Myc Binding Research Articles

1728-P: Transcriptional Activation of Myc by Glucose Requires Recruitment of ChREBP to the Pvt1 Promoter Regulating Proliferation in ß-Cells

Myc and Carbohydrate Response Element (ChoRE) Binding Protein (ChREBP) are glucose-responsive transcriptional regulators of β-cell proliferation. Myc requires ChREBP to drive glucose-mediated proliferation in β-cells, yet no ChoREs are present in Myc’s promoter. In primates and rodents, the Myc gene and the long non-coding RNA, PVT1 gene are syntenic, separated by approximately 60 kbp. Mutations in this loci are associated with malignancies and complications of diabetes but are unexplored in β-cells. In INS-1 cells, Myc and PVT1 mRNAs were induced in response to glucose by 3.5±0.02and 2.9±0.1 fold, respectively, and Myc protein levels increased by 4-fold ±0.17. Silencing of ChREBPβ significantly blocked the glucose response of Myc and Pvt1. ChREBP ChIPseq revealed a single ChoRE located approximately 100 bp upstream of the Pvt1 transcription start site and is highly conserved in primates and rodents. By Chromosome Conformation Capture (3C), we demonstrated that high glucose increased interaction between the Pvt1 and Myc promoters by a factor of 3.5±0.4. Using adenoviral delivery of CRISPR-xCas9-sgRNA targeting the Pvt1 ChoRE, we specifically attenuated ChREBP recruitment by 2.8±0.8 fold, while other known ChoREs were unaffected. We demonstrated by 3C that the chromatin looping in response to glucose was abolished by the Pvt1 ChoRE disruptor. Both in primary rat islets and in INS-1 cells, disruption of Pvt1’s ChoRE resulted in complete and significant blockage of Pvt1 and Myc mRNA upregulation in response to glucose, with no effect on other ChoRE-containing genes. Finally, disruption of the ChoRE on the Pvt1 promoter eliminated glucose-mediated proliferation of primary rat β-cells (a decrease of 9.8±1.9 fold on Ki67+ Ins+ staining). In conclusion, we identify a novel mechanism driving the ChREBP-dependent activation of the Myc and Pvt1 genes and proliferation of β-cells. Disclosure L.S.Katz: None. P.Wang: None. G.Brill: None. P.Zhang: None. J.Haldeman: Employee; Janssen Research & Development, LLC. C.B.Newgard: Advisory Panel; Eli Lilly and Company, Novo Nordisk, AstraZeneca. A.F.Stewart: None. A.Garcia-ocana: Consultant; Sun Pharmaceutical Industries Ltd. D.Scott: None. Funding National Institutes of Health (R01DK130300, P30DK020541)

MDB-37. CDK9 IS A DRUGGABLE MEDIATOR SUSTAINING MYC-DRIVEN TRANSCRIPTIONAL CIRCUITRY IN MEDULLOBLASTOMA

Abstract Though long recognized as a master regulator of cell proliferation across a wide range of cancers, Myc has proven elusive to direct therapeutic targeting. The CDK9-containing PTEFb, complexed with either BRD4 or SEC, facilitates Myc-driven transcriptional programs and is necessary for sustaining expression of Myc itself. Advances in development of clinical-grade CDK9 inhibitors creates an opportunity to examine this as a rational therapy for Myc-driven medulloblastoma (Myc-MB). In order to define the enhancer-promoter circuitry driving Myc expression in medulloblastoma, we performed chromosome conformation capture (Hi-C) from primary patient Myc-MB samples. Using a combination of CUT&RUN and RNA-seq, we find that treatment with the CDK9 inhibitor zotiraciclib depletes Myc binding and transcriptional activity at enhancer elements within the Myc topologically associated domain, largely abrogating transcriptional output from the Myc promoter. This leads to a decrease in Myc binding genome-wide with a concordant downregulation of hallmark Myc-driven transcriptional programs. Myc-MB cell lines are sensitive to CDK9 inhibition at low nanomolar concentrations, with a loss of fitness as measured by decreased proliferative or clonogenic potential and a marked induction of apoptosis. Clinically relevant CDK9 inhibitors show variable efficacy in vivo, but CNS-penetrant agents achieved a significant prolongation in xenograft survival. Together, these data demonstrate that CDK9 catalytic activity represents a druggable vulnerability underpinning Myc-driven transcriptional programs. The development of CNS-penetrant CDK9 inhibitors may open new avenues for rational therapy in these high-risk medulloblastomas.

ZNF692 promote proliferation through transcriptional repression of essential genes in clear cell renal carcinoma

Transcription deregulation is recognized as a prominent hallmark of carcinogenesis. However, our understanding of the transcription factors implicated in the dysregulated transcription network of clear cell renal carcinoma (ccRCC) remains incomplete. In this study, we present evidence that ZNF692 drives tumorigenesis in ccRCC through the transcriptional repression of essential genes. We observed overexpression of ZNF692 in various cancers, including ccRCC, and found that the knockdown or knockout of ZNF692 suppressed the growth of ccRCC. Genome-wide binding site analysis using ChIP-seq revealed that ZNF692 regulates genes associated with cell growth, Wnt signaling, and immune response in ccRCC. Furthermore, motif enrichment analysis identified a specific motif (5′-GCRAGKGGAKAY-3′) that is recognized and bound by ZNF692. Subsequent luciferase reporter assays demonstrated that ZNF692 transcriptionally represses the expression of IRF4 and FLT4 in a ZNF692 binding motif-dependent manner. Additionally, we observed MYC binding to the promoter regions of ZNF692 in most cancer types, driving ZNF692 overexpression specifically in ccRCC. Overall, our study sheds light on the functional significance of ZNF692 in ccRCC and provides valuable insights into its therapeutic potential as a target in cancer treatment.

