tbuckley/cabot-search huggingface dataset:
The ETO2 transcriptional cofactor maintains acute leukemia by driving a MYB/EP300‐dependent stemness program
Authors: Alexandre Fagnan, Zakia Aid, Marie Baille, Aneta Drakul, Elie Robert, Cécile K. Lopez, Cécile Thirant, Yann Lecluse, Julie Rivière, Cathy Ignacimouttou, Silvia Salmoiraghi, Eduardo Anguita, Audrey Naimo, Christophe Marzac, Françoise Pflumio, Sébastien Malinge, Christian Wichmann, Yun Huang, Camille Lobry, Julie Chaumeil, Eric Soler, Jean‐Pierre Bourquin, Claus Nerlov, Olivier A. Bernard, Juerg Schwaller, Thomas Mercher
Journal: HemaSphere (2024)

Abstract Transcriptional cofactors of the ETO family are recurrent fusion partners in acute leukemia. We characterized the ETO2 regulome by integrating transcriptomic and chromatin binding analyses in human erythroleukemia xenografts and controlled ETO2 depletion models. We demonstrate that beyond its well‐established repressive activity, ETO2 directly activates transcription of MYB, among other genes. The ETO2‐activated signature is associated with a poorer prognosis in erythroleukemia but also in other acute myeloid and lymphoid leukemia subtypes. Mechanistically, ETO2 colocalizes with EP300 and MYB at enhancers supporting the existence of an ETO2/MYB feedforward transcription activation loop (e.g., on MYB itself). Both small‐molecule and PROTAC‐mediated inhibition of EP300 acetyltransferases strongly reduced ETO2 protein, chromatin binding, and ETO2‐activated transcripts. Taken together, our data show that ETO2 positively enforces a leukemia maintenance program that is mediated in part by the MYB transcription factor and that relies on acetyltransferase cofactors to stabilize ETO2 scaffolding activity.
Dietary Acculturation Is Associated With Altered Gut Microbiome, Circulating Metabolites, and Cardiovascular Disease Risk in US Hispanics and Latinos: Results From HCHS/SOL
Authors: Yi Wang, Guo-Chong Chen, Zheng Wang, Kai Luo, Yanbo Zhang, Yang Li, Amanda C. McClain, Marta M. Jankowska, Krista M. Perreira, Josiemer Mattei, Carmen R. Isasi, Maria M. Llabre, Bharat Thyagarajan, Martha L. Daviglus, Linda Van Horn, David Goldsztajn Farelo, Luis E. Maldonado, Steven R. Levine, Bing Yu, Eric Boerwinkle, Rob Knight, Robert D. Burk, Robert C. Kaplan, Qibin Qi, Brandilyn A. Peters
Journal: Circulation (2024)

Dietary acculturation, or adoption of dominant culture diet by migrant groups, influences human health. We aimed to examine dietary acculturation and its relationships with cardiovascular disease (CVD), gut microbiota, and blood metabolites among US Hispanic and Latino adults.
Childhood Opportunity and Acute Interstage Outcomes: A National Pediatric Cardiology Quality Improvement Collaborative Analysis
Authors: Benjamin Zielonka, Emily M. Bucholz, Minmin Lu, Katherine E. Bates, Garick D. Hill, Nelangi M. Pinto, Lynn A. Sleeper, David W. Brown
Journal: Circulation (2024)

The interstage period after discharge from stage 1 palliation carries high morbidity and mortality. The impact of social determinants of health on interstage outcomes is not well characterized. We assessed the relationship between childhood opportunity and acute interstage outcomes.
Targeting RNA‐binding motif protein 39 for arginine reduction: unveiling metabolic vulnerability in arginine‐dependent liver cancer
Authors: Aoxue Li, Hongjuan Cui, Erhu Zhao
Journal: MedComm (2024)

