Motif Enrichment Research Articles

Breast cancer risk SNPs and associated expression QTLs focusing Bangladeshi population: An in silico analysis

BackgroundSingle Nucleotide Polymorphism (SNP)s in the genome and associated genes cause susceptibility to breast cancer, the most common cancer leading to death in women. Variation in different human races' genomes makes breast cancer prognosis challenging in terms of targeted drugs and therapies. The study aimed to compile the Breast cancer associated SNPs used for screening in the existing publications focusing Bangladeshi population, followed by the identification of Expression quantitative trait loci (eQTLs) associated with those SNPs from the eQTL database. eQTLs identify genes whose expression is regulated by specific SNPs. In silico characterization in terms of variant effect prediction, co-expression, Gene Ontology (GO) enrichment, protein-protein interaction, and sequence motif analysis narrowed down a specific set of candidate genes. MethodsPublished reports emphasizing the SNPs screened for Breast cancer in Bangladeshi population were analyzed in PancanQTL for identification of eQTLs which uses genotype and gene expression data from The Cancer Genome Atlas. The gene description and GO associated with identified eQTLs were retrieved from the Ensembl database and characterizations were performed using variant effect predictor, Coexpedia, MEME suite, and STRINGdb. ResultsIt was found from the published reports that not all variants showed strong association with the disease in Bangladeshi population. The cis-eQTLs associated with reported SNPs tested so far on Bangladeshi population are ZNF575, MRPL42P5, C15orf57, C15orf62, NFATC3, XRCC1, C14orf153, CKB, BAG5, KLC1, MARK3. Among them only ZNF575 was enlisted as breast cancer associated eQTL and the rest are linked with other types of cancer. These genes are mostly associated in DNA-binding transcription factor activity, protein binding, Intracellular protein transport II, transferase activity. Protein-protein interaction could predict some functional partners to connect the eQTLs with respective SNP harboring genes. Taking the commonly screened genes for breast cancer as targets breast cancer associated cis and trans eQTLs along with the associated survival eQTLs have been retrieved from the database and a list of specific variants are recommended for future studies to get a more comprehensive scenario about the disease prognosis. ConclusionSince it was found from the existing literature that the commonly used variants are not always associated with all human races, this simple and precise in silico study was carried out to analyze publicly available data. This helped limit specific candidate genes and variants which will be helpful in future population-based screenings in understanding breast cancer prognosis with a provision to develop population specific personalized drug.

Abstract B113: Characterization of the epigenomic landscape of the human pancreas and early pancreatic neoplastic lesions

Abstract Study of early pancreas neoplasia in humans had previously been limited by lack of available tissue. Recent work by our group on deceased donor pancreata identified pancreatic intraepithelial neoplasia (PanIN) lesions in non-diseased organs and defined a transcriptomic signature for the microenvironment of these pre-cancerous lesions. Prevalence of PanINs in healthy human tissue was higher than expected and established a novel model to expand understanding of the complex biology of these precursor lesions. Epigenetic changes in chromatin structure and the subsequent effects on gene expression are essential processes in neoplasia that have yet to be described at the single cell level in the human pancreas. We hypothesized that characterization of the epigenomic landscape in donor pancreata would identify differences in chromatin structure and gene expression between healthy human tissue and PanINs, thereby expanding prior knowledge and identifying novel targets of study in the biology of early neoplasia in the pancreas. Single nuclei from five donor pancreata (six total samples including one replicate sample from a single donor pancreas) were isolated for transposase-accessible chromatin preparation followed by high-throughput sequencing (ATAC-seq) using the 10x Genomics platform. Data analysis was conducted using CellRanger, Seurat, Signac, and AUCell to identify and label chromatin peaks in individual nuclei corresponding to acinar, ductal, and PanIN origin according to gene signatures identified by scRNA on matched pancreata (Carpenter et al 2023, Cancer Discovery). Using this method, cells corresponding to these gene signatures, including PanIN-like cells, were indeed identified in preliminary analysis. Differentially accessible regions of the genome were then analyzed for motif enrichment between these cell types. Motifs enriched in cells identified as PanINs compared to either ductal or acinar cells included several transcription factors implicated in tumorigenesis, including members of the AP-1/Fos/Jun family and multiple zinc-finger protein family members, such as the KLF. These results are similar to previously demonstrated essential factors in pancreatic neoplasia. Differentially expressed motifs between ductal and acinar cells included factors associated with differentiation, including Myod1, Ptf1a, and the TCF family of transcription factors. Together, this study demonstrates that PanINs can be identified in human pancreas tissue by ATAC-seq and that differentially expressed motifs can be identified this model, providing opportunity for further integration with transcriptomic information to elucidate detailed understanding of early neoplasia in the pancreas. Citation Format: Jamie N. Mills, Joyce Thompson, Jacqueline Morales, Padma Kadiyala, Ahmed M. Elhossiny, Howard Crawford, Eileen Carpenter, Marina Pasca di Magliano, Filip Bednar, Simone Benitz. Characterization of the epigenomic landscape of the human pancreas and early pancreatic neoplastic lesions [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B113.