Abstract A062: Alternative promoter usage is linked to transcriptional and epigenetic alterations during prostate cancer progression

Abstract Background: Prostate tumor progression is driven by transcription factors (TFs), most prominently the Androgen Receptor (AR), that drive proliferation and therapy resistance. Many genes have several promoters that can be bound by distinct TFs. It is unclear what role alternative promoter selection plays in tumor progression. We hypothesized that driver TFs target novel gene promoters during prostate tumor progression, and that understanding how this targeting occurs would reveal novel aspects of prostate tumor biology. Methods: We performed ultra-deep RNA sequencing on 104 metastatic Castration Resistant Prostate Cancer (mCRPC) biopsies, generating > 450M reads/sample (10X the typical depth), in samples with matched whole genome DNA and methylation sequencing. We combined these data with published deep transcriptomes in normal prostate and localized prostate cancer for a total of 274 samples. Promoter activity was evaluated in all 274 biopsies using the proActiv tool. Differential promoter activity levels were integrated with transcription factor motif enrichment, chromatin immunoprecipitation sequencing, and previously published somatic and methylation sequencing data in the mCRPC samples. Results: Using normal prostate tissue as a baseline, we identified 463 and 3,237 APs with differential activity in localized prostate cancer and mCRPC, respectively. Increased alternative promoter (AP) usage was associated with upregulation of prostate tumor driver genes. Elevated androgen signaling in both localized and mCRPC was correlated with increased AP use. In localized prostate tumors, APs preferentially switch to promoters harboring binding sites for the AR pioneer factor FOXA1. In mCPRC, APs were further enriched for binding of MYC, E2F1, and HIF1A. Furthermore, AP usage reflects transcriptional dysregulation related to lineage plasticity in response to therapy. APs in neuroendocrine prostate cancer (NEPC) were bound by neuroendocrine TFs such as ASCL1 and HAND2. While canonical promoters are usually unmethylated, methylation levels at APs were strongly linked to AP activity. Conclusions: Our data show that transcription initiated at APs is a key contributor to increased gene activity in prostate tumors. APs that are upregulated in prostate tumors are linked to transcription factors activated by recurrent somatic alterations and lineage plasticity. Methylation at APs is an important and underappreciated driver of promoter choice in mCRPC. Understanding how somatic alterations and epigenetic reprogramming of TFs affect APs is essential to understanding how these processes impact therapy resistance. Citation Format: Meng Zhang, Martin Sjöström, Raunak Shrestha, Arian Lundberg, Thaidy Moreno-Rodriguez, Adam Foye, Ha X. Dang, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Christopher A. Maher, Felix Y. Feng, David Quigley. Alternative promoter usage is linked to transcriptional and epigenetic alterations during prostate cancer progression [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A062.

Abstract A058: Lineage plasticity is associated with an altered MAX cistrome through super-enhancer remodeling

Abstract Background: Roughly 20% of late stage prostate cancer patients display a lineage conversion from typical androgen receptor (AR) driven castrate resistant prostate cancer (CRPC) to a particularly lethal neuroendocrine prostate cancer (NEPC) phenotype as a result of AR pathway inhibition (ARPI). Notably, the mutational landscape of CRPC and NEPC is quite similar, suggesting that epigenetic changes may guide this lineage conversion. Our objective was to explore changes in active epigenetic marks with a particular focus on super-enhancers (SEs) and identify factors that regulate these active regions during lineage plasticity. Methods: We performed ChIP-seq for H3K27ac, H3K4me3 and various TFs in our CRPC and ENZ resistant (ENZR) NEPC-like cell models. We leveraged publicly available H3K27ac data in cell lines as well as PDX models to validate our findings. RNA-seq was integrated with our ChIP-seq results to create a signature which we applied to patient data sets. GIGGLE analysis was used to identify candidate factors at SEs. Results: CRPC and NEPC showed similar active marks at promoters however, enhancer elements were significantly remodeled. We observed extensive remodeling of SEs in our ENZR model compared to CRPC and these unique regions showed greater H3K27ac signals in other ENZR models such as NCI-H660. SE linked genes are associated with stemness pathways and are strongly upregulated as a result of ARPI in vitro, and in vivo. Factor enrichment analysis of these regions showed enrichment for MAX and MYC family binding similar to small cell lung cancer cell lines. ChIPseq for MYC and MAX in our cell models revealed an expansion of MAX binding and contraction of MYC binding in our ENZR model compared to CRPC. In particular, we saw increased binding of MAX at plasticity SEs without MYC suggesting an interaction with MYCL or other factors since MYCN is not expressed in our models. Conclusions: This work improves our understanding of the epigenetic changes that occur during lineage plasticity and ARPI resistance. SE analysis in our models suggests that MAX may be activating these regions with MYCL or independently of the MYC family. MYCL expression is upregulated in NEPC and has higher expression than MYCN suggesting a potential role during lineage plasticity. Citation Format: Maxim Kobelev, Dwaipayan Ganguli, Takeshi Namekawa, Amina Talal, Joshua Scurll, Amina Zoubeidi. Lineage plasticity is associated with an altered MAX cistrome through super-enhancer remodeling [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A058.

