title: Transcriptional Memory Dampens Heat Shock Responses in Yeast: Functional Role of Mip6 and its interaction with Rpd3

city: València

first: Joan

last: Serrano Quílez

state: València

address: Jaume Roig, 11

institute: CSIC

summary: Cells must rapidly adapt to environmental fluctuations, including heat stress, to maintain homeostasis and ensure survival. A key adaptive mechanism is transcriptional memory, which enables cells to "remember" prior stress exposure and mount a faster or more con-trolled transcriptional response upon re-exposure. However, the molecular mecha-nisms underlying transcriptional memory in the heat shock response (HSR) remain in-completely understood. Here, we investigate the role of the RNA-binding protein Mip6 in regulating transcriptional memory during heat stress in Saccharomyces cerevisiae. Using qRT-PCR and RNA-seq, we demonstrate that prior heat shock exposure dampens the activation of heat-responsive genes upon a second stress, a phenomenon more pro-nounced in mip6Δ mutants. Our transcriptomic analyses reveal that transcriptional memory predominantly suppresses excessive gene expression changes, fine-tuning stress responses. Moreover, we identify a functional and physical interaction between Mip6 and the histone deacetylase Rpd3, a key regulator of transcriptional memory. Loss of both Mip6 and Rpd3 results in synthetic growth defects under heat stress and misregulation of Msn2/4-dependent transcripts, implicating Mip6 as a novel player in the coordination of chromatin and RNA-binding mechanisms during transcriptional memory. Additionally, we show that transcriptional memory modulates metabolic homeostasis and proteostasis. Collectively, our findings implicate Mip6 in the coordination of transcriptional memory in the HSR and reveal a novel link between the RNA-binding protein Mip6 and the chroma-tin modifier Rpd3 HDAC in stress adaptation. These insights provide a foundation for further exploration of transcriptional memory mechanisms across diverse stress condi-tions.

overall_design: A cell culture was split into two flasks. One of them (memory) was exposed to a first 20 min heat shock and, after a 60 min recovery phase at optimal conditions, to a second 20 min heat shock. In the meantime, the other flask (no memory) was only exposed to a single 20 min heat shock. The heat shocks were performed by adding media at 51 ºC.

first: Serrano-Quílez

last: Joan

first: Tejada-Colón

last: Ana

first: Nuño-Cabanes

last: Carme

first: Rodríguez-Navarro

last: Susana


title: Harnessing Notch Signaling to Enhance the Generation and Functionality of Human Conventional Type I Dendritic Cells for Cancer Immunotherapy Applications

status: Public on Jun 17 2025

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: Conventional dendritic cell type I (cDC1) are essential for an effective antitumor immune response, and their presence in the tumor microenvironment is positively correlated with clinical benefits. The extremely low frequency of these cell subsets in peripheral blood limits their application as a cellular vaccine for cancer immunotherapy. Developing a robust in vitro culture system for their large-scale generation from hematopoietic stem cells (HSCs) is a potential approach for generating cDC1-based cellular vaccines. We have developed a novel culture system by exploiting the Notch signaling requirement for cDC1 differentiation from HSCs and successfully generated billions of cDC1s from every million input CD34+ cells. We compared the gene expression profiles of cDC1s generated under feeder-free conditions or on feeders with or without Notch ligands using bulk RNA sequencing. Our results confirm that the in vitro-generated cDC1s are bona fide cDC1s and closely resemble naturally circulating cDC1s in vivo. The cDC1 generation system represents a significant opportunity to develop novel cellular vaccines for cancer immunotherapy, leveraging cross-presenting DC subsets.

