tbuckley/cabot-search huggingface dataset:
Abstract A019: CRISPR-based investigation of CHIP mutations reveals their role in CAR-T therapy-related inflammatory toxicities
Authors: Xiuli Wang, Scott R. Goldsmith, June-Wha Rhee, Stephen J. Forman, Chunyan Zhang, Saro Armenian
Journal: Cancer Research (2025)

Abstract Background: Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by somatic mutations (e.g. DNMT3A, TET2, and ASXL1I) in hematopoietic stem cells, and linked to age-related clonal expansions and inflammatory states. We previously showed that patients with CHIP receiving CAR-T cell therapy have a four-fold risk of developing clinically significant cytokine release syndrome (CRS) compared to those without CHIP (Transplant Cell Ther 2024). This prompted us to investigate the mechanisms through which CHIP mutations could contribute to CAR-T-related toxicities. Methods: We employed CRISPR-based gene editing to target CHIP-associated genes—DNMT3A, TET2, and ASXL1—in M1-like macrophages, which were differentiated from human monocytes in the presence of 20 ng/mL of GM-CSF. Gene perturbation was achieved with cell-penetrating phosphorothioated single-stranded DNA oligonucleotides to deliver the CRISPR-Cas9 and gRNA complex (PS-Cas9/gRNA). Editing was performed using multiple gRNAs for each gene: DNMT3A (2 gRNAs), TET2 (3 gRNAs), and ASXL1 (2 gRNAs), and decreased protein expression was confirmed post-editing. We co-cultured CS1 CAR-T cells targeting multiple myeloma (MM), MM.1S cells, and edited autologous macrophages at a 1:1:0.1 ratio for 24 hours to assess the inflammatory response. Cytokine secretion was quantified using the LEGENDplex™ Human Inflammation Panel 1 (13-plex). Results: Compared to non-edited macrophages, DNMT3A-, TET2-, and ASXL1-edited macrophages consistently secreted significantly higher levels of IL-6 (642, 920, 1338 pg/ml vs. 325 pg/ml respectively, P&amp;lt;0.05-0.001), MCP-1(90, 122, 151 pg/ml vs. 55 pg/ml, respectively, P&amp;lt;0.01-0.001), TNFα (2015, 1722, 1874 pg/ml vs. 1043 pg/ml, respectively P:ns - &amp;lt; 0.001), IL-1β (75, 99, 146 pg/ml vs. 38 pg/ml, respectively, P&amp;lt;0.05-0.001), and IL-8 (21, 19, 22 ng/ml vs. 15 ng/ml, respectively, P:ns- &amp;lt;0.001). Conclusions: These findings suggest CHIP mutations in human macrophages may exacerbate the inflammatory response in CAR-T therapy, highlighting a potential biomarker for stratifying patients at higher risk for toxicities such as CRS and guiding more personalized prophylactic interventions. Citation Format: Xiuli Wang, Scott R. Goldsmith, June-Wha Rhee, Stephen J. Forman, Chunyan Zhang, Saro Armenian. CRISPR-based investigation of CHIP mutations reveals their role in CAR-T therapy-related inflammatory toxicities [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 A019.
Abstract B013: Gene-body DNA methylation of ONECUT2 predicts its expression status and prostate cancer aggressiveness in clinic specimens
Authors: Gangning Liang, Gangning Liang
Journal: Cancer Research (2025)

Abstract ONECUT2 is a lineage plasticity driver and therapeutic target in aggressive prostate cancer (PCa). The goal of this study was to determine the role of ONECUT2 gene-body DNA methylation in regulating its expression and to evaluate its potential as a biomarker and therapeutic target for aggressive PCa. We observed a robust positive correlation between ONECUT2 expression levels and gene-body DNA methylation. This role was confirmed in prostate cancer cells through treatment with a DNA methylation inhibitor (DNMTi). Targeted bisulfite sequencing was performed to measure ONECUT2 gene-body DNA methylation in 208 needle biopsies from PCa patients, revealing a correlation between ONECUT2 gene-body hypermethylation and aggressive features. Thus, measuring ONECUT2 gene-body DNA methylation in clinical specimens can provide a predictive assessment of disease progression before surgery. Our results also suggest that downregulating ONECUT2 expression using DNMTi may be a viable therapeutic strategy for treating aggressive PCa. Citation Format: Gangning Liang, Gangning Liang. Gene-body DNA methylation of ONECUT2 predicts its expression status and prostate cancer aggressiveness in clinic specimens [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 B013.
Abstract PR004: Interplay between histone modifications and DNA methylation in cancer
Authors: Chao Lu
Journal: Cancer Research (2025)