Abstract A118: Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignancy and rapid recurrence

Abstract Pancreatic ductal adenocarcinoma (PDAC) disease progression involves complex cell state transitions in both malignant and non-malignant populations within the tumor microenvironment. To uncover PDAC cell states and epigenetic features associated with clinical outcome, we studied 42 PDAC samples (35 primary tumors and 7 metastases) from 41 patients with single cell ATAC-seq, along with 10 sample-matched single cell RNA-seq profiles. Our work uncovered thousands of chromatin regions with altered accessibility in malignant cells relative to normal ductal and acinar cells. Numerous epigenetic changes were universal to all PDAC clusters regardless of patient-of-origin and occurred proximal to genes involved in glycolysis, regulation of MYC, hypoxic response, extracellular matrix remodeling, and repression of transposable elements. Topic modeling of high dimensional chromatin data revealed networks of co-accessible cis-regulatory regions active in malignant cells, as well as networks specific to basal-like and classical PDAC molecular subtypes. Furthermore, our epigenomic data also suggest alternate paths of lineage infidelity across the classical-basal continuum: while basal-like PDAC cells acquire chromatin accessibility mimicking that of skin or mammary epithelial tissue, several classical subtype tumors featured a subpopulation of malignant cells with increased accessibility of neural-associated chromatin regions genome-wide. Within the immune compartment, we also identified a cis-regulatory network with increased activity in T-cells sampled from rapidly recurring PDAC tumors. Motif analysis of this network revealed enrichment for SMAD and FOXP1 motifs, suggesting widespread modification of T-cells by TGF-β. To our knowledge, our work is the largest single-cell resolution study of chromatin state in human PDAC to date, revealing key epigenetic features associated with PDAC subtype and clinical outcome. Citation Format: Kevin MacPherson, Jason M. Link, Patrick Worth, Brett Sheppard, Andrew Fields, Colin Daniel, Andrew Nishida, Carl Pelz, Trent Waugh, Ethan Agritelle, John Muschler, Andrew Adey, Rosalie Sears. Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignancy and rapid recurrence [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A118.

Abstract C025: Fibroblast-specific IL1R1-p38 MAPK signaling sustains stromal inflammation and contributes to therapeutic resistance in pancreatic cancer

Abstract Introduction: The desmoplastic stroma of pancreatic ductal adenocarcinoma (PDAC) perpetuates therapeutic resistance by impairing drug delivery and effector immune cell infiltration and activation. We have identified tumor cell-derived interleukin-1α (IL1α) as a critical activator of the stroma, comprised of cancer-associated fibroblasts (CAF), towards a pro-inflammatory phenotype via the IL1 receptor, IL1R1, and subsequent activation of p38 MAPK. Our hypothesis is that disruption of the CAF-specific IL1α/p38 MAPK signaling axis can improve chemotherapeutic resistance by remodeling the fibrotic stromal landscape and the overall immune microenvironment in PDAC. Methods: p38 MAPK was pharmacologically inhibited with pexmetinib and genetically with an shRNA lentiviral system. Bulk RNA and ATAC sequencing (RNAseq and ATACseq) were performed on human pancreatic stellate cells (hPSC). Gene set enrichment analyses and motif enrichment analyses were performed on the RNAseq and ATACseq datasets, respectively. Tumor cells (KPC-6694), derived from LSL-KrasG12D/+; LSL-Tp53R172H/+; Pdx1Cre/+ (KPC) murine tumors, were injected orthotopically into Col1a2Cre/+; Mapk14f/f and Col1a2Cre/+; Il1r1f/f mice, and tumors were harvested for downstream analysis. Ptf1aCre/+; LSL-KrasG12D/+; Tgfbr2flox/flox (PKT) mice were treated with pexmetinib (PEX, 30mg/kg, daily PO), anakinra (AKA, 50mg/kg IP, BID) or vehicle control for 2.5 weeks prior to sacrifice for downstream analyses and single-cell RNA sequencing (scRNA) on tumors. Results: In vitro inhibition of p38 MAPK prevented CAF activation into an inflammatory fibroblast, when stimulated with IL1α, demonstrated through bulk RNAseq and ATACseq. Bulk ATACseq revealed epigenetic regulation of the inflammatory CAF phenotype by IL1-mediated activation of p38 MAPK. Stromal-specific deletion of Il1r1 or Mapk14 resulted in signification reduction of tumor weight and intratumoral myeloid-derived suppressor cells. Additionally, pharmacologic blockade of both IL1R1 (AKA) and p38 MAPK inhibition (PEX) altered intratumoral immune cell and CAF populations, by flow cytometry and scRNA. Lastly, p38 inhibition or IL1R1 blockade combined with chemotherapy significantly reduced tumor burden and favorably altered the immune landscape in a PDAC genetically engineered mouse model. Conclusions: These findings provide important mechanistic data in preclinical PDAC models to explore p38 MAPK inhibition in combination therapy to target the fibrotic stroma and immunosuppressive tumor microenvironment. Citation Format: Samara P. Singh, Austin R. Dosch, Siddharth Mehra, Iago de Castro Silva, Vanessa Tonin Garrido, Anna Bianchi, Haleh Amirian, Edmond W. Box, Jashodeep Datta, Nagaraj S. Nagathihalli, Nipun B. Merchant. Fibroblast-specific IL1R1-p38 MAPK signaling sustains stromal inflammation and contributes to therapeutic resistance in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C025.

TGFβ macrophage reprogramming: a new dimension of macrophage plasticity.

