Single-cell ATAC-seq Research Articles

OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions.

Chromatin accessibility serves as a critical measurement of physical contact between nuclear macromolecules and DNA sequence, providing valuable insights into the comprehensive landscape of regulatory mechanisms, thus we previously developed the OpenAnnotate web server. However, as an increasing number of epigenomic analysis software tools emerged, web-based annotation often faced limitations and inconveniences when integrated into these software pipelines. To address these issues, we here develop two software packages named OpenAnnotatePy and OpenAnnotateR. In addition to web-based functionalities, these packages encompass supplementary features, including the capability for simultaneous annotation across multiple cell types, advanced searching of systems, tissues and cell types, and converting the result to the data structure of mainstream tools. Moreover, we applied the packages to various scenarios, including cell type revealing, regulatory element prediction, and integration into mainstream single-cell ATAC-seq analysis pipelines including EpiScanpy, Signac, and ArchR. We anticipate that OpenAnnotateApi will significantly facilitate the deciphering of gene regulatory mechanisms, and offer crucial assistance in the field of epigenomic studies. OpenAnnotateApi for R is available at https://github.com/ZjGaothu/OpenAnnotateR and for Python is available at https://github.com/ZjGaothu/OpenAnnotatePy.

Type I interferons induce an epigenetically distinct memory B cell subset in chronic viral infection

Memory B cells (MBCs) are key providers of long-lived immunity against infectious disease, yet in chronic viral infection, they do not produce effective protection. How chronic viral infection disrupts MBC development and whether such changes are reversible remain unknown. Through single-cell (sc)ATAC-seq and scRNA-seq during acute versus chronic lymphocytic choriomeningitis viral infection, we identified a memory subset enriched for interferon (IFN)-stimulated genes (ISGs) during chronic infection that was distinct from the T-bet+ subset normally associated with chronic infection. Blockade of IFNAR-1 early in infection transformed the chromatin landscape of chronic MBCs, decreasing accessibility at ISG-inducing transcription factor binding motifs and inducing phenotypic changes in the dominating MBC subset, with a decrease in the ISG subset and an increase in CD11c+CD80+ cells. However, timing was critical, with MBCs resistant to intervention at 4weeks post-infection. Together, our research identifies a key mechanism to instruct MBC identity during viral infection.

Abstract NG08: Dissecting and quantifying pancreatic cancer plasticity using single-cell multiomics, lineage tracing and functional genomics reveals novel mediators of therapy resistance

Abstract NG08: Dissecting and quantifying pancreatic cancer plasticity using single-cell multiomics, lineage tracing and functional genomics reveals novel mediators of therapy resistance

Abstract CT271: Neoadjuvant targeted therapy in stage I-III HER2-mutant lobular breast cancer

Abstract Background: Invasive lobular carcinoma (ILC) accounts for approximately 10-15% of all breast cancers and is characterized by hormone receptor positivity (HR+), low Ki-67 score, and loss of cell adhesion receptors such as E-cadherin. While these tumors tend to be indolent initially, late recurrences and distant metastasis are common, and ILC has very low rates of pathologic complete response (pCR) to both neoadjuvant chemotherapy and endocrine therapy (ET). HER2 (ERBB2) mutations are enriched in about 10% of unselected ILC, with some reports showing the prevalence as high as 27% in pleomorphic and higher grade ILCs. HER2 mutations in ILC are associated with ET resistance and a worse prognosis. Neratinib is a HER2 tyrosine kinase inhibitor (TKI) currently FDA-approved for adjuvant treatment of HER2-amplified (HER2+) early-stage breast cancer. It has shown safety and efficacy in combination with ET in metastatic HER2-mutant HR+ breast cancer. We hypothesize that neoadjuvant treatment with neratinib and ET will improve pathologic responses in newly diagnosed HER2-mutant HR+ ILC. Methods: This study (NCT05919108) is an open label multi-site Phase II clinical trial for 30 patients with Stage I-III ILCs and a HER2 activating mutation. Patients will be identified by next generation sequencing (NGS) of the diagnostic biopsy and randomized to 4 weeks of ET +/- neratinib; a biopsy will be done at the end of the lead-in phase. All patients will then receive ET and neratinib for 20 weeks prior to proceeding to surgery. To optimize tolerability, the first cycle of neratinib will include a dose escalation and antidiarrheal prophylaxis. The primary objective of this study will be the pre-operative endocrine prognostic index (PEPI) score, which will be compared to a historical PEPI-0 rate for patients with HR+ breast cancer treated with neoadjuvant ET. Secondary objectives will include pCR, residual cancer burden, and rates of breast conserving surgery. Correlative studies will include biomarkers of tumor cell cycle arrest, apoptosis, HER2 pathway activation, and gene expression on the pre- and on-treatment (4 week) biopsy from the lead-in phase to document molecular synergy between neratinib and ET. Patient-derived organoids from the 4-week biopsies will be established and subjected to single-cell RNA, ATAC seq, and DNA sequencing to study tumor evolution and elucidate epigenetic programs and somatic alterations that allow breast cancer survival despite continuous HER2-directed therapy. This is a first in kind, mechanism-based, molecularly targeted combination of a HER2 TKI and ET in HER2-mutant ILC. We posit results from this study may generate a clear signal of clinical activity leading to a randomized Phase III trial aimed at incorporating HER2-directed therapies as a treatment for operable, early stage ILC. This signal may also suggest for the first time the added value of NGS in patients with newly diagnosed HR+ breast cancer. Citation Format: Laura C. Kennedy, Nisha Unni, Ariella B. Hanker, Carlos L. Arteaga. Neoadjuvant targeted therapy in stage I-III HER2-mutant lobular breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT271.