The MYC-YBX1 Circuit in Maintaining Stem-like Vincristine-Resistant Cells in Rhabdomyosarcoma.

Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma that causes significant devastation, with no effective therapy for relapsed disease. The mechanisms behind treatment failures are poorly understood. Our study showed that treatment of RMS cells with vincristine led to an increase in CD133-positive stem-like resistant cells. Single cell RNAseq analysis revealed that MYC and YBX1 were among the top-scoring transcription factors in CD133-high expressing cells. Targeting MYC and YBX1 using CRISPR/Cas9 reduced stem-like characteristics and viability of the vincristine-resistant cells. MYC and YBX1 showed mutual regulation, with MYC binding to the YBX1 promoter and YBX1 binding to MYC mRNA. The MYC inhibitor MYC361i synergized with vincristine to reduce tumor growth and stem-like cells in a zebrafish model of RMS. MYC and YBX expression showed a positive correlation in RMS patients, and high MYC expression correlated with poor survival. Targeting the MYC-YBX1 axis holds promise for improving survival in RMS patients.

TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs.

Eukaryotic genomes contain several types of recurrent sequence motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial motifs. We present transCRISPR, the first online tool dedicated to search for sequence motifs in the user-provided genomic regions and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen motifs, for up to tens of thousands of target regions in 30 genomes, either for the Cas9 or dCas9 system. TransCRISPR provides user-friendly tables and visualizations, summarizing features of identified motifs and designed sgRNAs such as genomic localization, quality scores, closest transcription start sitesand others. Experimental validation of sgRNAs for MYC binding sites designed with transCRISPR confirmed efficient disruption of the targeted motifs and effect on expression of MYC-regulated genes. TransCRISPR is available from https://transcrispr.igcz.poznan.pl/transcrispr/.

Isolation and Activity Analysis of Phytoene Synthase (ClPsy1) Gene Promoter of Canary-Yellow and Golden Flesh-Color Watermelon

Watermelon (Citrullus lanatus) is an economically important cucurbit crop. Its pulp is rich in antioxidant carotenoids, which confer a variety of flesh colors. ClPsy1 (Phytoene Synthase) is the rate-limiting enzyme for carotenoid synthesis; however, the promoter activity of ClPsy1 is still unknown. In the present study, promoter sequences were isolated from four watermelon accessions: Cream of Saskatchewan pale yellow (COS), canary yellow flesh (PI 635597), golden flesh (PI 192938), and red flesh (LSW-177), all of which express ClPsy1 at extremely high levels. Sequence alignment and cis-element analysis disclosed six SNPs between the four lines all in COS, two of which (at the 598th and 1257th positions) caused MYC and MYB cis-element binding sequence variations, respectively. To confirm ClPsy1 gene promoter activity, full-length and deletion fragments of the promoter were constructed and connected to a β-D-glucosidase (GUS) vector and transferred into tomato fruits. GUS staining was performed to analyze the key segment of the promoter. The activity of the PI 192938 ClPsy1 full-length promoter exceeded that of COS. The deletion fragment from −1521 bp to −1043 bp exhibited strong promoter activity, and contained a MYB transcription factor-binding site mutation. We combined RNA-seq with qRT-PCR to analyze the gene expression pattern between the MYB transcription factor Cla97C10G196920 and ClPsy1 gene and found that Cla97C10G196920 (ClMYB21) showed the same expression trend with ClPsy1, which positively regulates carotenoid synthesis and metabolism.

Abstract 1266: MYC mediated HIF-2α modulates the altruistic stemness reprogramming in leukemia stem cells

