectal carcinoma (CRC) represents a major hurdle towards personalized medicine. Efforts based on whole tumor profiling demonstrated that the CRC molecular subtypes were associated with specific tumor morphological patterns representing tumor subregions. We hypothesize that whole-tumor molecular descriptors depend on the morphological heterogeneity with significant impact on current molecular predictors. We investigated intra-tumor heterogeneity by morphology-guided transcriptomics to better understand the links between gene expression and tumor morphology represented by six morphological patterns (morphotypes): complex tubular, desmoplastic, mucinous, papillary, serrated, and solid/trabecular. Whole-transcriptome profiling by microarrays of 202 tumor regions (morphotypes, tumor-adjacent normal tissue, supportive stroma, and matched whole tumors) from 111 stage II-IV CRCs identified morphotype-specific gene expression profiles and molecular programs and differences in their cellular buildup. The proportion of cell types (fibroblasts, epithelial and immune cells) and differentiation of epithelial cells were the main drivers of the observed disparities with activation of EMT and TNF-α signaling in contrast to MYC and E2F targets signaling, defining major gradients of changes at molecular level. Several gene expression-based (including single-cell) classifiers, prognostic and predictive signatures were examined to study their behavior across morphotypes. Most exhibited important morphotype-dependent variability within same tumor sections, with regional predictions often contradicting the whole-tumor classification. The results show that morphotype-based tumor sampling allows the detection of molecular features that would otherwise be distilled in whole tumor profile, while maintaining histopathology context for their interpretation. This represents a practical approach at improving the reproducibility of expression profiling and, by consequence, of gene-based classifiers.

EXTH-06. GLIOBLASTOMA PATIENT SPECIFIC TRANSCRIPTOME REMODELING IN RESPONSE TO MDM2 ANTAGONIST TREATMENT OF WILD-TYPE P53 CANCER STEM CELLS IS ASSOCIATED WITH SENSITIVITY AND STRATEGIES FOR COMBINATION THERAPY

Abstract Over 70% of glioblastomas are p53 wild-type and these patients could benefit from p53 reactivation treatment. Here we determined the sensitivity of a glioblastoma patient-derived cancer stem cells (CSCs) panel to three MDM2 antagonists (MDM2a) to test to what extent transcriptional reprogramming is affected by genomic background and correlates to response to acute treatment with MDM2 antagonists. IC50 concentrations and area above the curve (AAC) were measured from dose response curves obtained from 4 and 7-day treatment. The inhibitors were specific to wt-p53 CSCs, but these presented a wide range of sensitivity. Seven wt-p53 CSCs were treated RG7112 IC50 concentrations or DMSO control for 24h (n=4). RNA was isolated for Illumina Truseq stranded mRNA libraries sequenced at 30M depth. Quantified raw counts were processed using NOISeq R package to determine differentially expressed genes (DEG) between control and treated samples. In addition to the expected high representation of upregulated p53 targets in all cell lines, we observed significan cell specific transcriptome alterations, including enrichment of survival pathways, such as mTOR, ERK and NFkB in the less sensitive CSC lines, which did not readily correlate with the individual genomic landscapes. E2F targets, G2-M cell cycle check point and DNA-repair pathways were highly enriched in the downregulated genes. Combination of MDM2a with radiation treatment (RT) was synergistic to a subset of CSCs. As validation we found that MDM2a treatment was effective in sensitizing a resistant orthotopic mouse glioblastoma PDX to fractionated RT, with maximum efficacy when treatment started 24h prior to RT vs simultaneously (Log-rank Mantel-Cox test: p=0.0006 vs 0.0277). The integration of the treatment-mediated transcriptional patterns with differential sensibility to MDM2 antagonists and genomic landscape of the CSC panel provides a platform to identify targets for combination therapies, which is the most promising clinical application of the reactivation of wt-p53 in GBMs.

Multi-Omics Analysis Reveals That TET2 Loss Epigenetically Primes Monocytes for Inflammatory Responses Via AP-1 Signaling