The August 2023 article in Science Signaling, "TGF-β uncouples glycolysis and inflammation in macrophages and controls survival during sepsis," challenges the traditional M1/M2 macrophage classification by investigating the impact of transforming growth factor β on macrophage metabolism and function. Despite its conventional anti-inflammatory role, transforming growth factor β-treated macrophages exhibit a distinct phenotype marked by heightened glycolysis, suppressed proinflammatory cytokines, and increased coagulation factor expression. The study identifies phosphofructokinase, liver type as a crucial glycolytic enzyme regulated by transforming growth factor β via the mTOR-c-MYC pathway. Epigenetic changes induced by transforming growth factor β, such as increased Smad3 activation and reduced proinflammatory transcription factor motif enrichment, contribute to the anti-inflammatory profile. The research extends its implications to sepsis, revealing the role of transforming growth factor β in exacerbating coagulation and reducing survival in mouse models. This effect involves upregulation of coagulation factor F13A1, dependent on phosphofructokinase, liver type activity and glycolysis in macrophages. Connections to COVID-19 pathology are drawn, as transforming growth factor β-treated macrophages and SARS-CoV-2 E protein-exposed cells display similar metabolic profiles. Bioinformatic analysis of COVID-19 patient data suggests correlations between myeloid expression of TGFβR1, PFKL, and F13A1 with disease severity. The study challenges the M1/M2 classification, emphasizing the complexity of macrophage responses influenced by transforming growth factor β, proposing transforming growth factor β as a potential therapeutic target for conditions like sepsis and COVID-19 where dysregulated coagulation is significant. Overall, the research provides valuable insights into transforming growth factor β-mediated immunometabolic regulation, paving the way for future investigations and potential therapeutic interventions.

A low-cost, low-input method establishment for m6A MeRIP-seq.

N6-methyladenosine (m6A) is a highly prevalent modification found in mammal mRNA molecules that plays a crucial role in the regulation of cellular function. m6A RNA immunoprecipitation sequencing (MeRIP-seq) has been frequently used in transcriptomics research to identify the location of m6A. MABE572 (Millipore) is the most widely utilized and efficient anti-m6A antibody for MeRIP-seq. However, due to the high dose and price of this antibody, which has also been taken off the market, we discovered that CST's anti-m6A antibody can be used instead of MABE572 to map the m6A transcriptome. In the present study, we performed different concentrations of the CST anti-m6A antibodies with the corresponding initiation RNA of HEK293T cells, 2.5 μg antibody with 1 μg total RNA, 1.25 μg antibody with 0.5 μg total RNA, and 1.25 μg antibody with 0.1 μg total RNA. By comparing the m6A peak calling, enriched motifs, alternative splicing events, and nuclear transcripts modified by m6A between the CST and Millipore libraries, it was found that the CST library presented similar data to Millipore, even at incredibly low doses. The volume and cost of antibodies are significantly reduced by this refined MeRIP-seq using CST antibody, making it convenient to map future large-scale sample m6A methylation.

THE EPIGENETIC LANDSCAPE IN SOFT-TISSUE FIBROSIS

Dupuytren's disease (DD) is a fibroproliferative soft tissue disease affecting the palmar fascia of the hand causing permanent and irreversible flexion contracture. Aberrant fibrosis is likely to manifest through a combination of extrinsic, intrinsic, and environmental factors, including genetics and epigenetics. However, the role of epigenetics in soft tissue fibrosis in diseases such as DD is not well established. Therefore, we conducted a comprehensive multi-omic study investigating the epigenetic profiles that influence gene expression in DD pathology. Using control (patients undergoing carpal tunnel release) and diseased fibroblasts (patients undergoing Dupuytren's fasciectomy), we conducted ATAC-seq to assess differential chromatin accessibility between control and diseased fibroblasts. Additionally, ChIP-seq mapped common histone modifications (histone H4; H3K4me3, H3K9me3, H3K27me3, H4K16Ac, H4K20Me3) associated with fibrosis. Furthermore, we extracted RNA from control and DD tissue and performed bulk RNA-seq.ATAC-seq analysis identified 2470 accessible genomic loci significantly more accessible in diseased fibroblasts compared to control. Comparison between diseased and control cells identified numerous significantly different peaks in histone modifications (H4K20me3, H3K27me3, H3K9me3) associated with gene repression in control cells but not in diseased cells. Pathway analysis demonstrated a substantial overlap in genes being de-repressed across these histone modifications (Figure 1). Both, ATAC-seq and ChIP-seq analysis indicated pathways such as cell adhesion, differentiation, and extracellular matrix organisation were dysregulated as a result of epigenetic changes. Moreover, de novo motif enrichment analysis identified transcription factors that possibly contributed to the differential gene expression between control and diseased tissue, including HIC1, NFATC1 and TEAD2. RNA-seq analysis found that these transcription factors were upregulated in DD tissue compared to control tissue.The current epigenetic study provides insights into the aberrant fibrotic processes associated with soft tissue diseases such as DD and indicates that epigenetic-targeted therapies may be an interesting viable treatment option in future.For any figures or tables, please contact the authors directly.

Incorporating Sequence-Dependent DNA Shape and Dynamics into Transcriptome Data Analysis.