Abstract Cancer is increasingly acknowledged as a metabolic disease, characterized by metabolic reprogramming as its hallmark. However, the precise mechanisms behind this phenomenon and the factors contributing to tumorigenicity are still poorly understood. In a recent publication in Cell , Mossmann and colleague reported a study unveiling arginine as a molecule with second messenger‐like properties that reshapes metabolism to facilitate the tumor development in hepatocellular carcinoma (HCC). Their research revealed that the RNA‐binding motif protein 39 (RBM39)‐mediated increase in asparagine synthesis results in increased arginine uptake. This establishes a positive feedback loop that sustains elevated levels of arginine and facilitates oncogenic metabolic reprogramming. Additionally, Mossmann et al. demonstrated that depleting RBM39 with indisulam effectively disrupts the proto‐oncogenic metabolic reprogramming in HCC. This discovery presents a novel treatment strategy for arginine‐dependent liver cancers.
Comparison of genetic and epigenetic profiles of periodontitis according to the presence of type 2 diabetes
Authors: Junho Kang, Hansong Lee, Ji‐Young Joo, Jae‐Min Song, Hyun‐Joo Kim, Yun Hak Kim, Hae Ryoun Park
Journal: MedComm (2024)

Abstract Type 2 diabetes mellitus (T2DM) and periodontitis (PD) have intricated connections as chronic inflammatory diseases. While the immune response is a key factor that accounts for their association, the underlying mechanisms remain unclear. To gain a deeper understanding of the connection, we conducted research using a multiomics approach. We generated whole genome and methylation profiling array data from the periodontium of PD patients with DM (PDDM) and without DM to confirm genetic and epigenetic changes. Independent bulk and single‐cell RNA sequencing data were employed to verify the expression levels of hypo‐methylated genes. We observed a gradual rise in C&gt;T base substitutions and hypomethylation in PD and PDDM patients compared with healthy participants. Furthermore, specific genetic and epigenetic alterations were prominently associated with the Fc‐gamma receptor‐mediated phagocytosis pathway. The upregulation of these genes was confirmed in both the periodontal tissues of PD patients and the pancreatic tissues of T2DM patients. Through single‐cell RNA analysis of peripheral blood mononuclear cells, substantial upregulation of Fc‐gamma receptors and related genes was particularly identified in monocytes. Our findings suggest that targeting the Fc‐gamma signaling pathway in monocytes holds promise as a potential treatment strategy for managing systemic complications associated with diabetes.
Association of Metabolic Syndrome With Neuroimaging and Cognitive Outcomes in the UK Biobank
Authors: Danial Qureshi, Anya Topiwala, Shehab Uddin Al Abid, Naomi E. Allen, Elżbieta Kuźma, Thomas J. Littlejohns
Journal: Diabetes Care (2024)

Metabolic syndrome (MetS) has been linked to dementia. In this study, we examined the association of MetS with neuroimaging and cognition in dementia-free adults, offering insight into the impact of MetS on brain health prior to dementia onset.
Tyrosine kinase inhibitors in HER2‐positive metastatic breast cancer with trastuzumab emtansine resistance: insights from a multicenter retrospective real‐world study
Authors: Chunxiao Sun, Yijia Hua, Nan Jin, Xiaojia Wang, Jian Huang, Xinyu Wu, Tianyu Zeng, Xueqi Yan, Fan Yang, Yan Liang, Xiang Huang, Wei Li, Yongmei Yin
Journal: MedComm (2024)

Abstract The use of trastuzumab emtansine (T‐DM1) has revealed significant efficacy in HER2‐positive metastatic breast cancer (MBC). However, optimal therapeutic strategies following T‐DM1 failure remain a subject of debate in clinical practice. In this multicenter, retrospective, real‐world study, we sought to examine the effectiveness and safety of tyrosine kinase inhibitors (TKIs) as a therapeutic strategy in HER2‐positive MBC who developed T‐DM1 resistance. Between September 2018 and December 2022, 66 patients were enrolled. The median progression‐free survival of TKIs‐based therapy was 10.1 months (95% CI, 4.7–15.6). Objective response rate and clinical benefit rate were 18.2 and 66.7%, respectively. TKIs‐based therapy demonstrated better effectiveness in patients who had previously derived benefit from T‐DM1 and featured acquired resistance to trastuzumab. The most common adverse events were diarrhea (36, 54.5%), hand‐foot syndrome (31, 47.0%), and leucopenia (30, 45.5%). In conclusion, TKIs‐based therapy showed promising effectiveness and safety in HER2‐positive MBC patients after T‐DM1 failure.
Abstract PR07: <i>SETD1B</i> mutations confer apoptosis resistance and BCL2 independence in B-cell lymphoma
Authors: Ana Portelinha, Shenqiu Wang, Sara Parsa, Man Jiang, Sagarajit Mohanty, Soumya Sharma, Neeraj Arya, Omid Tavana, Jiayu Wen, Jude Fitzgibbon, Ahmet Dogan, Ana Younes, Ari M. Melnick, Hans-Guido Wendel
Journal: Blood Cancer Discovery (2024)