overall_design: RNA expression profiling of in vitro generated conventional type I dendritic cells in the presence or absence of notch ligands

first: Sreekumar

last: Balan

first: Kristen

last: Radford

first: Xuedi

last: Wang

first: Nina

last: Bhardwaj


title: Single-Cell RNA Sequencing of Lungs Infected for 24 Hours with Avirulent Coccidioides posadasii (Δcts2/Δard1/Δcts3)

city: Livermore

first: Dina

last: Weilhammer

state: California

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

summary: The innate immune responses to Coccidioides are not well understood, particularly regarding which immune cells initiate the response upon infection. This study uses mouse models 24 hours post-infection to explore the initial immunological response to Coccidioides. Data sets include CD45+ MACS bead-sorted lung immune cells labeled with Coccidioides to differentiate which immune cells were directly interacting with the fungus versus bystander cells. The unlabeled Coccidioides data set includes all immune cells from the lungs. Using fungal fluorescent labeling and single-cell RNA sequencing, we identified CD274 (PD-L1) expressing neutrophils and contact-dependent Spp1+ macrophages as dominant responders, indicating an anti-inflammatory initial response. These findings elucidate the early dynamics of host immune interactions with Coccidioides, providing a foundation for further understanding host-pathogen interactions in fungal respiratory infections.

overall_design: We utilized 10X Genomics to conduct single-cell RNA sequencing to characterize the phenotypes of immune cells during the initial Coccidioides infection. The data sets include CD45+ MACS bead-sorted lung immune cells labeled with Coccidioides to distinguish immune cells that were directly interacting with the fungus versus bystander cells. The unlabeled Coccidioides data set includes all immune cells from the lungs. All single-cell RNA sequencing data were collected from 6 mice, pooled into 2 groups, and sequenced with n=3.

first: Nadia

last: Miranda

first: Oscar

middle: A

last: Davalos

first: Katrina

middle: K

last: Hoyer

middle: R


title: Identification of PRMT5 as a therapeutic target in cholangiocarcinoma [RNA-seq I]

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

summary: Cholangiocarcinoma is a very aggressive cancer whose incidence is increasing. Moreover, chemotherapies are little effective and the response to immune checkpoint inhibitors is low. We have identified protein arginine-methyltransferase 5 (PRMT5) as a novel therapeutic target in cholangiocarcinoma. PRMT5-targeting drugs markedly inhibited CCA cells proliferation, synergizing with cisplatin and gemcitabine, and hindered the growth of cholangiocarcinoma organoids. PRMT5 inhibition blunted the expression of oncogenic genes involved in chromatin remodeling and DNA repair, consistently inducing the formation of RNA-loops and promoting DNA damage. Our findings support the evaluation of PRMT5 inhibitors in clinical trials.

overall_design: To study the effect of PRMT5 inhibition in cholangiocarcinoma (CCA), the human CCA cell line HuCCT-1 was treated with PRMT5 inhibitor JNJ-64619178 or vehicle (DMSO) and we then performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicates of each condition.

first: Jasmin

last: Elurbide

first: Leticia

last: Colyn

first: Maria

middle: U

last: Latasa

first: Iker

last: Uriarte

first: Amaya

middle: L

last: Pascual

first: Emiliana

middle: V

last: Goiricelaya

first: Borja

middle: C

last: Uribe

last: Barrena

first: Matias

last: Avila


title: Identification of PRMT5 as a therapeutic target in cholangiocarcinoma [RNA-seq II]

summary: Cholangiocarcinoma is a very aggressive cancer whose incidence is increasing. Moreover, chemotherapies are little effective and the response to immune checkpoint inhibitors is low. We have identified protein arginine-methyltransferase 5 (PRMT5) as a novel therapeutic target in cholangiocarcinoma. Treatment with PRMT5 inhibitor significantly restrains the growth of experimental cholangiocarcinoma model TAZ/AKT without adverse effects. Our findings support the evaluation of PRMT5 inhibitors in clinical trials.

overall_design: To study the effect of PRMT5 inhibition in tumor progression, cholangiocarcinoma (CCA) was induced in C57BL/6J mice by hydrodynamic tail vein injection (HTVI) of plasmids coding for mutant TAZ, myr-AKT and the sleeping beauty transposase (TAZAKT). One group of mice was treated with PRMT5 inhibitor JNJ-64619178 (TAZAKT_JNJ) and control mice received the vehicle (TAZAKT_V). C57BL/6J mice without HTVI injection nor treatment were used as healthy controls (C). We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different mice of each group.