Differentially expressed genes in a cellular context may be co-regulated by the same transcription factor. However, in the absence of a concurrent transcription factor binding data, such interactions are difficult to detect, especially at the single cell expression level. Motif enrichments in such genes can be used to gain insight into differential expressions caused by the shared upstream TFs. However, it is now established that many genes are co-regulated by the same TF due to a shared DNA shape or sequence-dependent conformational dynamics instead of sequence motif. In this work, we demonstrate how, starting from a gene expression data, such DNA shape and dynamics signatures can be potentially detected using publicly available tools, including DynaSeq, developed in our group for predicting the sequence-dependent components of these DNA shapefeatures.

Evidence of innate training in bovine γδ T cells following subcutaneous BCG administration.

The Bacillus Calmette Guerin (BCG) vaccine has been shown to induce non-specific protection against diseases other than tuberculosis in vaccinated individuals, attributed to the induction of trained immunity. We have previously demonstrated that BCG administration induces innate immune training in mixed peripheral blood mononuclear cells and monocytes in calves. Gamma Delta (γδ) T cells are non-conventional T cells that exhibit innate and adaptive immune system features. They are in higher proportion in the peripheral blood of cattle than humans or rodents and play an essential role in bovine immune response to pathogens. In the current study, we determined if BCG administration induced innate immune training in bovine γδ T cells. A group of 16 pre-weaned Holstein calves (2-4 d age) were enrolled in the study and randomly assigned to vaccine and control groups (n=8/group). The vaccine group received two doses of 106 colony forming units (CFU) BCG Danish strain subcutaneously, separated by 2 weeks. The control group remained unvaccinated. Gamma delta T cells were purified from peripheral blood using magnetic cell sorting three weeks after receiving the 1st BCG dose. We observed functional changes in the γδ T cells from BCG-treated calves shown by increased IL-6 and TNF-α cytokine production in response to in vitro stimulation with Escherichia coli LPS and PAM3CSK4. ATAC-Seq analysis of 78,278 regions of open chromatin (peaks) revealed that γδ T cells from BCG-treated calves had an altered epigenetic status compared to cells from the control calves. Differentially accessible peaks (DAP) found near the promoters of innate immunity-related genes like Siglec14, Irf4, Ifna2, Lrrfip1, and Tnfrsf10d were 1 to 4-fold more accessible in cells from BCG-treated calves. MOTIF enrichment analysis of the sequences within DAPs, which explores transcription factor binding motifs (TFBM) upstream of regulatory elements, revealed TFBM for Eomes and IRF-5 were among the most enriched transcription factors. GO enrichment analysis of genes proximal to the DAPs showed enrichment of pathways such as regulation of IL-2 production, T-cell receptor signaling pathway, and other immune regulatory pathways. In conclusion, our study shows that subcutaneous BCG administration in pre-weaned calves can induce innate immune memory in the form of trained immunity in γδ T cells. This memory is associated with increased chromatin accessibility of innate immune response-related genes, thereby inducing a functional trained immune response evidenced by increased IL-6 and TNF-α cytokine production.

Analysis of Chromatin Accessibility and DNA Methylation to Reveal the Functions of Epigenetic Modifications in Cyprinus carpio Gonads.

Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are limited. In this study, we conducted the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and Bisulfite sequencing (BS-seq) to explore the roles of epigenetic modifications in the common carp gonads. We identified 84,207 more accessible regions and 77,922 less accessible regions in ovaries compared to testes, and some sex-biased genes showed differential chromatin accessibility in their promoter regions, such as sox9a and zp3. Motif enrichment analysis showed that transcription factors (TFs) associated with embryonic development and cell proliferation were heavily enriched in ovaries, and the TFs Foxl2 and SF1 were only identified in ovaries. We also analyzed the possible regulations between chromatin accessibility and gene expression. By BS-seq, we identified 2087 promoter differentially methylated genes (promoter-DMGs) and 5264 gene body differentially methylated genes (genebody-DMGs) in CG contexts. These genebody-DMGs were significantly enriched in the Wnt signaling pathway, TGF-beta signaling pathway, and GnRH signaling pathway, indicating that methylation in gene body regions could play an essential role in sex maintenance, just like methylation in promoter regions. Combined with transcriptomes, we revealed that the expression of dmrtb1-like, spag6, and fels was negatively correlated with their methylation levels in promoter regions. Our study on the epigenetic modifications of gonads contributes to elucidating the molecular mechanism of sex differentiation and sex maintenance in the common carp.

Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

BackgroundDrought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far.ResultsIn the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes.ConclusionsThese results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information.

The Molecular Mechanism of Relatively Low-Temperature-Induced Broccoli Flower Bud Differentiation Revealed by Transcriptomic Profiling