Abstract During solid tumor development, gene-poor and lamina-associated genomic regions undergo progressive loss of DNA methylation, whereas promoter CpG islands become DNA hypermethylated. We report evidence suggesting that the recruitment of DNMT3A by histone modifications contributes to this cancer-associated DNA methylome reprogramming. The genomic targeting of DNMT3A is regulated by the competition between NSD1-mediated histone H3K36 methylation and polycomb-mediated H2AK119 ubiquitination, via DNMT3A's PWWP domain and N-terminal ubiquitin-interacting region, respectively. Mutations in NSD1, DNMT3A reader domains or polycomb complexes perturb DNMT3A recruitment and can recapitulate patterns of DNA methylation observed in patient tumors. Lastly, tumors exhibiting progressive hypomethylation, such as those harboring NSD1 mutations, are paradoxically immune-cold despite the increased expression of retrotransposons. These results suggest that DNA hypomethylation and aberrant retrotransposon activation are significant bottlenecks to tumor development and may represent promising therapeutic targets. Citation Format: Chao Lu. Interplay between histone modifications and DNA methylation in cancer [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 PR004.
Abstract B022: TEDEdb: Transposable element differential expression database
Authors: Gennaro H Calendo, Morgan Chaunzwa, Iman Dehzangi, Jozef Madzo, Jean-Pierre Issa
Journal: Cancer Research (2025)

Abstract Epigenetic therapies that induce global DNA hypomethylation activate transcriptionally repressed transposable elements (TEs). The activation of a class of TEs known as human endogenous retroviruses (HERVs) can trigger an innate antiviral response in cells called “viral mimicry”. Viral mimicry induced by aberrantly expressed HERVs stimulates interferon signaling genes resulting in an adaptive immune response that can ultimately lead to immunogenic cell death. This heightened immune activity can enhance the efficacy of immune checkpoint inhibitor therapies. Identifying cancers that are susceptible to a viral mimicry response or treatment regimens that induce aberrant transcription of TEs has not yet been fully explored. Recent computational tools enable the measurement of TE signal from short-read RNA-seq data and several large-scale reprocessing pipelines have uniformly processed RNA-seq data of cancer cell lines treated with epigenetic and cytotoxic drugs. However, these large-scale pipelines omit the quantification of TEs. To address this gap and fully utilize publicly available data, we have developed a computational pipeline and database of TE expression for more than 7,000 samples from 220 cancer cell lines treated with over 700 cytotoxic and epigenetic drugs, yielding over 2,100 differential expression experiments. To illustrate the usefulness of this database, we ranked drugs by %TE activation and found that the top three targets were DNMT (Decitabine), CDK9 (MC180295), and Topoisomerase II (Doxorubicin). We enable the exploration of this dataset by implementing several meta-analysis methods and visualizations made available as an interactive web application. This database and web application can serve as a valuable resource for the cancer and epigenetics community by enabling hypothesis generation and providing insights into how specific drugs may induce TE expression. Citation Format: Gennaro H Calendo, Morgan Chaunzwa, Iman Dehzangi, Jozef Madzo, Jean-Pierre Issa. TEDEdb: Transposable element differential expression database [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 B022.
Abstract IA007: DNA methylation in cancer: From knowledge to applications
Authors: Manel Esteller
Journal: Cancer Research (2025)