Loss of function mutations in TET2 are common in clonal hematopoiesis (CH) and myelodysplastic syndromes (MDS). Increased inflammation and stem cell capacity have been reported in Tet2 KO mouse models, but molecular mechanisms and cell type-specific contributions to explain this phenotype are lacking. To create models of CH-like TET2 deficiency, we transplanted Mx1-CRE Tet2 fl/fl (Tet2 KO) or Tet2 fl/fl (both CD45.1 +) in CD45.2 + recipientsfollowing radiation-free conditioning with ACK2 (anti-cKit) antibody injection. Six months post-transplant, we flow sorted CD45.1 +Tet2 KO and Tet2 fl/fl Lin -Sca-1 +cKit + (LSK) cells, granulocyte-monocyte progenitors (GMP), and monocytes for RNA and assay for transposase-accessible chromatin (ATAC) sequencing. Differential gene expression analysis identified 902 (468 up, 434 down) differentially expressed genes (DEGs) in LSK, 134 (95 up, 39 down) in GMP, and 474 (125 up, 349 down) in monocytes (p adj&amp;lt;0.05). Gene set enrichment analysis (GSEA) identified that the top Hallmark gene sets in Tet2 KOLSK cells were related to MYC targets, oxidative phosphorylation, and E2F targets. In contrast, GMP and monocytes were most enriched for IFN-alpha and gamma gene sets along with IL6/JAK/STAT3 signaling. ATACseq revealed increased accessibility of myeloid-related transcription factor (TF) binding motifs in Tet2 KOLSK cells (CEBPA, PU.1-IRF(ETS:IRF), and AP-1 TF FOSL2(bZIP)), while prediction of cis-regulating regions via GREAT identified downregulated peaks associated with stem cell maintenance and upregulated peaks associated with myeloid mediated immunity. Peaks upregulated in Tet2 KOGMP cells were enriched for the motifs recognized by CEBPE, ISRE(IRF)) and the AP-1 TF JUND, while upregulated peaks in monocytes were enriched for RUNX1 and CEBPA motifs, as well as AP-1 TF FOS::JUNB. GREAT analysis in GMPs identified cis-regulatory regions related to myeloid mediated immunity, while monocytes possessed those associated with biotic stimuli. To better dissect heterogeneity across primitive and mature cell types driven by TET2 loss, we performed scRNAseq on Tet2 KO and Tet2 WT wholebone marrow (WBM) and sorted LSK cells. We identified 18 transcriptionally distinct cell subsets in a combined analysis of WBM. Tet2 KOprogenitor and myeloid subsets were all enriched for gene sets related to IFN-alpha and gamma and immune signaling. Interestingly, primitive and cycling HSPCs were also enriched for MYC target and oxidative phosphorylation gene sets, while these were negatively enriched for GMP, monocyte progenitor, and monocyte Tet2 KO subsets. Further, the IL-6/JAK/STAT3 signaling gene set was enriched in later myeloid cell types, but not in early or cycling HSPCs. These observations led us to hypothesize that Tet2 KO BM cell populations have differentially enhanced phosphoprotein signaling responses to key cytokines. We used a 36-antibody mass cytometry panel to perform deep immunophenotyping and signaling response studies in Tet2 KO BM. FlowSOM analysis identified clusters corresponding to cKIT +CD34 + myeloid progenitors, a Ly6C +CD34 +cKIT + progenitor, and Ly6Chi monocyte clusters were enriched in Tet2 KO BM, while manual gating revealed expansion of LSK, MPP3, and monocytes. We found that activation of pSTAT3 and pSTAT1, in response to either IL-6 or IFNγ, respectively, were significantly higher in Tet2 KO Ly6Chi monocytes, while the more primitive Ly6C +CD34 +cKIT + progenitors demonstrated only an increased response to IFNγ at pSTAT1. Further, prolonged exposure to IL-6 in immortalized Tet2 KO Hoxb8-ER GMP-like cells led to significantly higher levels of pSTAT3 over 4 hours. Since AP-1 TFs are drivers of inflammation and were enriched in our ATACseq dataset, we tested the effects of an AP-1 inhibitor on the Tet2 KO Hoxb8-ER cells. We found that the AP-1 inhibitor T5224 dose dependently reduced the expansion of Tet2 KO Hoxb8 progenitor cells in base media and inhibited the IL-6 mediated expansion of Tet2 KO Hoxb8 cells. Our data show that TET2 loss rewires BM HSPCs towards an inflammatory, myeloid phenotype. Starting at the GMP stage, we see increases in phosphoprotein responses to IFNγ, and then the addition of hypersensitivity to IL-6 in monocytes. TET2 loss leads to an increase in accessible AP-1 motifs in Tet2 KO cells, while inhibition of AP-1 reduces fitness of cells, suggesting a possible therapeutic strategy for TET2-mutated myeloid malignancy.