Abstract The translocation t(14;18) activates BCL2 and is considered the initiating genetic lesion in over ninety percent of follicular lymphomas (FL). Surprisingly, FL patients respond poorly to clinically approved inhibitor, venetoclax. The mechanisms underlying BCL2 independence in FL are poorly understood, and it has been speculated that epigenetic rewiring of cell death programs may play a role. We performed separate genome-wide CRISPR/Cas9 screens to explore the mechanisms of resistance to Venetoclax and an experimental MCL-1 inhibitor (S63845) and unveiled the histone lysine methyltransferase SETD1B (KMT2G) as an unexpected mechanism of resistance to both inhibitors in lymphoma. We show that mutations and deletions affecting SETD1B occur in 7% of FLs and 16% of diffuse large B cell lymphomas (DLBCL). In vivo, SETD1B acts as a tumor suppressor gene and cooperates with the related histone-lysine N-methyltransferase 2D (KMT2D) gene leading to a more aggressive disease presentation. This oncogenic cooperation is reflected in the genomes of human lymphoma, where SETD1B mutations typically co-occur with KMT2D mutations. Mechanistically, SETD1B is required to express pro-apoptotic BCL2 family proteins like BIM and BIK. Inhibitors of the KDM5 histone H3K4 de-methylase restore the expression of BIM and BIK, venetoclax sensitivity and lead to synergistic drug effects in SETD1B deficient lymphoma xenografts. Our results highlight a role for SETD1B in the epigenetic regulation of cell death proteins in B cell lymphomas, connecting the loss of SETD1B to lymphoma development and reduced sensitivity to venetoclax. Citation Format: Ana Portelinha, Shenqiu Wang, Sara Parsa, Man Jiang, Sagarajit Mohanty, Soumya Sharma, Neeraj Arya, Omid Tavana, Jiayu Wen, Jude Fitzgibbon, Ahmet Dogan, Ana Younes, Ari M. Melnick, Hans-Guido Wendel. SETD1B mutations confer apoptosis resistance and BCL2 independence in B-cell lymphoma [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PR07.
Abstract PO-012: Gain-of-function small molecules to reprogram oncogenic transcription in lymphoma
Authors: Sai Gourisankar, Roman Sarott, Basel Karim, Sabin Nettles, Haopeng Yang, Brendan Dwyer, Juste Simanauskaite, Jason Tse, Hind Abuzaid, Stephen M Hinshaw, Michael R Green, Gerald R Crabtree, Nathanael S Gray
Journal: Blood Cancer Discovery (2024)

Abstract Conventional pharmacotherapy in oncology centers on target-centric silencing of aberrant protein function through small molecule inhibitors, degraders, or CRISPR/RNAi. In contrast, here we leverage induced proximity to develop pharmacology that activates dominant signaling pathways for a therapeutic effect. To develop this concept, we describe a new class of bivalent small molecules that reprogram cancer-driving gene expression to activate cell death signaling in diffuse large B cell lymphomas (DLBCL). These molecules, called Transcriptional Chemical Inducers of Proximity (TCIPs), operate at fractional occupancy of their protein targets, without genomic modifications to the cell or organism. The first TCIPs transiently re-localized elongation factors such as BRD4 (TCIP1, PMID 37495688) to loci regulated by the transcription factor BCL6, inducing the expression of pro-apoptotic genes regulated by BCL6. In new, unpublished work, CDK-TCIPs have been made to re-direct the activity of transcriptional elongation kinases such as CDK9, CDK12, or CDK13 to induce the expression of pro-apoptotic BCL6-target genes. Profiling in ∼900 barcoded cancer cell lines show that the molecules exhibit potent cell killing potency in a highly DLBCL lineage-restricted manner. Cytotoxicity to healthy lymphocytes is 100- to 10,000-fold lower, although germinal center B cells are ablated in a dose-dependent manner consistent with the role of BCL6 in the germinal center. Biochemical, cell biological, proteomic, and genomic studies demonstrate that CDK-TCIPs operate via a gain-of-function mechanism reliant on the ternary complex formed by the bivalent molecule. Instead of global enzyme inhibition or degradation, CDK-TCIPs borrow and re-localize a fraction of total CDK activity to BCL6-bound chromatin, producing pharmacology from the induction of pro-apoptotic gene transcription. The findings suggest a path to rational design of new gain-of-function chemotherapeutic strategies to rewire cell signaling using induced proximity. Citation Format: Sai Gourisankar, Roman Sarott, Basel Karim, Sabin Nettles, Haopeng Yang, Brendan Dwyer, Juste Simanauskaite, Jason Tse, Hind Abuzaid, Stephen M Hinshaw, Michael R Green, Gerald R Crabtree, Nathanael S Gray. Gain-of-function small molecules to reprogram oncogenic transcription in lymphoma [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-012.
Abstract PO-006: ABBV-319: A CD19–targeting glucocorticoid receptor modulator antibody-drug conjugate therapy for B-cell malignancies
Authors: Chewei (Anderson) Chang
Journal: Blood Cancer Discovery (2024)