Abstract Potential cell surface markers specifically enriching the leukemia stem cell (LSC) subfraction based on stemness genes expression have not yet been identified. Previously, we reported ABCG2, a drug efflux pump, enriches a subpopulation of cells exhibiting a very high level of stemness genes expression in ES cells. These ABCG2+ ES cells exhibited high HIF-2α, which in cooperation with MYC-regulated Nanog and Sox-2. ABCG2+ cells demonstrated highly cytoprotective altruistic behavior by secreting high levels of glutathione. In the present study, we evaluated whether ABCG2+ subfraction of human LSCs exhibits high level of stemness genes and altruistic behavior. We isolated the ABCG2+ cell subfraction from cervical lymph node and blood of human T-ALL(n=5) and CML(n=7) patients exhibiting high levels of stemness genes in addition to MYC and HIF-2α. We investigated the altruistic stemness phenotype of the ABCG2+ cells by studying the molecular signature of MYC binding to HIF-2α. siRNA HIF-2α treatment led to ABCG2+ cell loss of proliferative capacity and reduced GSH levels, suggesting reduction of cytoprotective altruistic behavior in vitro. Treatment of ABCG2+ cell harboring mice with FM19G11 led to marked loss in the secondary engraftment in NOD/SCID mice, indicating loss of ABCG2+ cell self-renewal capacity. We found siRNA MYC inhibition led to loss of HIF-2α expression, suggesting that MYC might be regulating HIF-2α mediated altruistic stemness program in the ABCG2+ cells. Overall, we found that ABCG2 can be a probable marker to enrich the LSC subfraction having high expression of stemness genes and altruistic stemness phenotype. Citation Format: Shirsajit Mitra, Lekhika Pathak, Partha Jyoti Saikia, Bidisha Pal, Bikul Das. MYC mediated HIF-2α modulates the altruistic stemness reprogramming in leukemia stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1266.

RGS12 represses oral squamous cell carcinoma by driving M1 polarization of tumor-associated macrophages via controlling ciliary MYCBP2/KIF2A signaling

Tumor-associated macrophages (TAMs) play crucial roles in tumor progression and immune responses. However, mechanisms of driving TAMs to antitumor function remain unknown. Here, transcriptome profiling analysis of human oral cancer tissues indicated that regulator of G protein signaling 12 (RGS12) regulates pathologic processes and immune-related pathways. Mice with RGS12 knockout in macrophages displayed decreased M1 TAMs in oral cancer tissues, and extensive proliferation and invasion of oral cancer cells. RGS12 increased the M1 macrophages with features of increased ciliated cell number and cilia length. Mechanistically, RGS12 associates with and activates MYC binding protein 2 (MYCBP2) to degrade the cilia protein kinesin family member 2A (KIF2A) in TAMs. Our results demonstrate that RGS12 is an essential oral cancer biomarker and regulator for immunosuppressive TAMs activation.

MYC-activated LINC00607 promotes hepatocellular carcinoma progression by regulating the miR-584-3p/ROCK1 axis.

There have been many reports of long non-coding RNAs (lncRNAs) in tumors, and abnormally expressed lncRNA is closely related to hepatocellular carcinoma (HCC). The mechanism of LINC00607 in HCC has not been reported. We utilized qPCR to evaluate the RNA expression level. The mechanism of MYC binding to the LINC00607 promoter was revealed through chromatin immunoprecipitation assay and dual luciferase reporter assay. The proliferation and invasive ability were evaluated by CCK-8 and transwell assays. The relation between LINC00607 and miR-584-3p was assessed by RNA immunoprecipitation assay and dual luciferase reporter assay. The level of ROCK1 was evaluated by qPCR and western blot. In this research, we found that the expression of LINC00607 was higher in HCC tissues when compared with that in the adjacent non-tumor tissues. Meanwhile, MYC was observed to interact with the LINC00607 promoter, leading to the upregulation of LINC00607 in HCC. We further revealed that LINC00607 functioned as a sponge for miR-584-3p. Cell proliferation and migration assays showed that miR-584-3p may inhibit the HCC progression. Moreover, we found that the miR-584-3p inhibitor could reverse the effects of LINC00607 downregulation in HCC through rescue experiments. Through verification, miR-584-3p bound to the 3' UTR of ROCK1 to downregulate its expression. LINC00607 regulated by MYC can promote the proliferation, migration and invasion of HCC cells through the miR-584-3p/ROCK1 axis.

Regulator of G protein signaling 12 drives inflammatory arthritis by activating synovial fibroblasts through MYCBP2/KIF2A signaling

Synovial fibroblasts are the active and aggressive drivers in the progression of arthritis, but the cellular and molecular mechanisms remain unknown. Here, our results showed that regulator of G protein signaling 12 (RGS12) maintained ciliogenesis in synovial fibroblasts, which is critical for the development of inflammatory arthritis. Deletion of RGS12 led to a significant decrease in ciliogenesis, adhesion, migration, and secretion of synovial fibroblasts. Mechanistically, RGS12 overexpression in synovial fibroblasts increased the length and number of cilia but decreased the protein level of kinesin family member 2A (KIF2A). The results of LC-MS analyses showed that RGS12 interacted with MYC binding protein 2 to enhance its ubiquitination activity, through which the KIF2A protein was degraded in synovial fibroblasts. Moreover, overexpression of KIF2A blocked the increases in cilia length and number. Mice with RGS12 deficiency or treatment of RGS12 shRNA nanoparticles significantly decreased the clinical score, paw swelling, synovitis, and cartilage destruction during inflammatory arthritis by inhibiting the activation of synovial fibroblasts. Therefore, this study provides evidence that RGS12 activates synovial fibroblasts' pathological function via promoting MCYBP2-mediated degradation of KIF2A and ciliogenesis. Our data suggest that RGS12 may be a potential drug target for the treatment of inflammatory arthritis.

MYCBP2 expression correlated with inflammatory cell infiltration and prognosis immunotherapy in thyroid cancer patients.