Abstract For the last thirty years an increasing amount of evidence has shown the relevance of epigenetics in cell biology and tissue physiology, being DNA methylation aberrations in cancer the flag-ship for the recognition of its disturbance in human diseases. From the candidate gene approaches, new powerful technologies such as comprehensive DNA methylation microarrays and whole genome bisulfite sequencing has recently emerged that have reinforced the notion of epigenetic disruption in the crossroad of many sickness. From the poster-boy case of MGMT hypermethylation in the prediction of alkylating drug response to the personalized treatment of leukemia with small molecules targeted to fusion proteins involving histone modifiers, the field has walked a long path. The current talk will focus in the epigenetic profiling, basically at the level of DNA methylation and histone modifications, that is starting to provide clinical value in the diagnosis, prognosis and prediction of response to drug therapies. For cancer, we have already a wide view of the undergoing DNA methylation events that expand beyond classical promoter CpG islands of tumor suppressor genes and we have a growing list of mutated chromatin remodeler genes that contributes to the tumorigenesis process. It is time to apply this knowledge in practical clinical situations like the diagnosis of cancers of unknown primary, the screening of malignancies in high-risk populations or a biomarker selection of the patients that should receive treatment with anticancer drugs, including immunotherapy. Beyond cancer, DNA methylation is starting to be recognized as playing a major role in infectious diseases, and in this regard, the present lecture will also address the epigenomic component of COVID-19. Most important, Epigenomics can be added to Genomics, Transcriptomics and Proteomics plus Bioinformatics to create a Multomics view of human diseases. Citation Format: Manel Esteller. DNA methylation in cancer: From knowledge to applications [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 IA007
Abstract B012: The effect of a novel therapy on DNA methylation in Ewing Sarcoma
Authors: Emily Isenhart, Ajay Gupta, Joyce Ohm
Journal: Cancer Research (2025)

Abstract Ewing sarcoma (EwS) is a rare and aggressive disease affecting the bone and soft tissue of children and young adults. A FET::ETS fusion protein, typically EWSR1-FLI1 is pathognomonic for this disease. EwS is genomically quiet with widespread dysregulation driven by aberrant fusion activity leading to elevated endogenous levels of replication stress and epigenetic drift. While five-year survival rates are moderate for localized primary disease (∼70%), metastasized, relapsed, and refractory disease have much lower rates of survival (15-35%) and are associated with increased epigenetic heterogeneity. Treatment options are currently limited to systemic therapies which have not seen major advancement since the development of interval compression of chemotherapy and often lead to secondary complications for these patients. Our lab has identified a novel combination of replication stress response inhibitors (RSRi), DDK (DDKi) and WEE1 (WEE1i), which sensitize EwS cells to their own elevated levels of replication stress by removing repair strategies and forcing mitotic catastrophe and apoptosis. In one in vivo study, cell line derived xenografts in NSG mice were treated with DDKi (simurosertib) and WEE1i (adavosertib) in the following design: 1) vehicle control (n=5), 2) Irinotecan + Temozolomide (n=9), 3) Irinotecan (full dose) + DDKi + WEE1i (n=7), 4) Irinotecan (half dose) + DDKi + WEE1i (n=9), for a total of 30 samples. We have shown that this RSRi combination is able to effectively limit tumor growth over time even in the context of decreased chemotherapeutic dose. As increased replication stress can cause epigenetic drift, changes in methylation associated with treatment condition were investigated by reduced representation bisulfite sequencing. Differential methylation analysis was performed on individual CpG sites, CpG structures (islands, shores) and transcriptional elements (promoters, enhancers, transcription start sites). In this context, key pathways were found to be differentially methylated between treatment conditions, including those involved in cell signaling, motility, metabolism, and neuronal processes. Overall, this targeted therapy presents a promising therapeutic option for this pediatric patient population. Citation Format: Emily Isenhart, Ajay Gupta, Joyce Ohm. The effect of a novel therapy on DNA methylation in Ewing Sarcoma [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 B012.
Abstract A010: Dnmt3a2 ensures proper enhancer DNA methylation during embryonic development
Authors: Minmin Liu, Guillermo A Urrutia, Rachel Shereda, Gangning Liang, Peter A Jones
Journal: Cancer Research (2025)