Abstract Glucocorticoids such as prednisone (P) and dexamethasone (D) are key components in standard-of-care immuno-chemotherapy regimens (e.g., R-CHOP, EPOCH-R, Hyper-CVAD) for the treatment of B-cell malignancy. However, prolonged systemic glucocorticoid treatment is associated with several adverse events that often result in dose reduction and reduced therapeutic efficacy. ABBV-319 is a CD19-targeting antibody-drug conjugate (ADC) with a glucocorticoid receptor modulator (GRM) payload engineered to reduce glucocorticoid-associated toxicities while possessing three distinct mechanisms of action (MOA) to increase therapeutic efficacy: (1) CD19 receptor-mediated delivery of potent glucocorticoid receptor modulator (GRM) payload to induce apoptosis, (2) inhibition of B-cell receptor (BCR) stimulated CD19 signaling, and (3) enhanced Fc-mediated effector function via afucosylation of the antibody backbone. ABBV-319 elicited potent GRM-driven anti-tumor activity against multiple malignant B-cell lines in vitro as well as in cell line-derived xenografts (CDXs) and patient-derived xenografts (PDXs) in vivo. Remarkably, a single-dose of ABBV-319 induced sustained tumor regression and enhanced anti-tumor activity compared to repeat dosing of systemic prednisolone at the maximum tolerated dose (MTD) in mice. The unconjugated CD19 monoclonal antibody (mAb) also displayed anti-proliferative activity on a subset of B-cell lymphoma cell lines through the inhibition of PI3K signaling. Moreover, afucosylation of the CD19 mAb enhanced Fc-mediated antibody-dependent cellular cytotoxicity (ADCC), and this activity was maintained after conjugation with GRM payload. Notably, ABBV-319 displayed superior efficacy compared to afucosylated CD19 mAb in human CD34+ PBMC-engrafted NSG-tg(Hu-IL15) transgenic mice, demonstrating enhanced anti-tumor activity in vivo when multiple MOAs are enabled concurrently. ABBV-319 also showed potent anti-tumor activity across multiple B-cell lymphoma models, including non-germinal center B-cell (GCB) DLBCL and relapsed lymphoma treated with R-CHOP treatment. Collectively, these data support the ongoing evaluation of ABBV-319 for the treatment of B-cell malignancy in Phase I clinical trial (NCT05512390). Disclosures: All authors are employees of AbbVie. The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication. Citation Format: Chewei (Anderson) Chang. ABBV-319: A CD19–targeting glucocorticoid receptor modulator antibody-drug conjugate therapy for B-cell malignancies [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-006.
Abstract PO-035: Genome-wide CRISPR knockout screen identifies sialylation as a tumor suppressive mechanism in B-cell malignancies
Authors: Namratha Sheshadri, Rongrong Li, Muhammad Usama Tariq, Jianliang Shen, Jaeyong Jung, Junrong Yan, Kevin Lu, Zhiyuan Shen, Ping Xie, Wei-Xing Zong
Journal: Blood Cancer Discovery (2024)