Broccoli (Brassica oleracea L. var. italica) has a large, edible green flower head, which is one of its critical economic traits. A prerequisite of broccoli flower head formation is flower bud differentiation (FBD). Low-temperature treatment is an effective way to induce FBD in broccoli. However, the molecular mechanism underlying low-temperature-induced broccoli FBD remains largely unclear. In this study, using broccoli cultivar Zhongqing 10 as the experimental material, we investigated the effects of low-temperature treatment on FBD by comparing the plants grown at low temperatures (17 °C/9 °C, 16 h/8 h) with the control plants grown under normal temperature conditions (25 °C/17 °C, 16 h/8 h). After 15 days of different temperature treatments, the flower buds of the plants growing under the low-temperature condition started to differentiate. However, the control plants remained in the vegetative growth stage, indicating that low temperature successfully induced flower bud formation. Subsequently, a global transcriptomic analysis was conducted to detect the differentially expressed genes (DEGs) during low-temperature-induced FBD in broccoli. A total of 14 DEGs in five phytohormone signaling pathways, 42 DEGs in nine transcription factor families, and 16 DEGs associated with the floral development pathways were identified. More DEGs were present in the auxin signaling pathway than in other phytohormone signaling pathways, which indicated that the auxin signaling pathway played a critical role in modulating low-temperature-induced FBD in broccoli. Furthermore, four TF classes, including bZIP, GCM domain factors, MADS-box factors, and C2H2 zinc finger factors, possessed enriched motifs, indicating that their closely related DETFs ABI5, HY5L, WRKY11, WRKY15, WRKY22, SOC1, AGL8, FLC, SPL8, and SPL15 may be directly involved in the transcription regulation of broccoli FBD. This study provides an important basis for further investigation of the molecular regulatory mechanism of broccoli flower development under low temperatures.

10064-GGE-6 A MULTI-OMIC LANDSCAPE OF GLIOBLASTOMA, IDH-WILD TYPE

Abstract Glioblastoma (GBM) is the most common and highly resistant malignant brain tumor. Although the previous large-scale genomic analyses identified numerous driver genes, limited progress has been achieved in the development of novel treatments. To obtain further insights into the molecular mechanisms underlying the development of GBM, an integrated analysis including epigenetic and transcriptomic analyses, known to regulate malignant tumor progression, is imperative. We analyzed 289 whole-genome sequencing (WGS) including 159 unpublished deep WGS (≥ ×120 coverage) along with RNA-seq, DNA methylation array, whole-genome bisulfite sequencing, and assay for transposase-accessible chromatin with sequencing (ATAC-seq).Mutational analysis identified known driver alterations exhibiting inter-tumoral heterogeneity. Deep WGS enables us to delineate a fine view of clonal architecture demonstrating distinct mutational signatures between clonal and subclonal mutations, suggesting different mutational processes contribute to GBM pathogenesis depending on the developmental stage. Genetic alterations are strongly associated with gene expression subtypes and DNA methylation patterns. Transcriptional deconvolution analysis reveals the heterogeneous proportion of differentiated and stem-like cell states among cases. Tumors predominantly comprised of differentiated cells display genetic and epigenetic profiles that align with the classical subtype, whereas tumors predominantly composed of stem-like cells exhibit profiles consistent with the proneural subtype. Genome-wide chromatin accessibility patterns are well associated with expression subtypes of GBM. Motif enrichment analysis of open chromatin sites identified specific transcription factor binding sites, such as the SOX10 motif in the proneural subtype, known to regulate cell states, and the CREB motif in the mesenchymal and classical subtypes, which promote cell proliferation and angiogenesis through TGF-beta regulation. These findings support a model in which the difference in chromatin structure also regulates the progression of GBM.Our analysis encompassing multilayer molecular mechanisms reveals that GBM evolves through harboring genetic alterations and epigenetic modifications depending on the tumor initiation stage and cellular differentiation status.

MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks.

Our study aimed to identify biologically relevant transcription factors (TFs) that control the expression of a set of co-expressed or co-regulated genes. We developed a fully automated pipeline, Motif Over Representation Analysis (MORA), to detect enrichment of known TF binding motifs in any query sequences. MORA performed better than or comparable to five other TF-prediction tools as evaluated using hundreds of differentially expressed gene sets and ChIP-seq datasets derived from known TFs. Additionally, we developed EnsembleTFpredictor to harness the power of multiple TF-prediction tools to provide a list of functional TFs ranked by prediction confidence. When applied to the test datasets, EnsembleTFpredictor not only identified the target TF but also revealed many TFs known to cooperate with the target TF in the corresponding biological systems. MORA and EnsembleTFpredictor have been used in two publications, demonstrating their power in guiding experimental design and in revealing novel biological insights.

ScANANSE gene regulatory network and motif analysis of single-cell clusters

The recent development of single-cell techniques is essential to unravel complex biological systems. By measuring the transcriptome and the accessible genome on a single-cell level, cellular heterogeneity in a biological environment can be deciphered. Transcription factors act as key regulators activating and repressing downstream target genes, and together they constitute gene regulatory networks that govern cell morphology and identity. Dissecting these gene regulatory networks is crucial for understanding molecular mechanisms and disease, especially within highly complex biological systems. The gene regulatory network analysis software ANANSE and the motif enrichment software GimmeMotifs were both developed to analyse bulk datasets. We developed scANANSE, a software pipeline for gene regulatory network analysis and motif enrichment using single-cell RNA and ATAC datasets. The scANANSE pipeline can be run from either R or Python. First, it exports data from standard single-cell objects. Next, it automatically runs multiple comparisons of cell cluster data. Finally, it imports the results back to the single-cell object, where the result can be further visualised, integrated, and interpreted. Here, we demonstrate our scANANSE pipeline on a publicly available PBMC multi-omics dataset. It identifies well-known cell type-specific hematopoietic factors. Importantly, we also demonstrated that scANANSE combined with GimmeMotifs is able to predict transcription factors with both activating and repressing roles in gene regulation.

