Centromeres are essential chromosome components yet remain poorly understood due to their highly repetitive sequence architecture. Using fully-phased telomere-to-telomere diploid assemblies from a three-generation pedigree integrated with long-read epigenomes from matched peripheral blood mononuclear cells, induced pluripotent stem cells, and neural progenitor cells, we generate allele-resolved single basepair resolution maps of centromere genetic and epigenetic dynamics across inheritance, reprogramming, and differentiation. We show that centromeric dip regions (CDRs), which define the functional core of centromeres, are positionally stable across generations and cell-fate transitions. In contrast, CDR epigenetic architecture is highly dynamic. Reprogramming markedly attenuates CDR hypomethylation, which is partially restored during differentiation in parallel with global hypomethylation of active alpha-satellite arrays and coordinated changes in nucleosome organization and protein occupancy. Centromeric remodeling is insulated from X-chromosome status, including Xa, Xi, and erosion. Finally, de novo mutations arising during reprogramming are enriched in centromeric regions but depleted within functional centromeric cores.

When aligning next-generation sequencing (NGS) reads to a reference genome, differences between the true genome of the individual under study and the reference result in a biased interpretation of aligned data through systematic errors known as reference alignment bias (RAB). The degree to which RAB impacts functional readouts has not been thoroughly quantified. Leveraging resources from the Human Pangenome Reference Consortium, here we quantify RAB in functional genomics assays. Our results indicate that, on average, 0.2% of the genome is susceptible to bias in RNA sequencing (RNA-seq) studies, 1% in ATAC-seq, and 3% in WGBS when using the human reference hg38. Our study quantifies the effect of RAB on functional assays and highlights the importance of using an adequately representative reference genome.

The human genome reference established a shared coordinate system for genome function, but it is incomplete and not fully representative of human diversity. Here, we benchmark how genome representation and corresponding analytical frameworks for each representation shape functional genomics using chromatin accessibility sequencing (ATAC-seq), RNA sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) data from lymphoblastoid cell lines derived from five individuals with fully phased genome assemblies. We compare results across hg38, CHM13, the draft human pangenome, and each individual's maternal and paternal assemblies. Because current pipelines and quality control conventions are tuned to hg38, several of these comparisons reflect genome representation in the context of available methods, rather than sequence alone. Individual identity accounts for 57.52-78.47% of total variance in functional estimates, whereas genome choice contributes 0.002-7.85% and sample-by-genome interactions contribute 0.63-5.43%. About 2% of biological signals are detectable only with personal assemblies. Although these effects are modest overall, some biologically important features remain inaccessible to linear references. Consistent with this, graph-based DNA methylation analysis in the human pangenome reveals a non-reference AluY5a insertion within a putative TNKS enhancer at chromosome 8p23.1 that becomes visible and hypermethylated only in the pangenome.

Osteoarthritis (OA) is a joint disease with an etiology partially rooted in metabolic dysfunction, yet the underlying mechanisms in this context are not determined, limiting opportunities to develop therapeutic treatments. In this study, we used a multiomic approach combining RNA sequencing, ATAC-seq, MRE-seq, and metabolomics to reveal that OA articular chondrocytes induced by imbalanced transforming growth factor–β (TGF-β) and bone morphogenetic protein (BMP) signaling have increased fatty acid synthesis and oxidation processes regulated by nuclear factor I A (NFIA) up-regulation. Inhibition of NFIA suppressed the elevated gene expression of essential metabolic enzymes, including acetyl-CoA carboxylase A ( ACACA ) and carnitine palmitoyltransferase 2 ( CPT2 ), leading to the restoration of fatty acid metabolism and cellular homeostasis in both murine and human OA articular chondrocytes. Obese mice displayed metabolic stress with elevated expression of NFIA, ACACA, and CPT2 in joint tissues, and they simultaneously developed profound synovitis, cartilage degeneration, subchondral bone sclerosis, and pain after joint injury. Both Nfia inhibition and pharmacological suppression of fatty acid metabolism in obese mice preserved joint integrity and mitigated synovitis and pain in the context of injury-induced OA settings. Overall, this work identifies a role for NFIA in the regulation of fatty acid metabolism and articular chondrocyte homeostasis and highlights fatty acid metabolism as a potential therapeutic target for OA treatment, particularly under obesity conditions.