Immune checkpoint inhibitors (ICIs) have shown promising results for the treatment of multiple cancers. ICIs and related therapies may also be useful for the treatment of thyroid cancer (TC). In TC, Myc binding protein 2 (MYCBP2) is correlated with inflammatory cell infiltration and cancer prognosis. However, the relationship between MYCBP2 expression and ICI efficacy in TC patients is unclear. We downloaded data from two TC cohorts, including transcriptomic data and clinical prognosis data. The Tumor Immune Dysfunction and Exclusion (TIDE) algorithm was used to predict the efficacy of ICIs in TC patients. MCPcounter, xCell, and quanTIseq were used to calculate immune cell infiltration scores. Gene set enrichment analysis (GSEA) and single sample GSEA (ssGSEA) were used to evaluate signaling pathway scores. Immunohistochemical (IHC) analysis and clinical follow up was used to identify the MYCBP2 protein expression status in patients and associated with clinical outcome. A higher proportion of MYCBP2-high TC patients were predicted ICI responders than MYCBP2-low patients. MYCBP2-high patients also had significantly increased infiltration of CD8+ T cells, cytotoxic lymphocytes (CTLs), B cells, natural killer (NK) cells and dendritic cells (DC)s. Compared with MYCBP2-low patients, MYCBP2-high patients had higher expression of genes associated with B cells, CD8+ T cells, macrophages, plasmacytoid dendritic cells (pDCs), antigen processing and presentation, inflammatory stimulation, and interferon (IFN) responses. GSEA and ssGSEA also showed that MYCBP2-high patients had significantly increased activity of inflammatory factors and signaling pathways associated with immune responses.In addiation, Patients in our local cohort with high MYCBP2 expression always had a better prognosis and greater sensitivity to therapy while compared to patients with low MYCBP2 expression after six months clinic follow up. In this study, we found that MYCBP2 may be a predictive biomarker for ICI efficacy in TC patients. High MYCBP2 expression was associated with significantly enriched immune cell infiltration. MYCBP2 may also be involved in the regulation of signaling pathways associated with anti-tumor immune responses or the production of inflammatory factors.

Strategic optimization of conditions for the solubilization of GST-tagged amphipathic helix-containing ciliary proteins overexpressed as inclusion bodies in E. coli

Expression of affinity-tagged recombinant proteins for crystallography, protein–protein interaction, antibody generation, therapeutic applications, etc. mandates the generation of high-yield soluble proteins. Although recent developments suggest the use of yeast, insect, and mammalian cell lines as protein expression platforms, Escherichia coli is still the most popular, due mainly to its ease of growth, feasibility in genetic manipulation and economy. However, some proteins have a spontaneous tendency to form inclusion bodies (IBs) when over-expressed in bacterial expression systems such as E. coli, thus posing a challenge in purification and yield. At times, small peptides undergo degradation during protein production and hence using suitable tags could circumvent the problem. Although several independent techniques have been used to solubilize IBs, these cannot always be applied in a generic sense. Although tagging a GST moiety is known to enhance the solubility of fusion proteins in E. coli, resulting in yields of 10–50 mg/L of the culture, the inherent nature of the protein sequence at times could lead to the formation of IBs. We have been working on a Myc Binding Protein-1 orthologue, viz. Flagellar Associated Protein 174 (FAP174) from the axoneme of Chlamydomonas reinhardtii that binds to an A-Kinase Anchoring Protein 240 (AKAP240) which has been annotated as Flagellar Associated Protein 65 (FAP65). Using an in-silico approach, we have identified two amphipathic helices on FAP65 (CrFAP65AH1 and CrFAP65AH2) that are predicted to bind to FAP174. To test this prediction, we have cloned the GST-tagged peptides, and overexpressed them in E. coli that have resulted in insoluble IBs. The yields of these over-expressed recombinant proteins dropped considerably due to IB formation, indicating aggregation. An integrated approach has been used to solubilize four highly hydrophobic polypeptides, viz. two amphipathic helices and the respective proline variants of FAP65. For solubilizing these polypeptides, variables such as non-denaturing detergents (IGEPAL CA-630), changing the ionic strength of the cell lysis and solubilization buffer, addition of BugBuster®, diluting the cell lysate and sonication were introduced. Our statistically viable results yielded highly soluble and functional polypeptides, indiscreet secondary structures, and a yield of ~ 20 mg/L of the E. coli culture. Our combinatorial strategy using chemical and physical methods to solubilize IBs could prove useful for hydrophobic peptides and proteins with amphipathic helices.

Deep learning for MYC binding site recognition.