A Longitudinal Single-Cell Atlas of Treatment Response in Pediatric AML

Introduction: Pediatric acute myeloid leukemia (pAML) is a heterogeneous disease in terms of driver alterations, treatment response and patient outcomes. Although approximately 90% of pAML patients respond to initial treatment, tumours relapse frequently. Despite large-scale genomic sequencing efforts, it remains elusive why tumors relapse. Previously, mutations have been identified that affect transcriptional regulation, indicating that epigenetic processes may contribute to treatment resistance in pAML. We therefore studied how tumor epigenetic patterns, transcriptional regulation and cell populations change over the course of treatment using single-cell ATAC sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) in pediatric populations. Methods: We profiled 330,047 cells using scRNA-seq and 353,984 cells using scATAC-seq derived from 28 uniformly treated pAML patients, driven by either MLL fusions, CBFB fusions, RUNX1 fusions, FLT3-ITD or other aberrations (i.e. CEBPA mutations). All patients were enrolled in the AAML1031 trial (https://childrensoncologygroup.org/aaml1031), a randomized phase 3 clinical trial that investigated the addition of Bortezomib (BTZ) and Sorafenib to standard treatment modalities. Samples were obtained serially at diagnosis, at remission and at relapse and single-cell profiles were compared between these stages. Results: We identified malignant and non-malignant populations in the scATAC-seq and scRNA-seq data, showing that in all cases, malignant cells from patients at diagnosis were distinct from those taken at relapse. Major differences between diagnosis and relapse were associated with differentiation, and by inferring distinct cell populations we identified that relapsed cell populations appeared to shift towards a more primitive state. The extent of this shift was dependent on the genetic subtype and the effects were more pronounced in MLL-rearranged tumors. To identify the candidate mechanisms and transcription factors involved in this shift we studied the monocytic, lymphocytic and erythrocytic lineages in non-malignant cells and compared these to the tumor at diagnosis and relapse. Based on motif enrichment we found that across all different subgroups, transcription factors (TFs) that drive monocytic differentiation (i.e. CEBPA) have a lower activity while TFs driving erythrocytic and lymphocytic differentiation (i.e. TCF3) have a higher activity. Analysis of hematopoietic stem-like and progenitor-like cells (HSPC-like) confirmed this change, indicating that the “priming” towards other lineages is not only a result of shifts in cell populations but also a result of rewiring of early progenitors. To investigate this rewiring, we analysed regions of open chromatin that were enriched in malignant HSPCs compared to normal HSPCs across different subgroups. We found that those regions were highly specific to the driving alteration and were enriched for MEF2C binding sites in MLL-driven tumors and AP-1 binding sites in other tumors. Overall, upon relapse MEF2C expression and inferred TF activity appeared to increase, coinciding with an apparent increase in lymphoid priming and early lymphoid factors including LMO2, LYL1 and TCF3, among others. Two cases in the cohort appeared to switch lineage from a monocytic to lymphocytic phenotype and were enriched in CD19 and CD79A positive malignant cells upon relapse. Both cases shared the characteristic that MEF2C was upregulated upon relapse and showed upregulation of typical B-lymphoid transcription factors such as PAX5. Discussion: By generating a large dataset of pediatric AML patient samples collected at diagnosis, remission and relapse, we have identified changes in cellular hierarchies and transcriptional networks that occur upon relapse. Our study shows that shifts in cell populations readily occur upon treatment and are dependent on subgroup-defining alterations. Particularly MLL-rearranged tumors show a high level of plasticity that could explain the poor outcome of this group. Furthermore, we show that tumors appear to adapt their transcriptional programs towards a more “stem-like” state, with a likely higher propensity to differentiate towards other lineages such as the lymphoid lineage. We have identified MEF2C as a possible regulator of these processes, opening a new perspective to target the plasticity of these tumors.

Novel Fusion Gene Aven-NUTM1 Induces Mice Myeloid Leukemia Vulnerable to HDAC Inhibitors

Chromosomal rearrangements involving the NUTM1 gene produce fusion genes commonly found in NUT carcinoma. While recurring NUTM1 fusions have been reported in other neoplasms, including AML, their roles in leukemogenesis remain unclear. We identified the AVEN-NUTM1 (AN) fusion gene in an AML patient resistant to standard chemotherapy, and went to assess AN's leukemogenicity via bone marrow transduction and transplantation. Mice transplanted with AN-transduced hematopoietic stem/progenitor cells (HSPCs) developed transplantable myeloid leukemia with a median survival of 342 days. RNA sequencing revealed downregulation of genes related to hematopoietic cell lineage commitment and upregulation of genes related to early hematopoietic progenitors and MYC-targeted genes in AN-transformed leukemic cells. Co-immunoprecipitation confirmed that AVEN-NUTM1 can interact with and activate EP300 as previously reported. To determine whether AN's interaction with EP300 is related to its ability to induce malignant transformation, we mutated the interaction site and constructed mutants of other structural domains. Colony-forming and replating assays showed that HSPCs expressing AN with mutations in the EP300 binding site lost their ability to self-renew and form colonies. A CUT&RUN assay followed by sequencing showed that the most enriched motif in overlapping peaks between AN and EP300 were ETS motifs, suggesting the involvement of an ETS transcription factor family member in AN-activated EP300-induced leukemia. We further found that both the patient's primary cells and bone marrow cells from leukemic mice were especially vulnerable to HDAC inhibitors. These results demonstrate that the AVEN-NUTM1 fusion gene can drive the development of myeloid leukemia in mice, AN's ability to bind and activate P300 is closely linked to its leukemogenicity, and that HDAC inhibitors are effective in targeting AN leukemia cells. The study provids valuable insights for the targeted treatment of NUTM1-related leukemia patients.