Abstract 4406: Single cell multiomic analysis reveals how genomic, epigenomic and transcriptomic events drive progression of multiple myeloma precursor states

Abstract In this study we have leveraged Moffitt Cancer Center’s cohort of over 1,000 bone marrow (BMBX) aspirates from normal donors, MM precursor diseases (MGUS, SMOL), active therapy naïve disease (NDMM), as well as early (post 1-3 lines of therapy, ERMM) and late-relapse (3+ lines of therapy, LRMM) MM patients, characterized clinically, cytogenetically (FISH), genetically (WES), and transcriptomically (RNA-seq).Transcriptomic analysis identified a subset of cancer hallmarks differentially expressed between MGUS and NDMM samples (e.g. cell identity, adhesion and inflammatory signaling, etc.).Dimensionality reduction analysis, followed by unsupervised segmentation, identified clusters of co-expressing genes across this dataset. Enrichment analysis of aforementioned gene clusters, differentially expressed between MGUS and NDMM states, identified a number of putative transcription factors (GATA1/2, SUZ12, RUNX1, SOX2, TP63, NFE2L2, FOXM1 and NANOG), as well as polycomb complex and H3K27me3 as main drivers. Single cell ATAC-seq in 11 BMBX (4 SMOL, 4 NDMM, 1 ERMM, 2 LRMM) and single cell multiomics (simultaneous scATAC-seq/scRNA-seq) in additional 10 BMBX (2 healthy, 3 MGUS, 3 SMOL and 2 NDMM) confirmed that the H3K27me3 putatively regulated gene clusters were the only ones with significant chromatin accessibility changes. Single cell analysis confirmed differential expression and accessibility of cancer hallmarks identified in larger cohort, as well as putative driver TFs. Correlation between TF expression and motif accessibility produced an additional list of pioneer TFs putatively involved in progression from MM precursor states (ZEB1, EBF1, SPI1, PAX5, etc.).Investigation of scMultiomic data demonstrated that NDMM and SMOL samples contain subpopulations of cells in MGUS and normal “states” (cell clusters in scMultiomics UMAP), confirming intra-sample heterogeneity, and that divergence within the multiomic plane occurs in the transition between MGUS and SMOL. Through pseudotime and single cell copy number analysis (epiAneufinder/scATAC-seq and inferCNV/scRNA-seq) we were able to reconstruct how MM FISH cytogenetic abnormalities alter the multiome of these cells, creating aforementioned intra-sample heterogeneity. Despite different initiating events, all samples shared a common biology putatively regulated by epigenetic dysregulation, suggesting polycomb complex hijacking as a therapeutic opportunity for precursor MM. Citation Format: Rafael Canevarolo, Praneeth Sudalagunta, Maria Silva, Mark Meads, Rachid Baz, Melissa Alsina, Kenneth H. Shain, Ariosto Siqueira Silva. Single cell multiomic analysis reveals how genomic, epigenomic and transcriptomic events drive progression of multiple myeloma precursor states [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4406.