Motivation: The definition of the genome distribution of the Myc transcription factor is extremely important since it may help predict its transcriptional activity particularly in the context of cancer. Myc is among the most powerful oncogenes involved in the occurrence and development of more than 80% of different types of pediatric and adult cancers. Myc regulates thousands of genes which can be in part different, depending on the type of tissues and tumours. Myc distribution along the genome has been determined experimentally through chromatin immunoprecipitation This approach, although powerful, is very time consuming and cannot be routinely applied to tumours of individual patients. Thus, it becomes of paramount importance to develop in silico tools that can effectively and rapidly predict its distribution on a given cell genome. New advanced computational tools (DeeperBind) can then be successfully employed to determine the function of Myc in a specific tumour, and may help to devise new directions and approaches to experiments first and personalized and more effective therapeutic treatments for a single patient later on. Results: The use of DeeperBind with DeepRAM on Colab platform (Google) can effectively predict the binding sites for the MYC factor with an accuracy above 0.96 AUC, when trained with multiple cell lines. The analysis of the filters in DeeperBind trained models shows, besides the consensus sequence CACGTG classically associated to the MYC factor, also the other consensus sequences G/C box or TGGGA, respectively bound by the SP1 and MIZ-1 transcription factors, which are known to mediate the MYC repressive response. Overall, our findings suggest a stronger synergy between the machine learning tools as DeeperBind and biological experiments, which may reduce the time consuming experiments by providing a direction to guide them.

Functional Characterization of Cooperating MGA Deletions in RUNX1::RUNX1T1 Acute Myeloid Leukemia

Max-gene associated (MGA) is a dual-specificity transcription factor that is recurrently mutated in 2-5% of all cancers and commonly seen in lung adenocarcinoma, endometrial carcinoma, and colorectal cancer. Our group has previously described heterozygous loss-of-function mutations in 9% of RUNX1::RUNX1T1 pediatric AMLs. Similar loss-of-function mutations are seen in other hematopoietic malignancies, including chronic lymphocytic leukemia (CLL), natural killer/T-cell lymphoma, B-cell acute lymphoblastic leukemia (B-ALL), and T-cell acute lymphoblastic leukemia (T-ALL). MGA is a component of the non-canonical polycomb repressive complex (ncPRC1.6) containing an amino-terminal T-box domain and a carboxy-terminal Myc-like basic helix-loop-helix (bHLH) domain which are used to regulate MAX-network and T-box family targets. In hematological malignancies such as RUNX1::RUNX1T1 AMLs, MGA mutations disrupt or remove the Myc-like bHLH domain. The role of MGA in normal hematopoietic regulation and leukemic development are understudied. This is likely due to the lack of in vivo MGA deficiency models which are embryonic lethal. We hypothesize that the loss of MGA leads to disruption of the ncPRC1.6 complex, causing a loss in global transcriptional repression of many pathways, including Myc and E2F target genes, leading to enhanced hematopoietic cell growth and self-renewal, as well as shortening the latency of AML driven by RUNX1::RUNXT1. To test this hypothesis, we designed a multidisciplinary approach to characterize the hematopoietic function of MGA. IP-Westerns of overexpressed flag-tagged MGA and its subsequent variants in K562 cells revealed that MGA truncations disrupt interactions with components of the ncPRC1.6 complex. Because these truncations lead to the loss of MGA's molecular function, we next generated CRISPR/Cas9 to knockout MGA in Molm13 cells. Using RNA-Seq and CUT&RUN to assess the genomic localization of MGA, we determined that MGA binds to an average of 85,119 peaks and 17.7% of those sites are at transcription start sites, including cell cycle genes such as CCND2. Deletion of MGA led to the removal of repressive H3K27me3 marks and an increase in MYC binding as well as active histone marks such as H3K4me3 and H3K27Ac at the transcription start site of CCND2. This led to an increase in CCND2 expression (logFC 1.56, FDR 1.56E-12) which is supported by in vitro EdU assays showing a 10.43% increase in cells cycling into S-phase. To further define the hematopoietic function of MGA, we designed a conditional knockout Mga mouse model with LoxP sites flanking exon 3, leading to deletion of Mga in hematopoietic stem and progenitor cells (HSPCs) when crossed with Vav1-cre. Transcriptome profiling analysis of HSPCs isolated from heterozygous (Mga+/) and homozygous (Mga-/-) mice reveals that Mga-/- mice, but not Mga+/-, leads to up-regulation of cell cycle (FDR 4.2E-06), Myc (FDR 6.3E-10), and E2f (FDR 2.9E-17) signaling pathways. Ex vivo serial CFU replating and cell proliferation assays support this, showing that Mga-/- leads to increased stem cell self-renewal and cell growth. However, bone marrow and spleen analysis of both Mga+/- and Mga-/- mice reveal no changes in immunophenotype when compared to WT controls. Expression of RUNX1::RUNX1T1 isoform 9a (AML-ETO9a) in Mga+/- or Mga-/- HSPCs reveals a significant increase (69% and 74% respectively, p<0.01) in leukemic stem cell self-renewal, when compared to WT controls expressing AML-ETO9a at week 4. When transplanted in mice, Mga+/- and Mga-/- HSPCs expressing AML-ETO9a led to a rapid expansion of blasts (GFP+, lin-, cKit+) found in the peripheral blood as well as a shortened latency compared to wild-type controls expressing AML-ETO9a (Figure 1). These studies demonstrated MGA as a regulator of hematopoietic cell proliferation (Figure 2), and how MGA deficiency cooperates with oncogenes to create more aggressive leukemia. Because MGA mutations occur in many tumor types, these data also provide functional insights into ncPRC1.6 activity in leukemia and other tumor types with recurrent mutations in MGA or other components of this complex. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