Single-cell omics has been widely applied in oncology research for biomarker discovery, providing an in-depth understanding of cancer heterogeneity. While bulk sequencing methods lack the specificity afforded by single cell studies, single cell applications miss insights due to trade-offs for sensitivity at scale. Current high throughput single cell DNA-seq applications are limited to targeted sequencing approaches, while scaled single cell RNA-seq applications are limited to 3’ or 5’ end counting methods or only capture polyadenylated RNA transcripts. To address these challenges, we have developed a nanoliter dispensing instrument, library prep chemistries and a bioinformatics analyses suite that scales both single cell genomics and transcriptomics assays while maintaining whole genome and whole transcriptome coverage, respectively. To demonstrate the ability to scale a non-targeted single cell whole genome amplification (WGA) application, we applied our new WGA workflow to cancer cell lines and primary Clear Cell Renal Cell Carcinoma samples. The data revealed segmental aneuploidies and both germline and putative somatic variants in thousands of single cancer cells in a single day, at shallow sequencing depths of approximately 300,000 paired end reads per single cell. Addressing the limitation of scaled single-cell transcriptomic solutions, our new total RNA-seq workflow is capable of generating data on up to 100,000 single cells at a time in two days. We applied this high-throughput workflow on cancer cells treated and untreated with epigenetic therapy and selected 11,000 cells to reach a deeper sequencing depth. The results demonstrate the ability to identify new biomarkers through comprehensive profiling of both protein-coding and noncoding genes with full gene-body coverage, revealing significant expression differences across multiple RNA biotypes as well as identifying splice junction isoforms. Overall, our data highlights the advantages of complex and rich datasets generated from single-cell workflows, which, when paired with an unbiased, non-targeted approach, enable the discovery of novel genomic and transcriptomic events in oncology samples. Shuwen Chen, Peng Xu, Xuan Li, Joseph Liu, Yana Ryan, Kazuo Tori, Hima Anbunathan, Alan Du, Mike Covington, Raymond Mendoza, Samantha Leong, Tomoya Uchiyama, Mohammad Fallahi, Xuan Qu, Xiaoyun Xing, Bryan Bell, Patricio Espinoza, Ting Wang, Yue Yun, Andrew Farmer. Resolving tumor heterogeneity by uncovering novel genomic and transcriptomic events with a new scaled and automated workflow [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB047.

The ETS family transcription factor ETV2, VEGFA, and its receptor FLK1 are essential for hematopoietic, vascular, and cardiac development. Here, we combine dual Etv2 and Flk1 lineage tracing with molecular profiling to define how mesoderm progenitors are allocated to hematopoietic, endothelial, cardiomyocyte, and smooth muscle lineages. We demonstrate that hematopoietic, endothelial, and cardiac valves arise from dual Etv2+ and Flk1+ lineages and that Etv2+ and Flk1+ mesoderm contributing to the hemangiogenic fate is molecularly distinct from that generating muscle. Mechanistically, we show that ETV2 cooperates with the BAF chromatin remodeling complex to establish accessibility at ETV2 target loci. Loss of Baf155 expression reduces chromatin accessibility at ETV2 target loci and impairs hemangiogenic lineage specification. This work defines lineage relationships and the molecular circuitry underlying hemangiogenic specification during cardiovascular development.