Abstract Ba/F3 is a murine pro-B cell line that is dependent on interleukin-3 (IL-3) for its survival and proliferation. It has been widely used for identifying oncogenes and mechanisms of drug-resistance. Using this cell line, we conducted a genome-wide CRISPR knockout screen to identify genes whose loss can confer IL-3 independence, hence may be implied as tumor suppressor genes (TSGs). We identified several genes that map to human chromosome 6q, a frequent deletion hotspot in B-cell malignancies, that may act as TSGs. One of these putative novel TSGs is Slc35a1, which encodes the membrane solute carrier that facilitates the transport of nucleotide sugar (CMP-sialic acid) into the Golgi apparatus for subsequent sialylation. Interestingly, in addition to Slc35a1, pathway analysis of hits from the CRISPR screen identified several genes in the sialic acid metabolism pathway, Nans, Cmas, and St3gal5. We confirmed that their silencing led to decreased protein sialyation and could confer IL-3-independent cell survival and growth in Ba/F3 cells. We continued to characterize Slc35a1 since its homozygous and heterozygous deletions are seen in 7-40% of different types of B-cell malignancies, including approximately 40% of patients with Diffuse Large B-cell Lymphoma. Slc35a1 deletion in murine and human cell-lines conferred cytokine-independent growth. Tail-vein injection of Slc35a1-silenced Ba/F3 cells resulted in allograft tumor growth presenting with splenomegaly and lymphadenopathy. Using Maackia amurensis lectin II (MAL II) to pull down sialylated proteins for mass spectrometry, we identified proteins that were differentially sialylated in Slc35a1 wild-type and knockout cells, among which are the α and β subunits of the integrin receptor, lymphocyte functional antigen 1 (LFA-1). As integrin desialylation can promote its constitutive activation, we are currently studying the impact of LFA-1 sialylation on B-cell function and transformation. We have also developed mouse models with B-cell specific ablation of Nans and Slc35a1 to further evaluate the role of sialylation on B-cell development and tumorigenesis in vivo. Overall, our study demonstrates that sialylation may function as a tumor suppressive mechanism and serve as a therapeutic target in B-cell cancers. Citation Format: Namratha Sheshadri, Rongrong Li, Muhammad Usama Tariq, Jianliang Shen, Jaeyong Jung, Junrong Yan, Kevin Lu, Zhiyuan Shen, Ping Xie, Wei-Xing Zong. Genome-wide CRISPR knockout screen identifies sialylation as a tumor suppressive mechanism in B-cell malignancies [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-035.
Abstract PO-002: Intrinsically disordered regions -induced CAR condensation improves the cytotoxicity of CAR-Ts against low-antigen cancers
Authors: Xinyan Zhang, Qian Xiao, Longhui Zeng, Fawzaan Hashmi, Xiaolei Su
Journal: Blood Cancer Discovery (2024)

Abstract Chimeric antigen receptor (CAR)-T cell-based therapies demonstrate remarkable efficacy for the treatment of otherwise intractable cancers, particularly B-cell malignancies. However, CAR-T cells respond to only a subset of cancers and are limited by low signaling efficiency: a few hundred or thousand antigen molecules are required to activate a CAR T cell whereas a single peptide-loaded MHC molecule is sufficient to trigger the activation of a normal T cell. This low antigen sensitivity not only limits the current CAR-T therapy to high antigen-expressing cancers, but also results in high frequencies of relapse, during which high antigen-expressing cancers downregulate their antigen levels to escape CAR-T’s attacking. To improve the antigen sensitivity of CAR-T cells, we engineered CARs targeting CD19 by including intrinsically disordered regions (IDRs) that promote signaling condensation. The “IDR CARs” triggered enhanced membrane-proximal signaling in the CAR-T synapse, which led to an increased release of cytotoxic factors, a higher killing activity towards low antigen-expressing cancer cells in vitro, and an improved anti-tumor efficacy in vivo. No elevated tonic signaling was observed in IDR CAR-Ts. Together, we demonstrated IDRs as a new tool set to enhance CAR-T cytotoxicity and to broaden CAR-T’s application to low antigen-expressing cancers. Citation Format: Xinyan Zhang, Qian Xiao, Longhui Zeng, Fawzaan Hashmi, Xiaolei Su. Intrinsically disordered regions -induced CAR condensation improves the cytotoxicity of CAR-Ts against low-antigen cancers [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PO-002.