MYC Influences mRNA Processing and Nuclear Export to Initiate Acute Myeloid Leukemia

Background: Although MYC is a potent oncogene that is frequently associated with poor outcomes in many solid tumors, its precise role in Acute Myeloid Leukemia (AML) pathogenesis and outcomes are not clear. We recently discovered that intermediate-risk AML patients with long first remissions with standard chemotherapy have an unexpectedly high frequency of pathogenic MYC mutations in the dominant leukemia clone at diagnosis (6 of 26 [23%] cases, versus 1.8% of all AML patients, p=0.002). An analysis of all MYC mutations reported in AML, revealed that they are nearly always single base substitutions that localize to a hotspot in the MYC Box I domain (MBI - AAs hotspot 73-74); this stands in distinct contrast to other hematopoietic malignancies, where MYC mutations are scattered throughout the entire gene. In this study, we engineered mouse hematopoietic stem and progenitor cells (HSPCs) to express AML-associated MYC missense mutations and characterized their in-vitro and in-vivo cellular and molecular phenotypes. Results: We observed that constitutive expression of MYC MBI mutant proteins in mouse HSPCs significantly prolonged Myc half-life and conferred different degrees of growth advantage over both wild type MYC overexpression and overexpression of non-MBI mutant proteins. To determine whether these mutations are AML drivers, HSPCs expressing MYCWT or the MBI mutants MYCP74Q and MYCT73N were transplanted into lethally irradiated syngeneic recipient mice, which were then evaluated for the development of leukemia. Primary recipient mice transplanted with MYCWT-expressing cells developed leukemia with a median survival of 58 days for whereas mice transplanted with MYCP74Q- or MYCT73N-expressing cells displayed a median survival of 42 and 41.5 days, respectively (p<0.001). Furthermore, secondary recipient mice transplanted with MYCWT-, MYCP74Q- or MYCT73N-expressing AML cells from primary recipient mice also developed AML, indicating that expression of WT and MBI-MUT Myc leads to the development of frank leukemia in mice. Next, we investigated the impact of these point mutations on the transcriptional targets of Myc by comparing single-cell RNA-seq profiles of murine HSPCs expressing wild type, P74Q, or T73N Myc versus an empty vector control. From these analyses, we found that while each of these mutants retain many of the transcriptional activities of wild type Myc, they also display unique transcriptional signatures. To better understand how these mutations affect the transcriptional output of MYC, we performed ChIP-seq analysis of primary murine HSPCs expressing MYCWT-, MYCcP74Q- or MYCT73N. Despite MBI mutations causing persistent MYC protein expression (due to prolonged half-life), we detected an overall decrease in chromatin binding of MBI-MUT MYC, with preserved binding to transcriptional start sites of a core sets of genes involved in splicing and translation. Importantly, MBI mutations did not affect the canonical E-box Myc binding site, nor create novel binding sites, indicating that these mutations lead to an overall decrease in Myc occupancy at target promoters. Immunofluorescent staining for WT vs. MBI mutant MYC showed that despite their overall decrease in chromatin binding, Myc mutant proteins localized predominantly to the nucleus. However, a substantial number of nuclei showed a ring-like morphology of MBI-MUT MYC, suggesting that MBI mutations might enrich protein localization at the nuclear periphery. To determine whether the changes in staining pattern observed for MBI-MUT were associated with alterations in the ability of MYC to interact with its regulatory proteins, we employed a modified BioID proximity labeling system, "TurboID", to screen for differential protein interactions in murine HSPCs. This analysis showed that MBI mutations resulted in several gained interactions over WT MYC - most prominently with components of the nuclear pore complex (NUP98, NUP107, NUP133, XPOT, RAE1) supporting the idea that MBI-MUT might accelerate transformation by controlling translation and mRNA nuclear export. Conclusions: Collectively, these data indicate that AML-associated MYC mutations support leukemogenesis through non-canonical (transcription-independent) MYC proprieties. More broadly, these data suggest that aberrant mRNA processing and nuclear export might play an important role in the initiation of AML by MYC mutations.

In Situ Characterization of Chromatin Landscape in Progression of Smoldering Precursor Stage to Multiple Myeloma