Immunotherapy has been a promising treatment for various cancer types. This therapy heavily relies on the efficiency of the targeted neoantigens for T cell recognition and downstream immune responses. Neoantigens derived from tumor-specific nonsynonymous somatic mutations have been a great resource and manifested remarkable therapeutic effects, yet with high patient specificity and high dependency on mutation rate. Here, we propose a novel strategy for discovering neoantigens derived from epigenetic mutations, rather than genetic mutations, from transposable elements (TEs) sequences. TEs make up 50% of the human genome but have been long considered to be “junk DNA” and therefore overlooked in medical genomics. However, recent works from our lab have shown that, despite being epigenetically silenced in somatic cells, certain TEs contribute significantly to the evolution of regulatory networks and shape the cancer transcriptome landscape, including functioning as promoters and producing novel, tumor-specific TE-derived transcripts (TSTETs) that can be translated into proteins. Given the plasticity of epigenome, neoantigens resulted from epigenetic mutations could be pan-cancer with high recurrence. Thus, we hypothesize that cryptic promoters embedded in TEs can be re-activated due to epigenetic dysregulation in cancer, leading to the generation of highly recurrent, pan-cancer, TE-derived, tumor-specific protein products that could be employed as neoantigens for immuno-therapy. In this study, we developed a computational pipeline termed TE Promoter Finder 3 (TEProf3) to precisely identify TE-derived promoters and transcripts genome-wide from transcriptomic data, including data from both long-read and short-read sequencing. We applied TEProf3 to analyze 12,015 tumor samples encompassing 33 cancer types from The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) datasets. Our analysis revealed 14,417 of TSTETs and hundreds of tumor-specific TE-derived antigens (TSTEAs) from the tumor transcriptomic and mass spectrometry data, respectively. Notably, most TSTETs exhibited high recurrence rates, with over 10% recurrence in the majority and some exceeding 90% recurrence. Each tumor sample displayed a median number of 19 TSTETs. Certain cancer types showed a comparable landscape of tumor-specific TE-derived promoters, potentially due to similarities in epigenetic mutations and cell types of origin. The number of TSTETs correlated with tumor progression in some cancer types, suggesting a link between progressive dysregulation of TE-derived promoters and tumorigenesis. We further assessed the efficiency of antigen presentation in cancer cell lines as a proof of concept. We successfully identified T cell receptors sequences from CD8+ T cells that exhibited strong binding affinity for TSTEAs and demonstrated cytotoxicity effects on the cancer cell lines. In summary, this work represents one of the first comprehensive catalogs of TSTEAs, providing a valuable resource for future immunotherapy strategies. Citation Format: Yonghao Liang, Xiaoyun Xing, Ting Wang. Transposable elements activation produces pan-cancer tumor-specific neoantigens [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B024.

Following amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs shared by, or unique to, different regenerating cell types remain underinvestigated. Here, we mapped the regulatory landscape of fin regeneration by applying paired snRNA-seq and snATAC-seq on uninjured and regenerating fins. This map delineates the regulatory dynamics of predominant cell populations at multiple stages of regeneration. We observe a marked increase in the accessibility of chromatin regions associated with regenerative and developmental processes at 1 dpa, followed by a gradual closure across major cell types at later stages. This pattern is distinct from that of transcriptomic dynamics, which is characterized by several waves of gene upregulation and downregulation. We identified and in vivo validated cell-type-specific and position-specific regeneration-responsive enhancers and constructed regulatory networks by cell type and stage. Our single-cell resolution transcriptomic and chromatin accessibility map across regenerative stages provides new insights into regeneration regulatory mechanisms and serves as a valuable resource for the community.

Exposure to toxic substances, particularly early in life, can perturb epigenomic marks linked to disease susceptibility. Human studies of environmental exposures often rely on surrogate tissues such as blood, but toxicant accumulation differs across organs and results in tissue-specific responses. Thus, understanding whether exposure-induced epigenomic alterations in surrogate tissues such as blood reflect changes in toxicant target tissues, such as liver, is essential for designing and interpreting environmental epigenetic studies. To address this knowledge gap, we systematically analyzed 1,013 multi-omics data from the TaRGET II Consortium, comparing molecular responses in mouse liver and blood following perinatal exposure to arsenic, lead, bisphenol A, tributyltin, di-2-ethylhexyl phthalate, tetrachlorodibenzo-p-dioxin, or air pollution in the form of particulate matter < 2.5μm (PM2.5). Most toxicant-induced molecular changes were tissue-specific, yet we identified a subset of co-regulated genes and regulatory elements in liver and blood in response to early-life exposure to toxicants. Moreover, we discovered that specific pathways, such as immune-related processes, were commonly affected by exposures in both tissues, and transcription factors, including Klf, Jun, Ets1, and Cebp, emerged as shared regulators. While molecular alterations are infrequently conserved between tissues following toxicant exposure, the shared alterations in transcription factors and biological pathways may provide a strategy to link effects in surrogate tissues to target tissues.