Abstract 6932: Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in desmoplastic small round cell tumors

Abstract Background: Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, aggressive sarcoma primarily affecting young males. Despite being driven by the unique oncogenic transcription factor (TF) EWSR1-WT1, and a monotonous morphology, DSRCT cells display a polyphenotypic differentiation of unknown etiology. Methods: To explore DSRCT heterogeneity, we characterized a series of patient samples by single-cell, spatial, and bulk multi-omics. We integrated patients’ data with bulk RNA-sequencing, ChIP-sequencing, and ATAC-sequencing data generated in a DSRCT cell line model upon EWSR1-WT1 transcriptional silencing. Results: Single-cell RNA-sequencing (scRNA-seq) on 11 patient samples identified recurrent subpopulations of DSRCT tumor cells, including lineage-, metabolism-, and pseudostate-related clusters. These subpopulations showed overlapping gene modules and lacked copy number variation diversity, suggesting transcriptional plasticity as a potential source of tumor heterogeneity. We first investigated whether cell-intrinsic mechanisms may drive DSRCT intra-tumor heterogeneity. Using an in-house-developed assay, we found limited variability in EWSR1-WT1 transcript expression. Preclinical modeling defined an EWSR1-WT1 regulon, used as a surrogate for EWSR1-WT1 TF activity. Integration with scRNA-seq data showed that high EWSR1-WT1 activity was associated with lineage-related states, while glycolytic and profibrotic states correlated with low EWSR1-WT1 activity. Single-cell ATAC-seq with scRNA-seq (Multiome) on one patient sample identified TF motifs related to developmental processes - e.g., SOX, FOX, and GATA - as the most differentially enriched across clusters. Interestingly, EGR1 regulon activity showed an inverse correlation with EWSR1-WT1 and Androgen Receptor regulons’ activity, in line with preclinical data, where ATAC-seq showed increased accessibility of EGR1 upon EWSR1-WT1 silencing. We next investigated cell-extrinsic factors by spatial transcriptomics in six patient samples. Glycolytic and profibrotic subpopulations localized within hypoxic niches at the tumor periphery, in direct proximity to cancer-associated fibroblasts (CAFs), which promoted tumor growth in vitro, as assessed in DSRCT cells/CAFs co-culture assays. Finally focusing on inter-tumor heterogeneity, the prognostic evaluation of scRNA-seq-derived signatures revealed that a tumor cell epithelial signature correlated with improved patient survival in a cohort of 29 DSRCT samples profiled with bulk RNA-sequencing. Conclusion: DSRCT heterogeneity is driven by combined cell-intrinsic and -extrinsic mechanisms, including EWSR1-WT1 DNA-binding activity and interaction with CAFs. Gene signatures associated with specific DSRCT subpopulations correlated with prognosis, highlighting the clinical relevance of our findings. Citation Format: Clémence Henon, Julien Vibert, Thomas Eychenne, Nadège Gruel, Léo Colmet-Daage, Carine Ngo, Marlène Garrido, Nicolas Dorvault, Maria Eugenia Marques Da Costa, Antonin Marchais, Asuka Kawachi, Madison Lenormand, Clémence Astier, Roman Chabanon, Benjamin Verret, Rastislav Bahleda, Axel Le Cesne, Fatima Mechta-Grigoriou, Charles Honoré, Matthieu Faron, Olivier Delattre, Joshua J Waterfall, Sarah Watson, Sophie Postel-Vinay. Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in desmoplastic small round cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6932.