Narazaciclib, a Differentiated CDK4/6 Antagonist, Prolongs Cell Cycle Arrest and Metabolomic Reprogramming, Enabling Restoration of Ibrutinib Sensitivity in Btki-Resistant Mantle Cell Lymphoma

Bruton tyrosine kinase inhibitors (BTKi) have transformed the therapeutic landscape of mantle cell lymphoma (MCL); however, primary and acquired resistance to these agents remains a challenge. Previous studies have suggested that narazaciclib (ON123300), a second-generation, orally bioavailable and clinical-stage CDK4/6 inhibitor (CDKi), may trigger cell cycle arrest and significant tumor growth inhibition (TGI) in BTKi-resistant MCL. We compared the efficacy and safety profiles of narazaciclib with three health authority-approved CDKi (palbociclib, abemaciclib or ribociclib) in association with covalent (ibrutinib, acalabrutinib) and non-covalent (pirtobrutinib, ARQ-531) BTKi, across a panel of 10 MCL cell lines with distinct sensitivity to the first-in-class BTKi, ibrutinib. We integrated RNA sequencing and gene set enrichment analysis (GSEA) coupled to phospho-proteomics and kinase-substrate enrichment analysis (KSEA) to unravel the molecular bases of BTKi-CDKi drug interaction in MCL. CellTiter-Glo proliferation assay, FACS-mediated quantification of cell cycle and apoptosis, RT-PCR and western blot approaches followed by Seahorse-mediated metabolic assays were carried out for validation purposes. Finally, we evaluated the safety and efficacy of narazaciclib/ibrutinib combo in vivo in three immune-competent chicken embryo chorioallantoic membrane (CAM) MCL xenograft models. We found that narazaciclib exhibited the highest antitumor activity among MCL cell lines (mean IC 50: 3.61 ± 2.1 µM), regardless of the sensitivity of these to ibrutinib. Although there was no correlation between CDKi sensitivity and direct repression of the CDK4/CDK6-pRb pathway in MCL, transcriptomic and phenotypic analyses revealed a predominant downregulation of E2F target genes and G2/M checkpoint response upon narazaciclib treatment. This feature was linked to intracellular accumulation of p21, p16, and phospho-p27, decreased mitotic index, G1 cell cycle blockade, and apoptosis onset. When combined with ibrutinib, but not with the second-generation acalabrutinib, narazaciclib achieved significant synergistic antitumor activity in both BTKi-sensitive and BTKi-resistant cells. The combination was not associated with improved apoptosis, but rather with a slight but constant augmentation in G1 phase blockade and the down-modulation of cell cycle-associated transcriptome, although similar features were found when substituting narazaciclib with abemaciclib. The integration of transcriptomic and phospho-proteomic synergistic signatures further revealed that narazaciclib-ibrutinib combo modulated signatures related to DNA repair, P53 signaling, and glycolytic activity. Accordingly, in this model, narazaciclib/ibrutinib-exposed cells underwent a metabolic switch from glycolytic to oxidative phosphorylation (OxPhos) phenotype accompanied by intracellular accumulation of mitochondria and increased mtDNA copy number. This switch appeared to be specific to MCL cells rendered refractory to ibrutinib upon activation of alternative NFkB signaling, as it was not found in MCL-BTKmut cells. In vivo, while narazaciclib single agent achieved a moderate TGI in the CAM model, the narazaciclib/ibrutinib combo reduced tumor spreading by 65% and allowed a 50% reduction in malignant B cell infiltration into host bone marrow, with no detectable toxicity. In conclusion, our findings demonstrate that narazaciclib is safe and effective as a single agent in preclinical models of MCL, including BTKi-resistant cases. Its combination with ibrutinib achieved a synergistic tumoricidal effect in vitro and in vivo, accelerating cell cycle blockade and reverting the metabolic reprogramming characterizing MCL refractoriness to BTKi therapy.

Targeting the fibroblast growth factor pathway in molecular subtypes of castration-resistant prostate cancer.