last: Lopez Pascual

last: Valbuena Goiricelaya

last: Castello Uribe

last: Fernandez  Barrena


title: Identification of PRMT5 as a therapeutic target in cholangiocarcinoma

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing

city: Heidelberg

first: Dominik

last: Lindenhofer

address: Meyerhofstraße 1

country: Germany

institute: EMBL Heidelberg

summary: Genetic variants (both coding and noncoding) can impact gene function and expression, driving disease mechanisms such as cancer progression. The systematic study of endogenous genetic variants is hindered by inefficient precision editing tools, combined with technical limitations in confidently linking genotypes to gene expression at single-cell resolution. We developed single-cell DNA-RNA sequencing (SDR-seq) to simultaneously profile up to 480 genomic DNA loci and genes in thousands of single cells, enabling accurate determination of coding and noncoding variant zygosity alongside associated gene expression changes. Using SDR-seq, we associate coding and noncoding variants with distinct gene expression in human induced pluripotent stem cells. Furthermore, we demonstrate that in primary B cell lymphoma samples, cells with a higher mutational burden exhibit elevated B cell receptor signaling and tumorigenic gene expression. SDR-seq provides a powerful platform to dissect regulatory mechanisms encoded by genetic variants, advancing our understanding of gene expression regulation and its implications for disease.

overall_design: Several experiments were performed in this study. Proof-of-concept (01_POP) experiment test two different fixation conditions (PFA, glyoxal). Panel size experiment tested different tested different panels sizes of gDNA and RNA targets (02_Panel_size). Size of the panel is indicated in sample Title. CRISPRi experiment (03_CRISPRi) aimed to perturb TSS sites completely with a CROP-seq vector. PE experiment (04_PE) aimed to install eQTLs and STOP controls variants that have an impact on gene expression. BE experiment (05_BE) aimed to install eQTLs that have an impact on gene expression. (07_Species_Mix) tested cross-contamination of gDNA and RNA using SDR-seq.

first: Julia

last: Bauman

first: John

last: Hawkins

first: Donnacha

last: Fitzgerald

first: Umut

last: Yildiz

first: Haeyeon

last: Jung

first: Anastasiia

last: Korosteleva

first: Mikael

last: Marttinen

first: Moritz

last: Kueblbeck

first: Judith

middle: B

last: Zaugg

first: Kyung-Min

last: Noh

first: Sascha

last: Dietrich

first: Wolfgang

last: Huber

first: Oliver

last: Stegle

first: Lars

middle: M

last: Steinmetz


title: Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease

city: Saint Louis

first: Khai

last: Nguyen

state: MO

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: Background & Aims: Perianal fistulizing Crohn’s disease (PCD) is a common and debilitating complication with elusive pathophysiology. We examined biopsies from patients with PCD and related conditions using a multi-omics approach. Methods: Patients with PCD (n=24), CD without perianal disease (NPCD, n=10), and idiopathic perianal fistulas (IPF, or cryptoglandular fistulas, n=25) were recruited. Biopsies were taken from fistula tracts, fistula opening, and rectal mucosa during examination under anesthesia or colonoscopy. Single-cell RNA-sequencing (scRNA-seq), mass cytometry (CyTOF), spatial transcriptomics (ST), immunohistochemistry (IHC), and integrated analysis of published datasets were performed. Results: ScRNA-seq, CyTOF, and ST unraveled immune and non-immune cell compartments in PCD and IPF fistula tracts. PCD fistulas showed hyperactivated pathogenic pathways including interferon (IFN)G response, TNF signaling, and IL6-JAK-STAT3 in myeloid cells. Similarly, stromal cells from PCD fistulas exhibited elevated IFNG and TNF response, TNF signaling, and epithelial-mesenchymal transition (EMT). Further analysis revealed cellular modules associated with anti-TNF therapy in PCD patients. In addition to fistula tracts, intestinal cells from PCD patients also expressed greater levels of IFNG-responsive and EMT genes compared to CD patients without perianal disease. In addition, we showed that both fistula tracts and ileal mucosa from PCD patients harbored expanded IFNG+ Th17 cells, which expressed elevated inflammatory mediators. The findings were independently validated using ST and IHC. Conclusion: Multi-omics analysis revealed immune and nonimmune cell landscapes of PCD. and highlights the pathogenic role of hyperactivated IFNG signaling in both fistula tracts and luminal mucosa of patients with PCD. This study identified IFNG as a potential therapeutic target for PCD.