Abstract 1708: Transposable element derived enhancers in ovarian cancer

Abstract There is global epigenetic dysregulation during transformation from normal to cancerous cells. One of the many consequences of this global epigenetic dysregulation is the reactivation of transposable elements (TEs). TEs compose roughly half of the human genome and are normally repressed through epigenetic mechanisms such as DNA methylation and histone modifications. Endogenous retroviruses (ERVs) are a class of TEs that contain long terminal repeats (LTRs) with putative gene regulatory motifs. LTRs can be co-opted to be pro-tumorigenic by becoming non-canonical promotors for oncogenic genes. While several examples of TE-derived promotors have been reported in cancer, the potential significance of TE-derived enhancers remains largely unexplored. Here, we utilized publicly available multi-omics datasets (bulk and single-cell ATAC-seq, bulk and single-cell RNA-seq, and chromatin profiling) in the context of ovarian cancer to determine if there are tumor specific, TE-derived-enhancers that have gene regulatory function. We used CRISPRi technology to functionally validate a putative TE-derived enhancer and gene regulatory axis. We discovered that on the bulk tissue level, several TE families are enriched at open chromatin sites and sites marked by H3K27Ac (enhancer mark) of ovarian tumors, suggesting the presence of tumor specific, TE-derived enhancers. On the single-cell level, we discovered that ovarian cells have the highest expression of these TE transcripts compared to stromal and immune cells in the tumor microenvironment, suggesting that the increased TE-derived enhancer activity observed on the bulk level are specific to ovarian cells. Lastly, when we silenced a specific LTR18 locus upstream of a gene, TIPARP, TIPARP gene expression was also repressed, suggesting that these putative TE-derived enhancers have gene regulatory function. Determining the regulatory role of these TE-derived enhancers will provide novel insights into cancer-related transcriptomes. Citation Format: Lily L. Nguyen, Atma Ivancevic, Benjamin G. Bitler, Edward B. Chuong. Transposable element derived enhancers in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1708.

Abstract 7016: Plastic epigenome in youth: Insights from open chromatin in stem cells

Abstract The presence of plasticity in the epigenomes of young individuals is suggested by the aggressive phenotypes observed in cancers among adolescent and young adults (AYAs), including gastric cancers. To demonstrate the presence of this plasticity and identify the underlying epigenomic characteristics in gastric stem cells during youth, we examined organoids established from murine stomach tissue and conducted single-cell RNA-seq and ATAC-seq using murine antrum-pyloric tissues at ages of 3 weeks and 50 weeks, corresponding to human infancy and middle-age adult, respectively. Organoids established from infant mice showed higher dependence to niche factors, and stronger response to cytokine signals. Ligand-receptor analysis using single-cell RNA-seq data of tissues showed that infant epithelial stem cells and stromal cells had stronger interactions. Both supported the plastic nature of infant gastric epithelial cells. Single-cell ATAC-seq enabled us to identify epithelial stem cell population in infant and middle-aged mice, and 71 and 118 chromatin peaks were specific to infant and adult stem cells, respectively. Motif enrichment analysis showed an enrichment of binding sites for bZIP family transcription factors in infants, and an enrichment of binding sites of a chromatin remodeling factor and a family of transcription factors in adults. Additionally, comparison between differentiated epithelial cells, marked by the pit cell marker Muc5ac, and stem cells, marked by Lgr5, showed more pronounced differences: 46,772 peaks specific to pit cells and 39,076 peaks specific to stem cells. Interestingly, regions specific to pit cells were enriched in binding sites of the chromatin remodeling factor and the family of transcription factors, identical to the open regions specific to adult stem cells. This suggested that the chromatin accessibility profile of aged stem cells approaches to that of differentiated cells, leading to a loss of stemness. The single-cell RNA-seq data also revealed an increase in interactions between differentiated epithelial cells and fibroblasts in aged mice, as opposed to infant, suggesting the emergence of aberrant interactions in aged stomach tissue. Collectively, our data suggested that chromatin accessibility of gastric stem cells undergo an epigenomic shift during aging, approaching to the profiles of differentiated cells and losing their plasticity, and that a specific chromatin remodeling factor and a family of transcription factors could be involved in the process. Citation Format: Yu-Yu Liu, Chihiro Takeuchi, Satoshi Yamashita, Toshikazu Ushijima. Plastic epigenome in youth: Insights from open chromatin in stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7016.