Androgen receptor (AR) pathway inhibition remains the cornerstone for prostate cancer therapies. However, castration-resistant prostate cancer (CRPC) tumors can resist AR signaling inhibitors through AR amplification and AR splice variants in AR-positive CRPC (ARPC), and conversion to AR-null phenotypes, such as double-negative prostate cancer (DNPC) and small cell or neuroendocrine prostate cancer (SCNPC). We have shown previously that DNPC can bypass AR-dependence through fibroblast growth factor receptor (FGFR) signaling. However, the role of the FGFR pathway in other CRPC phenotypes has not been elucidated. RNA-Seq analysis was conducted on patient metastases, LuCaP patient-derived xenograft (PDX) models, and CRPC cell lines. Cell lines (C4-2B, VCaP, and 22Rv1) and ex vivo LuCaP PDX tumor cells were treated with enzalutamide (ENZA) and FGFR inhibitors (FGFRi) alone or in combination and sensitivity was determined using cell viability assays. In vivo efficacy of FGFRi in ARPC, DNPC, and SCNPC were evaluated using PDX models. RNA-Seq analysis of FGFR signaling in metastatic specimens, LuCaP PDX models, and CRPC cell lines revealed significant FGF pathway activation in AR-low PC (ARLPC), DNPC, and SCNPC tumors. In vitro/ex vivo analysis of erdafitinib and CH5183284 demonstrated robust and moderate growth suppression of ARPC, respectively. In vivo studies using four ARPC PDX models showed that combination ENZA and CH5183284 significantly suppressed tumor growth. Additional in vivo studies using four ARPC PDX models revealed that erdafitinib monotherapy was as effective as ENZA in suppressing tumor growth, and there was limited combination benefit. Furthermore, two of three DNPC models and two of four SCNPC models responded to CH5183284 monotherapy, suggesting FGFRi responses were model dependent. RNA-Seq and gene set enrichment analysis of end-of-study ARPC tumors treated with FGFRi displayed decreased expression of E2F and MYC target genes and suppressed G2M checkpoint genes, whereas end-of-study SCNPC tumors had heterogeneous transcriptional responses. Although FGFRi treatments suppressed tumor growth across CRPC phenotypes, our analyses did not identify a single pathway or biomarker that would identify tumor response to FGFRi. This is very likely due to the array of FGFR1-4 expression and tumor phenotypes present in CRPC. Nevertheless, our data nominate the FGFR pathway as a clinically actionable target that promotes tumor growth in diverse phenotypes of treatment-refractory metastatic CRPC.

Three E2F target-related genes signature for predicting prognosis, immune features, and drug sensitivity in hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) is extremely malignant and difficult to treat. The adenoviral early region 2 binding factors (E2Fs) target pathway is thought to have a major role in tumor growth. This study aimed to identify a predictive E2F target signature and facilitate individualized treatment for HCC patients. Methods: We constructed an E2F target-related gene profile using univariate COX and LASSO regression models and proved its predictive efficacy in external cohorts. Furthermore, we characterized the role of the E2F target pathway in pathway enrichment, immune cell infiltration, and drug sensitivity of HCC. Results: Lasso Cox regression created an E2F target-related gene signature of GHR, TRIP13, and CDCA8. HCC patients with high risk were correlated with shorter survival time, immune evasion, tumor stem cell characteristics and high sensitivity to Tipifarnib and Camptothecin drugs. Conclusion: Hepatocellular carcinoma prognosis was predicted by an E2F target signature. This finding establishes the theoretical usefulness of the E2F target route in customized identification and treatment for future research.

Pathway Mutations are Associated with Clinical Outcomes in Localized Pancreatic Cancer Treated with Neoadjuvant Chemoradiation Followed by Surgery

The purpose of this study was to determine if mutations in biological pathways are associated with clinical outcomes in patients with localized pancreatic cancer who undergo neoadjuvant chemoradiation followed by surgical resection. Patients treated with neoadjuvant chemoradiation followed by oncologic resection from 2015-2019 who also underwent next generation sequencing (NGS) of the primary tumor were included in this retrospective analysis. NGS was done using either Foundation One (n = 20), in-house Solid Tumor Panel (n = 121), or Tempus XT (n = 1). Genes were included in pathway analysis if at least one patient harbored a mutation in the gene. Pathways were defined from the Molecular Signatures Database Hallmark, KEGG, and Reactome gene sets. A pathway was deemed mutated if at least one gene within the pathway was mutated. Univariable Cox regression was performed to determine the association between pathway mutation status and overall survival (OS) as well as progression-free survival (PFS). In total, 142 patients met criteria for study inclusion. For pathway analysis, 329 genes met inclusion criteria. Patients were typically treated with neoadjuvant chemotherapy (either 5-fluorouracil-based or gemcitabine-based) followed by radiation. Patients received SBRT (n = 104, most commonly 33 Gy in 5 fractions) or conventionally fractionated radiation (n = 38, most commonly 50.4 Gy in 28 fractions). For clinical variables, worse OS was significantly associated with T stage (p = 0.036), N stage (p = 0.044), and lymphovascular invasion (LVI, p = 0.011); worse PFS was significantly associated with T stage (p = 0.0008), N stage (p = 0.022), LVI (p = 0.026), and conventional RT (p = 0.007). Mutations in major pathways were associated with worse OS, notably hedgehog signaling (p = 0.001), chromatin modifying enzymes (p = 0.002), WNT/beta-catenin signaling (p = 0.005), mismatch repair (0.006), E2F targets (p = 0.008), FLT signaling (p = 0.012), VEGF signaling (0.025), innate immune system (p = 0.026), and NOTCH signaling (p = 0.029). Pathway mutations associated with worse PFS included mismatch repair (p = 0.007) and hedgehog signaling (p = 0.013). For pancreatic cancer patients that undergo neoadjuvant chemoradiation followed by oncologic resection of the primary tumor, mutations in key biological pathways are associated with OS and PFS. Characterizing the importance of common pathway mutations may become increasingly valuable to help categorize less commonly mutated genes assayed by NGS.