Introduction Multiple myeloma (MM) is a fatal malignancy of plasma cells and is preceded by a precursor stage, smoldering myeloma (SMM). There is a 50% risk of progression from SMM to overt MM within five years of diagnosis. Most SMM patients do not receive treatment until progression to overt MM and early intervention is beyond the current standard of care. Large sequencing studies have revealed that SMM patients with similar genetic backgrounds experience varying rates of disease progression, overall survival, and treatment response. These findings indicate an unmet need to better define the molecular requirements of disease progression. We hypothesize that altered chromatin states in pre-myeloma cells act as priming events for clonal expansion and enable the transition from pre-myeloma conditions to MM. Characterization of the pre-myeloma epigenome at single-cell resolution may offer insights into the dynamic reprogramming that occurs during myeloma development and provide new biomarkers of disease progression. Methods Bone marrow (BM) aspirates were sampled from 26 patients and healthy donors at different stages of the disease. BM samples were enriched for plasma cells using CD138 microbeads and subjected to single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq, 10x Genomics). This cohort comprised five healthy donors, seven low risk (LR), five intermediate risk (IR), and three high risk (HR) SMM patients as well as six newly diagnosed (ND) MM patients based on the 2/20/20 risk stratification model. Batch effects, data denoising, and differential accessibility testing were performed using deep generative modeling via PeakVI. CytoTRACE was used to model cell plasticity and HOMER was used to infer enriched transcription factor footprints in differential accessibility regions (DARs). g:Profiler was used for gene ontology analyses. Results We analyzed >81,000 scATAC-seq profiles. To contextualize tumor cell emergence from normal plasma cells (NPCs), we supplemented our dataset with ~1,000 cells from a public dataset of relapsed refractory MM (RRMM) patients and healthy donors (Fredeet al., Nat Cell Biol, 2021). We identified ~17,000 LRSMM vs. NDMM DARs, ~24,000 HRSMM vs. LRSMM DARs and ~5,000 HRSMM vs. IRSMM DARs. Comparing cells from SMM and MM donors with NPCs revealed few or zero significant DARs, suggesting that intrasample heterogeneity must be properly resolved to accurately describe detailed molecular annotations of each cell group. We thus performed unsupervised clustering of all NPC, SMM, and MM cells to resolve 11 distinct clusters. We defined three NDMM clusters, three NPC/LRSMM clusters, and individual RRMM, NDMM/ HRSMM, HRSMM, IRSMM/LRSMM, NDMM/LRSMM clusters. Comparison of these clusters revealed ~13,000 LRSMM vs. NPCs DARs and ~1,600 IRSMM/LRSMM vs. NPC DARs. Gene ontology analysis of genes neighboring DARs (<50 kb) displayed signatures associated with the P38-MAPK, JNK, and WNT signaling pathways as well as differentiation and development, consistent with previous observations of de-differentiation and increased epigenomic plasticity in MM. BATF, POU3F3, SMAD2, IRF4, JUNB, MYC, FOSL1, and SP1 binding sites were enriched in DARs. We ordered these cell groups along an axis of disease progression, and work to build a deep, generative time-resolved model of MM emergence from pre-myeloma is ongoing. Conclusions We report the largest single-cell chromatin profiling experiment on primary MM cells, focusing on phenotypically early traits of SMM. We characterize distinct sub-groups of SMM patient BM cells and their corresponding regions of accessible chromatin. We are expanding this study through sample-matched WGS to delineate independent genetic and epigenomic contributions to MM progression. scATAC-seq analyses of the matched CD138-negative immune cell fractions are underway alongside analyses of single-cell transcriptome data for both CD138 positive and negative fractions. We anticipate that a deeper understanding of the chromatin states associated with the establishment of overt myeloma will lead to novel therapeutic targets and offer improved predictive prognostics for MM.

Inhibition of USP1 reverses the chemotherapy resistance through destabilization of MAX in the relapsed/refractory B-cell lymphoma

The patients with relapsed and refractory diffuse large B-cell lymphoma (DLBCL) have poor prognosis, and a novel and effective therapeutic strategy for these patients is urgently needed. Although ubiquitin-specific protease 1 (USP1) plays a key role in cancer, the carcinogenic effect of USP1 in B-cell lymphoma remains elusive. Here we found that USP1 is highly expressed in DLBCL patients, and high expression of USP1 predicts poor prognosis. Knocking down USP1 or a specific inhibitor of USP1, pimozide, induced cell growth inhibition, cell cycle arrest and autophagy in DLBCL cells. Targeting USP1 by shRNA or pimozide significantly reduced tumor burden of a mouse model established with engraftment of rituximab/chemotherapy resistant DLBCL cells. Pimozide significantly retarded the growth of lymphoma in a DLBCL patient-derived xenograft (PDX) model. USP1 directly interacted with MAX, a MYC binding protein, and maintained the stability of MAX through deubiquitination, which promoted the transcription of MYC target genes. Moreover, pimozide showed a synergetic effect with etoposide, a chemotherapy drug, in cell and mouse models of rituximab/chemotherapy resistant DLBCL. Our study highlights the critical role of USP1 in the rituximab/chemotherapy resistance of DLBCL through deubiquitylating MAX, and provides a novel therapeutic strategy for rituximab/chemotherapy resistant DLBCL.

Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains.

Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein-protein and protein-DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX. Our synthetic approach yields chemically stabilized tertiary domain mimetics that cooperatively bind the MYC/MAX consensus E-box motif with nanomolar affinity, exhibit specificity that is equivalent to or beyond that of full-length TFs and directly compete with MYC/MAX protein for DNA binding. A lead STR directly inhibits MYC binding in cells, downregulates MYC-dependent expression programs at the proteome level and inhibits MYC-dependent cell proliferation. Co-crystallization and structure determination of a STR:E-box DNA complex confirms retention of DNA recognition in a near identical manner as full-length bHLH TFs. We additionally demonstrate structure-blind design of STRs derived from alternative bHLH-TFs, confirming that STRs can be used to develop highly specific mimetics of TFs targeting other gene regulatory elements.