overall_design: Single-cell RNA-seq was performed on idiopathic and Crohn's perianal fistula biopsies (N = 6 and 9, respectively) using the 10X Chromium 5' protocol. Spatial transcriptomics was performed using 10X Visium on idiopathic and Crohn's perianal fistula (N =  3/group).

first: Siyan

last: Cao

first: Parakkal

last: Deepak

first: Marco

last: Colonna


title: POU3F2 regulates canonical Wnt signaling via SOX13 and ADNP to expand the neural progenitor population [CUTRUN_POU3F2NPCs]

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Loss-of-function mutations in the transcription factor POU3F2 have been identified in individuals with neurodevelopmental disorders. To elucidate the mechanistic role of POU3F2 in human neurodevelopment, we induced POU3F2 disruption in human neural progenitor cells (NPCs). Mutation of POU3F2 in NPCs causes reduced baseline canonical Wnt signaling and decreased proliferation, resulting in premature specification of radial glia. Additionally, POU3F2 levels across genetically diverse NPCs significantly associate positively with baseline canonical Wnt signaling and negatively with markers of radial glia specification. Through a series of unbiased analyses, we show that SOX13 and ADNP are transcriptional targets of POU3F2 which mediate POU3F2’s effects on Wnt signaling in human NPCs. Finally, we describe five individuals with autism spectrum disorder that harbor loss-of-function mutations in POU3F2, enhancing the genetic evidence for its critical role in human neurodevelopment. Together, these studies define POU3F2 as an activator of canonical Wnt signaling and mechanistically link two high-confidence autism genes, ADNP and POU3F2, in the regulation of neurodevelopment.

overall_design: CRISPR/Cas9-edited and respective control iPSC lines were differentiated into neural progenitor cells (NPCs) using a dual-SMAD inhibition protocol adapted from Topol, et al. (2015). POU3F2 WT and MUT NPCs were harvested at D21 and subjected to CUT&RUN-sequencing. This data is presented in Figure 6D-G.

first: Richard

last: Pearse

first: Tracy

last: Young-Pearse


title: POU3F2 regulates canonical Wnt signaling via SOX13 and ADNP to expand the neural progenitor population [RNAseq_LWnt3aNPCs]

overall_design: CRISPR/Cas9-edited and respective control iPSC lines were differentiated into neural progenitor cells (NPCs) using a dual-SMAD inhibition protocol adapted from Topol, et al. (2015). POU3F2 WT and MUT NPCs were treated with L or Wnt3a conditioned media for 24 hours and subjected to RNA-sequencing. This data is presented in Figure 2E-J.


title: Overcoming resistance to anti-VEGF therapy via epigenetic regulation of BARD1 [methylation]

city: Houston

first: Emine

last: Bayraktar

address: 1881 East Road

institute: MD Anderson Cancer Center

summary: Genome wide DNA methylation profiling of anti-VEGF resistant SKOV3 tumor samples treated with B20 and/or Azacytidine. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in SKOV3 tumors. Samples included 2 control IgG, 2 Azacytidine, 2 B20 and 2 B20+Azacytidine treated SKOV3ip1 tumors.

overall_design: Bisulphite converted DNA from 8 samples were hybridised to the HumanMethylation 450 K Infinium Methylation BeadChip (Illumina)

first: Cristian

last: Rodriguez-Aguayo

first: Elaine

last: Stur

first: Sudhir

last: Kumar

first: Lingegowda

middle: S

last: Mangala

first: Nicholas

last: Jennings

first: Nazende

middle: N

last: Bayram

first: Sara

last: Corvigno

first: Mark

last: Kim

first: Thanh

last: Vu

first: Pahul

last: Hanjra

first: Adrian

last: Ahumada

first: Sanghoon

last: Lee

first: Anna

last: Szymanowska

first: Hulya

last: Oztatlici

first: Abhinav

last: Jain

first: John

middle: P

last: Hagan

first: Stephen

last: Baylin

first: Jinsong

last: Liu

first: Gabriel

last: Lopez-Berestein

first: Sunila

last: Pradeep

first: Anil

last: Sood


title: Overcoming resistance to anti-VEGF therapy via epigenetic regulation of BARD1 [SKOV3 BARD1 siRNA-RNASeq]