Understanding the interaction between genetic and epigenetic variation remains a challenge due to confounding environmental factors. We propose that human induced Pluripotent Stem Cells (iPSCs) are an excellent model to study the relationship between genetic and epigenetic variation while controlling for environmental factors. In this study, we have created a comprehensive resource of high-quality genomic, epigenomic, and transcriptomic data from iPSC lines and three iPSC-derived cell types (neural stem cell (NSC), motor neuron, monocyte) from three healthy donors. We find that epigenetic variation is most strongly associated with genetic variation at the iPSC stage, and that relationship weakens as epigenetic variation increases in differentiated cells. Additionally, cell type is a stronger source of epigenetic variation than genetic variation. Further, we elucidate a utility of studying epigenetic variation in iPSCs and their derivatives for identifying important loci for GWAS studies and the cell types in which they may be acting.

Increased myeloid lineage production, termed myeloid skewing, leading to decreased tumor immunity, is a hallmark of aberrant hematopoiesis associated with cancer. It is believed that myeloid skewing may occur at the hematopoietic stem and progenitor cells (HSPCs) level to elicit hematopoietic changes. However, our understanding of the underlying molecular mechanisms remains incomplete. Here, we characterize the transcriptional and chromatin accessibility landscapes of bone marrow and splenic hematopoietic progenitors in the MMTV-PyMT mouse model of breast cancer using single-cell ATAC + RNA sequencing. We show that HSPCs in the bone marrow (BM) of the tumor-bearing mice show a modest upregulation of the myeloid-bias transcriptional signature without significant chromatin accessibility changes. By contrast, dendritic cell (DC) progenitors exhibit the most prominent transcriptional and chromatin changes, showing a signature of STAT3, CEBP, and non-DC myeloid gene activation. Compared to BM, splenic HSPCs exhibit a Notch signaling signature associated with erythroid commitment rather than further upregulation of the myeloid-bias signature. In addition, we also identify a cluster of splenic HSPCs in tumor-bearing animals with a transcriptional signature of mobilization. Our paired chromatin data suggest that AP-1 factors play a crucial role in driving this HSPC mobilization signature. Overall, we provide a comprehensive dataset for understanding the hematopoietic consequences of cancer.

Environmental exposures to toxic chemicals can profoundly alter the transcriptome and epigenome in both humans and animals, contributing to disease development across the lifespan. To elucidate how early-life exposure to toxicants exerts such persistent effects, the Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription II (TaRGET II) Consortium generated a landmark resource comprising 2,570 epigenomes and 1,043 transcriptomes from longitudinal studies in mice. All data are publicly available through the TaRGET II data portal and the WashU Epigenome Browser. This resource from target (liver, brain, lung, heart) and surrogate (blood) tissues at weaning (3 weeks) and two adult time-points (5 and 10 months) characterized the molecular response to arsenic (As), lead (Pb), bisphenol-A (BPA), di-2-ethylhexyl phthalate(DEHP), tributyltin (TBT), tetrachlorodibenzo-p-dioxin (TCDD), and particulate matter with a diameter of <2.5μm (PM2.5). The findings revealed persistent, toxicant-specific, sex-dependent epigenomic and transcriptomic perturbations, resulting in disrupted expression of 14,908 genes, altered chromatin accessibility at 87,409 regulatory elements, DNA methylation changes at 113,186 genomic regions, and chromatin state switching of histone modifications. The resulting high-resolution map of how environmental exposures reprogram the epigenome and transcriptome is broadly accessible via ToxiTaRGET database, offering unparalleled opportunities for the scientific community to investigate the molecular underpinnings of environmental toxicant exposures and their contributions to disease pathogenesis.

Environmental exposures to toxic chemicals can profoundly alter the transcriptome and epigenome in both humans and animals, contributing to disease development across the lifespan. To elucidate how early-life exposure to toxicants exerts such persistent effects, the Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription II (TaRGET II) Consortium generated a landmark resource comprising 2,564 epigenomes and 1,043 transcriptomes from longitudinal studies in mice. All data are publicly available through the TaRGET II data portal and the WashU Epigenome Browser. This resource from target (liver, brain, lung, heart) and surrogate (blood) tissues at weaning (3 weeks) and two adult time-points (5 and 10 months) characterized the molecular response to arsenic (As), lead (Pb), bisphenol-A (BPA), di-2-ethylhexyl phthalate(DEHP), tributyltin (TBT), tetrachlorodibenzo-p-dioxin (TCDD), and particulate matter with a diameter of <2.5μm (PM2.5). The findings revealed persistent, toxicant-specific, sex-dependent epigenomic and transcriptomic perturbations, resulting in disrupted expression of 14,908 genes, altered chromatin accessibility at 87,409 regulatory elements, DNA methylation changes at 113,186 genomic regions, and chromatin state switching of histone modifications. The resulting high-resolution map of how environmental exposures reprogram the epigenome and transcriptome is broadly accessible via ToxiTaRGET database, offering unparalleled opportunities for the scientific community to investigate the molecular underpinnings of environmental toxicant exposures and their contributions to disease pathogenesis.

The relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling of TE expression dynamics under the regulation of TP53 provides valuable resources for more clarity in TP53's roles in cancer. In this study, we characterized the TE transcriptomic landscape using long-read RNA-seq and short-read RNA-seq in three cancer cell lines varying only in TP53 genetic status. To identify transcripts that use TEs as potential promoters, we developed a computational pipeline, TEProf3, and identified in total 1942 transcripts with high confidence. Among these TE-derived transcripts, 239 are activated by TP53 and 221 are repressed by TP53. These TP53-responsive TE-derived transcripts are mainly driven by members of the ERV and LINE families. Following knockdown of wild-type (WT) TP53 expression, rescuing WT TP53 expression allows for partial recovery of the TE expression profile observed in the context of chronic TP53 expression. TP53 mutations R175H and R273H manifest their oncogenic characteristic partially through activating TE promoters in a cell type-specific manner. Lastly, we identified important sequence motifs that help govern the interactions between TEs and TP53, where TP53 activates TEs with TP53 binding motifs through direct binding and represses TEs indirectly via other pathways. Overall, we present a comprehensive profiling of the impact of TP53 on the activity of TE-derived promoters in isogenic cancer cell lines and provide a high-confidence TE expression atlas of TE promoters that are direct and indirect targets of TP53.

Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.

Inhibiting epigenetic modulators can transcriptionally reactivate transposable elements (TEs). These TE transcripts often generate unique peptides that can serve as immunogenic antigens for immunotherapy. Here, we ask whether TEs activated by epigenetic therapy could appreciably increase the antigen repertoire in glioblastoma, an aggressive brain cancer with low mutation and neoantigen burden. We treated patient-derived primary glioblastoma stem cell lines, an astrocyte cell line and primary fibroblast cell lines with epigenetic drugs, and identified treatment-induced, TE-derived transcripts that are preferentially expressed in cancer cells. We verified that these transcripts could produce human leukocyte antigen class I-presented antigens using liquid chromatography with tandem mass spectrometry pulldown experiments. Importantly, many TEs were also transcribed, even in proliferating nontumor cell lines, after epigenetic therapy, which suggests that targeted strategies like CRISPR-mediated activation could minimize potential side effects of activating unwanted genomic regions. The results highlight both the need for caution and the promise of future translational efforts in harnessing treatment-induced TE-derived antigens for targeted immunotherapy. Treatment of primary glioblastoma cell lines with epigenetic therapy reactivates transposable elements (TEs). TE-derived transcripts can produce human leukocyte antigen class I-presented antigens, which could potentially be therapeutically targeted.