Abstract Proper enhancer function and switching is essential for the development of vertebrates and is known to be controlled by DNA cytosine methylation. We used isoform-specific knockouts of the two known DNA methyltransferase variants, Dnmt3a1 and Dnmt3a2 to probe their roles in enhancer methylation in embryogenesis and in postnatal development. Mouse embryos lacking Dnmt3a1 showed minimal loss of genomic methylation confirming that this isoform is not required for embryonic development. However, they were smaller than their littermates and died about 4 weeks after birth with considerable demethylation in the brain as has been previously reported. On the other hand, embryos lacking Dnmt3a2 showed widespread genomic hypomethylation which was particularly prevalent in enhancers and imprinted genes. Interestingly these methylation deficits were largely repaired after birth, presumably by the remaining Dnmt3a1 isoform. The mice were viable; however, they showed an increased prevalence of sporadic phenotypes including anophthalmia, hydronephrosis, hydrocephalus and male infertility which have previously been observed in laboratory mice. Hypomethylation of several imprinted genes was also observed in sperm which might potentially explain the infertility phenotype. There is therefore an interplay between the 2 isoforms which is developmentally regulated and a key role for Dnmt3a2 might be the stabilization of enhancer states which lessening the chance of sporadic phenotypes arising after birth. Citation Format: Minmin Liu, Guillermo A Urrutia, Rachel Shereda, Gangning Liang, Peter A Jones. Dnmt3a2 ensures proper enhancer DNA methylation during embryonic development [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 A010.
Abstract B010: Concurrent analysis of multiple methylated CpG sites using multiplex MethyLight assay for epithelial ovarian cancer detection
Authors: Deepa Bisht, Manisha Sachan
Journal: Cancer Research (2025)

Abstract Objective: Epithelial ovarian cancer (EOC), a heterogeneous and aggressive gynaecologic malignancy, remains a leading cause of cancer-related death due to the lack of reliable, sensitive, and specific early diagnostic biomarkers. Methods: This study employed a cost-effective, CpG site-specific Amplification Refractory Mutation System PCR (ARMS-PCR) to assess the methylation frequency of six diagnostically potent CpG sites (cg18878992, cg00480298, cg029572270, cg10636246, cg10061138, and cg12910797) in 45 EOC samples and 25 normal controls. Methylation patterns (methylated, unmethylated, partially methylated) were confirmed through image analysis and Combined Bisulfite Restriction Analysis (COBRA). Three top methylated CpG sites were chosen to form two biomarker panels, which were subsequently tested for diagnostic efficiency. Furthermore, a TaqMan-based quantitative PCR (MethyLight) assay was developed, integrating the three most hypermethylated CpG sites (cg02957270, cg00480298, and cg10061138) in a triplex format. Results: ARMS-PCR revealed the diagnostic potential of two hypermethylated CpG sites (cg02957270, cg10061138) and one hypomethylated site (cg10061138). The sensitivity of the singleplex and multiplex panels reached 80%, 73.3%, and 82.3%, respectively. The MethyLight assay demonstrated an enhanced sensitivity of 86% and specificity of 92% for the multiplex panel (cg02957270 and cg00480298) along with control col2A1. ROC curve analysis revealed AUC values of 0.96, 0.91, and 0.84 for the singleplex assays and 0.97 for the multiplex panel. While ARMS-PCR showed limited correlation with clinicopathological characteristics, significant associations were found in the MethyLight assay (p &amp;lt; 0.05). Conclusions: This discovery opens a new frontier in DNA methylation research, suggesting the potential to harness clinically relevant, independent CpG sites, in hypermethylated state for the development of novel biomarkers. Citation Format: Deepa Bisht, Manisha Sachan. Concurrent analysis of multiple methylated CpG sites using multiplex MethyLight assay for epithelial ovarian cancer detection [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 B010.
Abstract IA011: Heterochromatin deregulation during hematopoietic stem progenitor cell (HSPC) aging
Authors: Tingting Hong, Lei Guo, Anna Guzman, James You, Margaret Goodell, Yubin Zhou, Yun Huang
Journal: Cancer Research (2025)