Retinoic Acid and Ascorbate Remodel the Epigenome of Leukemia Cells to Improve Therapeutic Efficacy By Enhancing TET Activity

Ten-eleven translocation (TET) enzymes are commonly mutated in leukemia, leading to aberrant DNA methylation and impaired hydroxymethylation. All-trans retinoic acid (ATRA) is a vitamin A derivative and cofactor of retinoic acid receptors (RARs) which, in combination with arsenic trioxide, can curatively treat acute promyelocytic leukemia. ATRA has also been shown to upregulate expression of Tet2 and Tet3 in murine embryonic stem cells, and retinol and ascorbic acid (vitamin C) have been shown to enhance pluripotent stem cell reprogramming through increasing hydroxymethylcytosine and promoting DNA demethylation. Our previous work has demonstrated ascorbate can slow disease progression in vivo and, combined with the PARP inhibitor Olaparib, promote cell cycle dysregulation and induce cellular differentiation in acute myeloid leukemia (AML) models both in vitro and in vivo. Here, we show ATRA can induce TET2 and/or TET3 expression in AML cells, and, combined with ascorbate, increase genome-wide oxidized methylcytosine in a TET-dependent manner. Combination treatment with ATRA and ascorbate also induces transcriptional reprogramming, leading to upregulation of DNA repair genes and pathways leading to increased expression of myeloid differentiation markers. Additionally, we observe chromatin remodeling associated with an enrichment for ETS motifs including genes and regions regulated by the transcription factor PU.1, an essential modulator of hematopoietic cell fate. We also show enrichment of retinoic acid receptor A (RARA) at the TET2 locus and at several RAR elements in response to ATRA in AML cells. Using very low dose ascorbate and ATRA, we show that the combination treatment can enhance the efficacy of Olaparib and Venetoclax to alter the cell cycle, promote differentiation, and induce apoptosis of AML cells. These data demonstrate the potential for ATRA and ascorbate to increase TET activity and drive myeloid differentiation and death of AML cells that can be exploited as an adjuvant therapy for the treatment leukemia.

Genotype-Phenotype Mapping Via Single-Cell Multi-Omics Identifies Therapeutic Vulnerabilities in Vexas Syndrome

VEXAS (Vacuoles E1 enzyme X-linked Autoinflammatory Somatic) syndrome originates from hematopoietic stem cells (HSCs) carrying a somatic UBA1 p.M41 mutation. UBA1 p.M41 mutation leads to systemic inflammation and bone marrow failure, with poor survival. Other than allogenic stem cell transplantation, no curative therapy is available for VEXAS. This arises from the challenge of defining the phenotypic effects of the UBA1 p.M41 mutation in primary human samples, confounded due to the mixture of wildtype and mutated cells. Thus, it is essential to resolve the admixture of wildtype and UBA1 p.M41 mutated cells to understand the effect of the UBA1 p.M41 mutation in the disease-initiating HSCs. By doing so, we can identify potential mutant-specific therapeutic vulnerabilities to specifically eliminate UBA1 p.M41 HSCs. To map genotype-phenotype relationship in human VEXAS samples, we deployed and developed single-cell multi-omics including Genotyping of Transcriptomes (GoT) and Genotyping of Targeted loci with Chromatin Accessibility (GoT-ChA), allowing the capture of UBA1 genotype, cell identity, transcriptome, chromatin accessibility and signaling pathways at single cell resolution ( Fig.1a). We applied GoT to CD34+ enriched bone marrow mononuclear cells (BMMNCs) from VEXAS primary human samples ( n = 31,406 cells across 6 patients). Integrating UBA1 genotyping with gene expression data showed an enrichment of the mutation in myeloid-committed cells and depletion in B and T cells. Interestingly, this mutation is also enriched in natural killer (NK) cells and plasmacytoid dendritic cells (both originating from lymphoid progenitors), which have not been previously reported. This suggests that VEXAS HSPCs display a skewed differentiation towards myeloid, NK, and plasmacytoid dendritic cells, which may contribute to inflammation in VEXAS. High-resolution mapping of UBA1 p.M41 vs. UBA1 wt HSCs revealed myeloid priming of mutated HSCs. UBA1 p.M41 HSCs showed an increased inflammation signature (Interferon alpha and gamma response pathways) along with increased unfolded protein response (UPR), glycolysis and decreased autophagy pathways. We validated UPR pathway activity by showing the expected increase in XBP1 splicing in UBA1 p.M41 HSPCs using targeted capture of the unconventional splice site. Interestingly, transcriptome data also showed a global translational downregulation accompanied by specific ATF4 target gene enrichment ( Fig.1b). These results suggest a preferential induction of the PERK arm of the UPR. Surface protein expression analysis supported the transcriptomic data, showing upregulation of CD38, CD13 and HLA-DR, denoting myeloid bias and increased inflammatory response in UBA1 p.M41 HSCs. Next, we performed GoT-ChA on CD34 + cells from VEXAS patients (n = 27,894 cells across 3 patients) to study mutant-specific chromatin accessibility. Complementary to the transcriptome data, UBA1 p.M41 HSCs showed increased motif accessibility for TFs associated with myelopoiesis, indicative of myeloid priming. We also observed enrichment for ATF4 and CEPBD TF motifs - downstream of PERK pathway of UPR ( Fig.1b). To validate these findings, we developed GoT-ChA integrated with intracellular protein capture and demonstrated an increased expression of phosphorylated eIF2 and ATF4 proteins in the UBA1 p.M41 HSCs. Finally, to functionally validate the specific role of the PERK pathway on the fitness of UBA1 p.M41 HSCs, we performed assays using mobilized CD34 + cells in-vitro. UBA1 Inhibition in normal CD34 + cells led to ATF4 up-regulation, which correlated with cell survival. The addition of PERK inhibition reduced ATF4 expression and resulted in markedly reduced CD34+ viability. In contrast, inhibiting IRE1 pathway along with UBA1 inhibition did not affect HSC viability. Altogether, we demonstrated that human VEXAS HSCs show a cell-intrinsic inflammatory phenotype and are myeloid biased. Moreover, mutated HSCs tolerate proteome toxicity through activation of the PERK pathway as a part of UPR, providing a fitness advantage to the UBA1 p.M41 mutated HSCs. Targeting the PERK pathway may thus represent a new strategy for overcoming VEXAS syndrome via precision targeting of UBA1 p.M41 mutated HSCs.