Abstract Objective: Single-cell RNA-seq (scRNA-seq) analysis has been widely applied in oncology research for biomarker discovery. Although droplet-based methods are commonly used for such studies owing to their high throughput, they still miss important insights due to their lack of full-length transcript coverage. While full-length methods are available, to date, they have not been able to meet the throughput demands of many researchers. Moreover, both droplet and full-length scRNA-seq methods do not currently provide adequate readouts for non-coding genes, thereby limiting investigation of gene regulatory networks to protein coding genes. To close these gaps, we have developed a new high-throughput full-length scRNA-seq workflow that comprehensively profiles both protein-coding and non-coding genes in up to 60,000 cells within two days. Methods: Our new high-throughput workflow uses two rounds of combinatorial indexing, starting with a 96-well plate format for the first barcoding step followed by an automated second barcoding step in a 5,184-nanowell chip using an automated nanodispensing system. Initial testing demonstrated that our method could handle up to 60,000 cells without generating significant levels of doublets due to barcode collisions. To further illustrate the capacity of the new scRNA-seq approach, we profiled a total of approximately 11,000 isogenic A549 cells that either express WT TP53 or are TP53 null. In addition, both isogenic cell lines were treated with epigenetic therapy or mock treatment. Libraries were generated and sequenced using an Illumina® NextSeq®2000 sequencer. The sequencing data was then analyzed to define differential gene expression for both protein-coding and non-coding transcripts as a function of TP53 genotype and treatment condition, using Cogent™ NGS software. Results: Preliminary analysis showed that, on average, approximately 11,000 genes and 40,000 transcripts were detected per single cell at a read depth of 100,000 reads per cell. UMAP-based clustering confidently separated the cells according to their genotypes and treatment conditions using either protein-coding genes or non-coding genes. Furthermore, differential expression analysis identified both protein-coding and non-coding transcripts with significant expression differences, underscoring biological significance. Conclusion: Our new high-throughput full-length scRNA workflow enables preparation of high-quality full-length RNA-seq libraries for up to 60,000 cells with only two rounds of barcoding and shows high sensitivity and specificity in gene/transcript detection and quantification. The technology significantly improves the ability to identify new biomarkers by enabling comprehensive profiling of both protein-coding and non-coding full length transcripts. Citation Format: Peng Xu, Joseph Liu, Yana Ryan, Kazuo Tori, Xuan Li, Hima Anbunathan, Mike Covington, Tomoya Uchiyama, Mohammad Fallahi, Xuan Qu, Xiaoyun Xing, Ting Wang, Bryan Bell, Shuwen Chen, Yue Yun, Andrew Farmer. A novel, high-throughput full-length scRNA-seq workflow for improved biomarker discovery [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 316.

Abstract Hematopoietic abnormalities, including myeloid-skewing, anemia, and extramedullary hematopoiesis, are often observed in cancer patients, with evidence suggesting that they promote the development of myeloid-derived suppressor cells. However, our understanding of the mechanisms underlying these hematopoietic phenotypes remains incomplete. Here, using the MMTV-PyMT mouse model of breast cancer, we characterize the transcriptional and chromatin accessibility landscapes of bone marrow and spleen hematopoietic progenitors using single-cell ATAC+RNA sequencing. We show that for the uncommitted hematopoietic stem and progenitor cells (HSPCs) in the bone marrow (BM), tumor growth induces a moderate upregulation of the myeloid-bias transcriptional signature and no significant chromatin accessibility changes. Compared to BM HSPCs, spleen HSPCs do not show a further upregulation of the myeloid-bias signature, and instead show the signature of Notch signaling, which has been associated with erythroid commitment. In addition, we also identify a cluster of spleen HSPCs in tumor-bearing animals with a transcriptional signature of mobilization, while our paired chromatin data suggest that AP-1 factors play a key role in HSPC mobilization. Furthermore, in contrast to the subtle tumor-induced changes in BM HSPCs, prominent transcriptional and chromatin changes are observed in dendritic cell (DC) progenitors, consistent with known cancer-associated DC defects. Our chromatin data also confirms, in an unbiased manner, that Stat3 and CEBP are both key contributors to DC defects. Overall, we provide a comprehensive dataset for understanding the hematopoietic consequences of cancer. Citation Format: Changxu Fan, Jun Wu, Xiaoyun Xing, Derek A. G. Barisas, Kyunghee Choi, Ting Wang. Transcriptional and chromatin accessibility landscapes of hematopoietic progenitors in a mouse model of breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2024 Oct 18-21; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2024;12(10 Suppl):Abstract nr B027.

Chromatin priming promotes cell-type-specific gene expression, lineage differentiation, and development. The mechanism of chromatin priming has not been fully understood. Here, we report that mouse hematopoietic stem and progenitor cells (HSPCs) lacking the Baf155 subunit of the BAF (BRG1/BRM-associated factor) chromatin remodeling complex produce a significantly reduced number of mature blood cells, leading to a failure of hematopoietic regeneration upon transplantation and 5-fluorouracil (5-FU) injury. Baf155-deficient HSPCs generate particularly fewer neutrophils, B cells, and CD8+ + T cells at homeostasis, supporting a more immune-suppressive tumor microenvironment and enhanced tumor growth. Single-nucleus multiomics analysis reveals that Baf155- deficient HSPCs fail to establish accessible chromatin in selected regions that are enriched for putative enhancers and binding motifs of hematopoietic lineage transcription factors. Our study provides a fundamental mechanistic understanding of the role of Baf155 in hematopoietic lineage chromatin priming and the functional consequences of Baf155 deficiency in regeneration and tumor immunity.