Abstract 1424: Epigenetic activation of tumoral IFNγresponse and pyroptosis overcomes immunotherapy resistance in hepatocellular carcinoma

Abstract Background: Immune checkpoint blockade (ICB) therapies by antibodies have revolutionized the treatment paradigm for a variety of cancers. Although subsets of people exhibit durable responses, resistance and relapse are common in hepatocellular carcinoma (HCC). We therefore aim to delineate the mechanism underlying the failure of ICB therapy in HCC, and more importantly to identify ICB-sensitizing therapeutic approaches. Methods: ICB-resistant orthotopic-grafted murine models were established via a serial selection of HCC cells in ICB-treated mice. Integrated multi-omics analysis (single-cell RNA-seq, single-cell ATAC-seq and ChIP-seq) were applied to decode the mechanisms underlying the ICB resistance and an epigenetic-mediated ICB response. Results: We successfully established the ICB-resistant murine models of HCC, in which tumor intrinsic interferon-gamma (IFNγ) response was most significantly suppressed and characterized by a “cold” tumor microenvironment with decreased lymphocyte activation and intratumoral infiltration. On the other hand, single cell RNA-seq analysis of human HCC biopsies revealed that patients with HDAC1/2/3-high HCC exhibit poor survival upon ICB therapy. Notably, we found that a novel specific HDAC1/2/3 inhibitor CXD101 synergized with PD-(L)1 antibody to induce immunogenic cell death, eradicate tumor and prolong survival in our ICB-resistant mouse models, which was accompanied by enhanced intratumoral infiltration, activation and anti-tumor memory formation of cytotoxic lymphocytes. Mechanistically, CXD101 combined with PD-(L)1 inhibition synergistically reactivated tumor IFNγ pathway via enhancing chromatin accessibility of downstream genes associated with antigen presentation and lymphocytes recruitment. Moreover, the activated immune system induced tumor cell pyroptosis, further igniting antitumor immunity and ICB response. Conclusions: Our findings suggest that corruption of tumor intrinsic IFNγ signaling may confer ICB resistance upon ICB therapy, which can be rectified by class I HDAC inhibitor mediated IFNγ response and tumor cell pyroptosis. Based on these findings, we have commenced a Phase II clinical study of a new epigenetic immunotherapy (CXD101 plus anti-PD-1) for HCC patients resisting anti-PD-(L)1 alone. This project is supported by the CRF (C4045-18W), GRF (14115820), TRS (T11-706/18-N), Li Ka Shing Foundation, CUHK Strategic Seed Funding for Collaborative Research Scheme. We also acknowledge support (funding and study medications) by Celleron Therapeutics. Citation Format: Yalin Tu, Haoran Wu, Chengpeng Zhong, Zhewen Xiong, Jing Wang, Patrick Pak-Chun Wong, Weiqin Yang, Jiahuan Lu, Zhixian Liang, Shufen Chen, Lingyun Zhang, Siyun Chen, Jingying Zhou, Ka-Fai To, Joseph Jao-Yiu Sung, Stephen Lam Chan, David Kerr, Nick La Thangue, Alfred Sze-Lok Cheng. Epigenetic activation of tumoral IFNγresponse and pyroptosis overcomes immunotherapy resistance in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1424.

Abstract 6545: Reversing lineage plasticity and drug resistance in lethal prostate cancer

Abstract Although major mechanisms of resistance to targeted therapies include mutation of the drug target, recent evidence suggests cell-adaptive mechanisms as alternative avenues for escaping treatment. In several cancers, tumor cells become plastic in response to target inhibition, changing their identity and molecular programs without acquiring further mutations. In the case of castration-resistant prostate cancer (CRPC) treated with standard-of-care, next-generation anti-androgens enzalutamide, tumor cells often switch lineage to survive drug pressure, acquiring neuroendocrine (NE) features and thereby transforming into neuroendocrine prostate cancer (CRPC-NE). Existing targeted therapies for CRPC and CRPC-NE provide limited benefit, representing an unmet clinical need. Hence, the elucidation of tumor plasticity and consequent heterogeneity that contribute to drug resistance is of paramount importance to identify novel therapeutic opportunities. We have recently developed a network-based precision cancer medicine framework to characterize molecular and drug sensitivity profiles of ~100 Genetically-Engineered Mouse Models (GEMM)-derived tumors of prostate cancer (Vasciaveo, et al. 2023). This study revealed that tumors derived from GEMMs with the loss of function of both Pten and Trp53 (NPp53) align with CRPC patients and exhibit high heterogeneity in regulatory programs and histopathologic features, including NE differentiation. We then adopted the NPp53 model to generate several 3D organoid lines in order to study tumor plasticity and heterogeneity. To elucidate their tumors’ regulatory programs, we reverse-engineered genome-wide regulatory networks using multimodal single-cell RNASeq and ATACSeq data to identify Master Regulator (MR) proteins implementing tumor cell identities and characterize their epigenetic landscape. Our network-based regulatory analysis identified several distinct cell populations, including cells activating epithelial-to-mesenchymal (EMT) programs and NE differentiation, all resistant to enzalutamide treatment. Cross-species analysis aligned these cells to human CRPC and CRPC-NE tumors. In particular, our analyses have shed light into the roles of NSD2, a known MR of lethal prostate cancer, whose ablation restored sensitivity to enzalutamide. In summary, we leveraged single-cell, multimodal data from CRPC and CRPC-NE 3D mouse organoids to elucidate regulatory programs of drug resistant, lethal prostate cancer and characterize its heterogeneity. Importantly, we also identified a mechanism that can be exploited for therapeutic intervention to restore tumor cells’ sensitivity Citation Format: Alessandro Vasciaveo, Jia J. Li, Dimitrios Karagiannis, Xiao Chen, Andrea Califano, Chao Lu, Michael M. Shen. Reversing lineage plasticity and drug resistance in lethal prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6545.

Txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16−/−) model. Our study of CC16−/− nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.

Integrative Single-Cell RNA-Seq, Single Cell ATAC-Seq, and Spatial RNA-Seq Analysis of Heterogeneity in HPV-Related Head and Neck Squamous Cell Carcinoma

Integrative Single-Cell RNA-Seq, Single Cell ATAC-Seq, and Spatial RNA-Seq Analysis of Heterogeneity in HPV-Related Head and Neck Squamous Cell Carcinoma

Chronic SIV-Induced neuroinflammation disrupts CCR7+ CD4+ T cell immunosurveillance in the rhesus macaque brain.

CD4+ T cells survey and maintain immune homeostasis in the brain, yet their differentiation states and functional capabilities remain unclear. Our approach, combining single-cell transcriptomic analysis, ATAC-Seq, spatial transcriptomics, and flow cytometry, revealed a distinct subset of CCR7+ CD4+ T cells resembling lymph node central memory (TCM) cells. We observed chromatin accessibility at the CCR7, CD28, and BCL-6 loci, defining molecular features of TCM. Brain CCR7+ CD4+ T cells exhibited recall proliferation and interleukin-2 production ex vivo, showcasing their functional competence. We identified the skull bone marrow as a local niche for these cells alongside CNS border tissues. Sequestering TCM cells in lymph nodes using FTY720 led to reduced CCR7+ CD4+ T cell frequencies in the cerebrospinal fluid, accompanied by increased monocyte levels and soluble markers indicating immune activation. In macaques chronically infected with SIVCL757 and experiencing viral rebound due to cessation of antiretroviral therapy, a decrease in brain CCR7+ CD4+ T cells was observed, along with increased microglial activation and initiation of neurodegenerative pathways. Our findings highlight a role for CCR7+ CD4+ T cells in CNS immune surveillance, and their decline during chronic SIV highlights their responsiveness to neuroinflammation.

The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling

Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regionswas conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.

The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis.

Chromatin accessibility plays a critical role in the regulation of cell fate decisions. Although gene expression changes have been extensively profiled at the single-cell level during early embryogenesis, the dynamics of chromatin accessibility at cis-regulatory elements remain poorly studied. Here, we used a plate-based single-cell ATAC-seq method to profile the chromatin accessibility dynamics of over 10000 nuclei from zebrafish embryos. We investigated several important time points immediately after zygotic genome activation (ZGA), covering key developmental stages up to dome. The results revealed key chromatin signatures in the first cell fate specifications when cells start to differentiate into enveloping layer (EVL) and yolk syncytial layer (YSL) cells. Finally, we uncovered many potential cell-type specific enhancers and transcription factor motifs that are important for the cell fate specifications.