first: Emine

last: Bayraktar

summary: Despite widespread use of anti-vascular endothelial growth factor (VEGF) antibody (AVA) for cancer therapy, most patients develop progressive disease after initial response. Therefore, novel strategies are needed to understand and overcome AVA resistance. Here, we identify an unexpected role of BRCA1-associated RING domain 1 (BARD1) in overcoming adaptive resistance to AVA. We investigated the effects of epigenetic modulation on cellular response to AVA; in particular, the molecular effects of both global and targeted DNA methylation. Using in vitro assays, BARD1 was identified as being specifically involved in angiogenesis. Sequential treatment with azacytidine overcame AVA therapy resistance in cancer models in vivo. We further demonstrated that specifically targeting BARD1 with either small-interfering RNA or CpG-targeted demethylation reduced tumor growth when combined with AVA therapy (compared with AVA alone) in mouse models of ovarian cancer. These results identify a previously unrecognized role for BARD1 in tumor angiogenesis and show that targeted restoration of BARD1 can enhance the efficacy of AVA therapy in cancer models.

overall_design: To understand the effect of BARD1 silencing on tumor angiogenesis pathways, we performed RNA sequencing of BARD1-silenced SKOV3ip1 cells. We transfected SKOV3ip1 cells with BARD1 siRNA or control siRNA for 48h, then subjected to RNA isolation follewed by RNAsequencing.

first: Cristian

last: Rodriguez-Aguayo

first: Elaine

last: Stur

first: Sudhir

last: Kumar

first: Lingegowda

last: Mangala

first: Nicholas

last: Jennings


title: Time-resolved transcriptomics of S. cerevisiae and S. pastorianus in response to plasma membrane stresses

city: Kunigami-gun

first: Yuta

last: Yamazaki

address: Tancha 1919-1

country: Japan

institute: Okinawa Institute of Science and Technology

summary: Yeasts are beneficial microorganisms for human society and are utilized for academic and industrial purposes. For academic purposes, S. cerevisiae is a well-investigated model for studying eukaryotic cellular processes. For industrial purposes, S. pastorianus, which has a hybrid genome of S. cerevisiae and S. eubayanus, has been served for lager beer production. During fermentation, S. pastorianus produces ~7% of EtOH, which induces plasma membrane (PM)/cell wall stress in yeast. Therefore, S. pastorianus may experience PM stress and adapt to the self-forming environment during fermentation. However, how yeast adapts to PM stress remains unclear. Here, we investigated the temporal cellular responses of S. cerevisiae and S. pastorianus during adaptation to PM stresses by time-resolved mRNA-seq analysis. Our data showed different transcriptional phenotypes between S. cerevisiae and S. pastorianus during adaptation. The results may reflect the distinct nature of the two yeasts that have evolved in different nutritional environments. The dataset presented here would provide a promising resource for studying the characteristic nature of these differentially domesticated yeasts upon PM stresses.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces pastorianus

overall_design: Time-resolved RNA seq profiling of S. cerevisiae and S. pastorianus in response to plasma membrane stresses.

first: Fumihiko

last: Omura

first: Eiichiro

last: Ono

first: Nozomu

last: Kamada

first: Keiko

last: Kono


title: Spatial Proteomics and Transcriptomics Reveal Early Immune Cell Organization in Pancreatic Intraepithelial Neoplasia