Abstract Aging is one of the major negative factors affecting normal hematopoiesis. Aged hematopoietic stem and progenitor cells (HSPCs) exhibit reduced self-renewal and increased myeloid bias during lineage specification, thereby sabotaging the immune system and increasing the risk of malignant transformation. Epigenetic dysregulation is a hallmark feature of aging and significantly contributes to age-related dysfunction across multiple biological systems. DNA methylation drift is commonly observed during aging, especially within late-replicated heterochromatin. DNA methylation and demethylation are maintained by DNMT and TET enzymes. Mutations in DNMT3A and TET2 are frequently observed in age-related clonal hematopoiesis (CH) and hematological malignancies. The impact of DNMT3A or TET2 loss-of-function on heterochromatin has recently gained recognition. Although heterochromatin is generally regarded as a gene-less region, it plays an important role in maintaining genome stability. Recently, we compared the impact of aging on WT and Tet2 knockout (KO) HSPCs. We observed that aging has less impact on Tet2KO HSPCs, which retain considerable clonal expansion capability during aging. However, WT HSPCs exhibited functional decline with age. At the molecular level, we identified the spatial relocation of heterochromatin from the nuclear periphery to the intranuclear region in aged WT HSPCs, but not in Tet2KO HSPCs. This relocation resulted in the upregulation of endogenous retroviruses (ERVs) and the promotion of innate immune responses in WT HSPCs, contributing to their functional decline during aging. This study adds a new dimension to understanding the functional interplay between DNA methylation and histone modifications in maintaining heterochromatin integrity and genome stability during stem cell aging. Citation Format: Tingting Hong, Lei Guo, Anna Guzman, James You, Margaret Goodell, Yubin Zhou, Yun Huang. Heterochromatin deregulation during hematopoietic stem progenitor cell (HSPC) aging [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 IA011
Abstract B015: Collection and purification of microgram amounts of cfDNA from urine for methylation analysis
Authors: Floyd Taub, Lindsey Ray, Charles Preston Neff, Elijah Barstis, Charles Henry, Kirsten Arnold
Journal: Cancer Research (2025)

Abstract Background: DNA methylation studies often require relatively large amounts of DNA, typically methods suggest hundreds of nanograms to a microgram per assay. While this is easy to obtain if genomic DNA (gDNA) is used, preforming similar studies on circulating cell free DNA (cfDNA) may be difficult. Plasma, especially that from normal individuals needed for comparison, may yield only 10 ng to 20 ng per ml. Thus, experimental designs involving multiple repeat analysis of the same specimen, or applying different complementary methylation methods to one specimen, may be limited by the amount of cfDNA in a blood sample. It is known that urine contains cfDNA, but reports on the amount vary from very low to being comparable to blood; the conflicting data may be due in part to the low yield some methods of isolation have reported to have when the DNA is small. Hypothesis: We postulated that a system which filtered hundreds of mls of urine and captured the DNA based on charge rather than absorption to silica, could capture adequate amounts of cfDNA from urine for repeat studies. Results: Initially, filtering large amounts of urine was problematic due to clogging. A system of stacked filters was devised. The method uses 200- 250 ml size syringes and 5 cm filter cartridges. It allows full voids, in fact up to 1 liter, to be filtered. The urine is first collected in a measuring cup containing preservatives, it is immediately filtered. This is simple enough to be done by a patient at home. The first of the stacked filters, collects urothelial and other cells that may be used to analyze gDNA; it also clarifies the urine sufficiently to pass through a second lower pore size filter modified to be highly positively charged. On average, a 150 ml void provides 2100 nanograms of cfDNA. The binding to the filter is sufficiently strong that DNases cannot bind or digest the DNA. Thus, the DNA is stable in the cartridge for four days and allows for shipping without special handling. The in-lab purification consists of separating the filters, then washing the cfDNA trapping filter, followed by elution of the DNA. It takes under 10 minutes and results in purified DNA that is suitable for downstream analysis. Conclusions: Microgram amounts of cfDNA can be easily extracted from urine to facilitate initial analyses sufficient for statistically robust studies and banking of specimens for future testing. Citation Format: Floyd Taub, Lindsey Ray, Charles Preston Neff, Elijah Barstis, Charles Henry, Kirsten Arnold. Collection and purification of microgram amounts of cfDNA from urine for methylation analysis [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 B015.