Mechanisms of PML::Rara and GATA2 Protein Interactions in Hematopoietic Cells

Despite excellent outcomes for Acute Promyelocytic Leukemia (APL) patients with combined ATRA and Arsenic Trioxide therapy, the underlying molecular mechanisms by which the PML::RARA fusion oncoprotein initiates APL are not yet clear. We recently found that the ability of PML::RARA to initiate aberrant serial replating (a surrogate for self-renewal) is dependent upon its ability to bind to DNA, since PML::RARA with a missense mutation (C88A) that prevents the binding of RARA to DNA eliminates aberrant replating. Currently, however, there is no consensus regarding the genomic binding sites of PML::RARA in myeloid progenitor cells and APL cells. Also, the transcriptional and epigenetic consequences of PML::RARA expression in primary hematopoietic cells remain unclear. To define the genomic binding sites of PML::RARA, we generated V5 epitope tagged PML::RARA constructs in MSCV-based retroviral vectors, and transduced mouse hematopoietic stem progenitor cells (HSPCs) with retroviruses containing V5-PML::RARA WT, V5-PML::RARA C88A, or an empty vector. Anti-V5 ChIP-seq revealed that PML::RARA binds to 2,677 distinct loci in primary mouse hematopoietic cells, and 2,064 sites in primary human hematopoietic cells. We previously demonstrated that Gata2 expression is induced with PML::RARA, and indeed, we identified strong PML::RARA binding to the distal Gata2 enhancer in both human and mouse HSPCs. Surprisingly, ATAC-seq revealed that the vast majority of PML::RARA binding sites are found in regions that are chromatin-accessible even in WT promyelocytes, suggesting that these regions are “open” prior to PML::RARA expression, perhaps because of the normal binding of “pioneer” transcription factors to these regions in WT cells. Indeed, evaluation of transcription factor binding motifs in the regions occupied by PML::RARA revealed significant enrichment for RARA binding motifs, and also GATA motifs. We therefore performed ChIP-seq on GATA2 in HSPCs, which confirmed enrichment in binding at the same sites. These data suggested that PML::RARA and GATA2 may bind in close proximity at hundreds of loci in the genome. To test this, we performed proximity labeling studies followed by mass spectrometry using PML::RARA WT vs. PML::RARA C88A fused to the biotin ligase TurboID in primary HSPCs. This approach revealed that the interactions of several proteins with PML::RARA (including GATA2) are dependent on the binding of PML::RARA to DNA; this suggests that DNA may in fact act as a scaffold to stabilize these protein:protein interactions ( Figure 1). To determine whether Gata2 may induce increased chromatin accessibility following PML::RARA expression, we performed ATAC-seq following Gata2 or PML::RARA overexpression in WT hematopoietic progenitor cells. 3,157 regions shared increased accessibility with either PML::RARA or Gata2 overexpression. Moreover, at a transcriptional level, we found that 535 (27.4%) of PML::RARA differentially expressed genes were coordinately regulated by Gata2 in WT cells. This suggests that PML::RARA indirectly regulates many of its gene targets via the upregulation of Gata2, and that Gata2 may be required for PML::RARA to initiate its transcriptional program. To test this, we performed serial replating assays using cells where Gata2 was knocked out either before or after PML::RARA expression. Consistent with our previous study, knock out of Gata2 following PML::RARA expression led to increased self-renewal capacity. However, knock out of Gata2 before PML::RARA expression prevented self-renewal. These data suggest a model in which GATA2 “opens” specific chromatin regions in early myeloid cells, which are then accessible to RARA or PML::RARA. The two proteins interact at these sites, tethered by their mutual interactions to their respective DNA binding motifs. PML::RARA binding promotes a pre-leukemic transcriptional program mediated in part by positively regulating Gata2. Gata2 is therefore initially required for PML::RARA to establish its transcriptional program. However, once that program is established, Gata2 paradoxically acts as a tumor suppressor, performing a normal role to limit proliferative excess in hematopoietic stem and progenitor cells.