Integrative bioinformatics analysis of WDHD1: a potential biomarker for pan-cancer prognosis, diagnosis, and immunotherapy

BackgroundAlthough WD repeat and high-mobility group box DNA binding protein 1 (WDHD1) played an essential role in DNA replication, chromosome stability, and DNA damage repair, the panoramic picture of WDHD1 in human tumors remains unclear. Hence, this study aims to comprehensively characterize WDHD1 across 33 human cancers.MethodsBased on publicly available databases such as TCGA, GTEx, and HPA, we used a bioinformatics approach to systematically explore the genomic features and biological functions of WDHD1 in pan-cancer.ResultsWDHD1 mRNA levels were significantly increased in more than 20 types of tumor tissues. Elevated WDHD1 expression was associated with significantly shorter overall survival (OS) in 10 tumors. Furthermore, in uterine corpus endometrial carcinoma (UCEC) and liver hepatocellular carcinoma (LIHC), WDHD1 expression was significantly associated with higher histological grades and pathological stages. In addition, WDHD1 had a high diagnostic value among 16 tumors (area under the ROC curve [AUC] > 0.9). Functional enrichment analyses suggested that WDHD1 probably participated in many oncogenic pathways such as E2F and MYC targets (false discovery rate [FDR] < 0.05), and it was involved in the processes of DNA replication and DNA damage repair (p.adjust < 0.05). WDHD1 expression also correlated with the half-maximal inhibitory concentrations (IC50) of rapamycin (4 out of 10 cancers) and paclitaxel (10 out of 10 cancers). Overall, WDHD1 was negatively associated with immune cell infiltration and might promote tumor immune escape. Our analysis of genomic alterations suggested that WDHD1 was altered in 1.5% of pan-cancer cohorts and the “mutation” was the predominant type of alteration. Finally, through correlation analysis, we found that WDHD1 might be closely associated with tumor heterogeneity, tumor stemness, mismatch repair (MMR), and RNA methylation modification, which were all processes associated with the tumor progression.ConclusionsOur pan-cancer analysis of WDHD1 provides valuable insights into the genomic characterization and biological functions of WDHD1 in human cancers and offers some theoretical support for the future use of WDHD1-targeted therapies, immunotherapies, and chemotherapeutic combinations for the management of tumors.

Identification of senescence-related lncRNA prognostic index correlating with prognosis and radiosensitivity in prostate cancer patients.

An increasing number of studies are shown how crucial a role cellular senescence plays in tumor development. In this study, we developed a senescence-related lncRNA prognostic index (SRLPI) to forecast radiosensitivity and the probability of biochemical recurrence (BCR) in patients with prostate cancer (PCa). PCa cohorts in TCGA and GEO databases were downloaded. Senescence-and prognosis-related lncRNA with differential expression in tumor and normal samples were identified and used to establish the SRLPI score. Mutation landscape, function pathway, tumor stemness and heterogeneity and tumor immune microenvironment were also analyzed. We performed the analysis using R 3.6.3 and the appropriate tools. A SRLPI score was constructed based on SNHG1 and MIAT in the TCGA cohort. Our classification of PCa patients into high- and low-risk groups was based on the median SRLPI score. When compared to the low-SRLPI group, the high-SRLPI group was more vulnerable to BCR (HR: 3.33). In terms of BCR-free survival and metastasis-free survival, the GSE116918 showed similar findings. Surprisingly, the SRLPI score demonstrated a high level of radiosensitivity for diagnosis (AUC: 0.98). Age, Gleason score, T stage, N stage, positive lymph nodes, and residual tumor were all significantly greater in patients with high SRLPI scores. Furthermore, this score was significantly related to markers of senescence. Protein secretion and androgen response were found to be substantially enriched in the low-SRLPI group, whereas E2F targets were found to be strongly enriched in the high-SRLPI group for pathway analysis. For the tumor microenvironment assessment, B cells, CD8+ T cells, immune score and TIDE score were positively related to SRLPI score while endothelial level was negatively associated with SRLPI score with statistical significance. We developed a SRLPI score that was related to prognosis and radiosensitivity and might be helpful in clinical practice.