Abstract B047: Epigenetic reprogramming by CBP/P300 bromodomain inhibition of triple-negative breast cancer and the immune microenvironment

Abstract Triple-negative breast cancer (TNBC) is a biologically heterogeneous and clinically important breast cancer subtype because if considered a distinct disease, TNBC would rank as the 5th leading cause of cancer deaths in women. TNBC patients resistant to standard-of-care therapies have poor survival. Tumor-associated immune cells such as neutrophils and macrophages can display a pro-tumoral phenotype and contribute to therapy resistance. Epigenetic enzymes have been shown to reprogram both the tumor cells and tumor-associated immune cells. Thus, targeting epigenetic enzymes is a potential strategy to improve the response of TNBC to standard-of-care therapies. Previously, our laboratory performed an epigenetic drug screen and identified several epigenetic inhibitors. We selected IACS-70654, a novel selective p300/CBP BRD inhibitor, to be the primary focus of this study. We determined the effects of IACS-70654 in our unique syngeneic TNBC mouse models. In a neutrophil-enriched luminal-like TNBC model 2208L, IACS-70654 as a single agent initially caused tumor regression and then durably prevented tumor growth, which is not usually observed for single agents in these aggressive TNBC models. IACS-70654 also substantially decreased infiltrated neutrophils. In the peripheral blood and bone marrow of 2208L tumor-bearing mice, IACS-70654 reduced neutrophils to the same level as non-tumor-bearing mice. Based on this finding, we treated 2208L tumors with IACS-70654 in combination with immune checkpoint blockade anti-PD1 and docetaxel. After 27 days, all treatments besides anti-PD1 were stopped, and the combination-treated tumors grew slower than the ones only treated with IACS-70654. More importantly, in tumors treated with IACS-70654 in combination with anti-PD1, there was a substantial increase in CD8+ T cell infiltration. In addition, B cell infiltration was induced in the tumor stroma, indicating that IACS-70654 stimulated immune response in the tumor microenvironment. In contrast, IACS-70654 failed to significantly reduce the growth of T12, a Claudin-low macrophage-enriched model. Therefore, we hypothesized that the infiltrated immune profiles, specifically myeloid cell infiltration, might partially account for this differential response. Accordingly, we studied the effects of IACS-70654 in two additional models, basal-like T6 and luminal-like 2250L tumors, which also have relatively high neutrophil infiltration. However, one of the principal differences in immune profiles between the two models and 2208L is that they also are infiltrated with twice as many macrophages. The response of infiltrated immune cells to IACS-70654 in those two models differed from those of 2208L tumors. IACS-70654 reduced monocytic myeloid-derived suppressor cells and pro-tumor macrophages. These results illustrate the immune heterogeneity among our tumor models. We are currently performing ChIP-seq and single-cell ATAC-seq to elucidate potential mechanisms and pathways employed by IACS-70654 in both tumor and tumor-associated immune cells. Citation Format: Xueying Yuan, Michael Soth, Na Zhao, Philip Jones, Jeffrey Rosen. Epigenetic reprogramming by CBP/P300 bromodomain inhibition of triple-negative breast cancer and the immune microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B047.

Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis.

Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data provided new insights into the understanding of epigenetic heterogeneity and transcriptional regulation. With the increasing abundance of dataset resources, there is an urgent need to extract more useful information through high-quality data analysis methods specifically designed for scATAC-seq. However, analyzing scATAC-seq data poses challenges due to its near binarization, high sparsity and ultra-high dimensionality properties. Here, we proposed a novel network diffusion-based computational method to comprehensively analyze scATAC-seq data, named Single-Cell ATAC-seq Analysis via Network Refinement with Peaks Location Information (SCARP). SCARP formulates the Network Refinement diffusion method under the graph theory framework to aggregate information from different network orders, effectively compensating for missing signals in the scATAC-seq data. By incorporating distance information between adjacent peaks on the genome, SCARP also contributes to depicting the co-accessibility of peaks. These two innovations empower SCARP to obtain lower-dimensional representations for both cells and peaks more effectively. We have demonstrated through sufficient experiments that SCARP facilitated superior analyses of scATAC-seq data. Specifically, SCARP exhibited outstanding cell clustering performance, enabling better elucidation of cell heterogeneity and the discovery of new biologically significant cell subpopulations. Additionally, SCARP was also instrumental in portraying co-accessibility relationships of accessible regions and providing new insight into transcriptional regulation. Consequently, SCARP identified genes that were involved in key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to diseases and predicted reliable cis-regulatory interactions. To sum up, our studies suggested that SCARP is a promising tool to comprehensively analyze the scATAC-seq data.

Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types

Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized cell types at high resolution, and studies integrating GWAS with scRNA-seq have shown promise, but studies integrating GWAS with scATAC-seq have been limited. Here, we identify disease-critical fetal and adult brain cell types by integrating GWAS summary statistics from 28 brain-related diseases/traits (average N = 298 K) with 3.2 million scATAC-seq and scRNA-seq profiles from 83 cell types. We identified disease-critical fetal (respectively adult) brain cell types for 22 (respectively 23) of 28 traits using scATAC-seq, and for 8 (respectively 17) of 28 traits using scRNA-seq. Significant scATAC-seq enrichments included fetal photoreceptor cells for major depressive disorder, fetal ganglion cells for BMI, fetal astrocytes for ADHD, and adult VGLUT2 excitatory neurons for schizophrenia. Our findings improve our understanding of brain-related diseases/traits and inform future analyses.

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 A109: Single-cell epigenomic analysis reveals an important role of the receptor kinase Ror2 in the erosion of cellular identity during pancreatic carcinogenesis

Abstract Introduction The major driver for pancreatic ductal adenocarcinoma (PDAC) is oncogenic KRAS. However, adult acinar cells, a probable origin of PDAC, are largely refractory to KrasG12D-mediated oncogenic transformation. With the concomitant loss of transcription factors that regulate acinar cell differentiation, such as Pdx1 (Pancreatic and Duodenal Homeobox 1), acinar cells undergo a rapid cell identity switch, known as acinar-to-ductal metaplasia (ADM). How loss of cell identity cooperates with oncogenic Kras to induce pancreatic transformation is largely unclear. Methods To elucidate mechanisms responsible for the accelerated cellular reprogramming in KrasG12D;Pdx1f/f animals, single-cell ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) from frozen pancreatic bulk tissue was performed. Chromatin accessibility states were captured at early stages of carcinogenesis and correlated to RNA-seq data. Differentially regulated genes were validated by multiplex RNAscope and immunohistochemistry staining and functionally studied in pancreatic cancer cell lines. Results Single-cell ATAC-seq proved a powerful tool for defining cell-type identity, cellular reprogramming and target genes in early metaplastic transformation of pancreatic tissue. Notably, acinar cells of KrasG12D;Pdx1f/f animals as well as a proportion of metaplastic lesions in both, KrasG12D and KrasG12D;Pdx1f/f mice, showed elevated accessibility and expression of the Ror2 (Receptor Tyrosine Kinase Like Orphan Receptor 2) gene. As a receptor tyrosine kinase, Ror2 controls noncanonical Wnt signaling and other essential signaling pathways, such as PI3K/AKT or Ras-MAPK. Genetic ablation of Ror2 in a mouse model of pancreatic neoplasia resulted in a shift in ADM cell identity, enriching ADM lesions with a senescent duct cell phenotype. In PDAC, ROR2 expression correlates with the more aggressive basal-like subtype. Overexpression of ROR2 in pancreatic cancer cell lines with a classical differentiation induced epithelial-to-mesenchymal transition, characterized by the downregulation of multiple epithelial markers and upregulation of mesenchymal genes. Knockout of ROR2 in pancreatic cancer cells significantly decreased cell proliferation. Conclusions Our in-depth sequencing data revealed that expression of KrasG12D with the concomitant loss of Pdx1 leads to vast alterations of acinar cell identity. We identified the receptor kinase Ror2 as a regulator of pancreatic cancer initiation and driver of pancreatic cancer cell aggressiveness. Citation Format: Simone Benitz, Malak Nasser, Alexander Steep, Jonathan Preall, Ujjwal Mahajan, Ian Loveless, Erick Davis, Hui-Ju Wen, Daniel Long, Michaela Louw, Samuel Zwernik, Donald Rempinski, Jacee Moore, Daniel Salas-Escabillas, Thomas Metzler, Ling Huang, Nina Steele, Ivonne Regel, Filip Bednar, Howard Crawford. Single-cell epigenomic analysis reveals an important role of the receptor kinase Ror2 in the erosion of cellular identity during pancreatic carcinogenesis [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 A109.