status: Public on Jun 16 2025

city: Baltimore

first: Neeha

last: Zaidi

address: 1650 Orleans Street

institute: Johns Hopkins

summary: Background: Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate largely due to late detection of disease. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease progression––this provides an opportunity to intercept PanIN–to–PDAC progression. However, immune interception strategies require a full understanding of PanIN and PDAC cellular architecture. Methods: Surgical specimens containing PanIN and PDAC lesions from a unique cohort of treatment-naïve patients with PDAC were surveyed using spatial-omics (proteomic and transcriptomic). Results: We uncovered, for the first time, the organization of lymphoid cells into tertiary lymphoid structures (TLSs) adjacent to PanIN lesions. These TLSs lack CD21+CD23+ B cells in comparison to more mature TLSs. Mature TLSs were found near the invasive PDAC border, despite patients being treatment-naïve. PanINs harbored mostly CD4+ T cells with fewer Tregs and exhausted T cells than PDAC tumors. Peri-tumoral space was enriched with naïve CD4+ and central memory T cells. Conclusions: These data show that early PanIN lesions recruit effector lymphoid populations capable of organizing into immature TLSs with few immune suppressive T cells relative to PDAC-associated TLS. These results implicate the opportunity to modulate the immune microenvironment in pre–malignant PanINs before immune exclusion and immunosuppression emerge during progression into PDACs.

overall_design:
Resected pancreas tissue from 5 treatment-naïve patients with PanIN and chronic pancreatitis in association with pancreatic ductal adenocarcinoma (PDAC) underwent profiling of immune infiltrates surrounding these lesions. Infiltrates surrounding normal pancreatic ducts, PanIN ducts, PDAC tumors, and regions of chronic pancreatitis were profiled and compared by imaging mass cytometry and Visium spatial transcriptomics. Visium spatial transcriptomic data from samples CP04, CP05B, NRL04, PANIN02A, PANIN02B, PANIN04, and PANIN03 are available from GEO accession GSE254829 (GSM8058249 - GSM8058255, respectively).

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Melissa

last: Lyman

first: Jacob

middle: T

last: Mitchell

first: Sidharth

last: Raghavan

first: Luciane

last: Kagohara

first: Amanda

last: Huff

first: Saurav

middle: D

last: Haldar

first: Sarah

last: Shin

first: Samantha

last: Guinn

first: Benjamin

last: Barrett

first: Gabriella

last: Longway

first: Alexei

last: Hernandez

first: Erin

last: Coyne

first: Xuan

last: Yuan

first: Lalitya

last: Andaloori

first: Jiaying

last: Lai

first: Yunzhoum

first: Rachel

last: Karchin

first: Anuj

last: Gupta

first: Ashley

last: Kiemen

first: André

last: Forjaz

first: Denis

last: Wirtz

first: Pei-Hsun

last: Wu

first: Atul

last: Deshpande

first: Todd

last: Armstrong

first: Nilofer

last: Azad

first: Jacquelyn

middle: W

last: Zimmerman

first: Laura

last: Wood

first: Robert

last: Anders

first: Elizabeth

last: Thompson

last: Jaffee

first: Elana

middle: J

last: Fertig


title: CDC42 inhibitors regulate genes involved in skin vasculaization

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 839 Health Science Ct.

department: Dermatology

institute: University of California, Irvine

summary: RhoJ protein has 55% homology with CDC42 and is highly expressed in endothelial cells. Both proteins regulate migration and contraction in endothelial cells through the activation of typrosine kinase receptors that control angiogenesis. To better understand how CDC42 inhibitors modulate angiogenesis, we performed bulk RNA sequening on wildtype skin treated with 12 mg/kg ARN22089 or vehicle twice a day for a week. Expression profiling showed that CDC42 inhibitors modulate skin vascularization. Some of the genes downregulated after CDC42 inhibitor treatment in wildtype skin involves CDC42 signaling and cell adhesion and putative angiogenesis regulators including CD177, CCL12, and CD34. Endothelial markers such as Lyve1 and Cd34 were also downregulated.

overall_design: RNA-seq profiling of wildtype (WT) mouse skin and WT skin from WT mouse treated with 12 mg/kg of ARN22089 twice a day for one week.

first: Linh M

last: Vuong

first: Anand K


title: Treatment of LNCaP cells with novel PRMT5:MEP50 protein:protein interaction inhibitors

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: We developed a novel compound for inhibition of PRMT5:MEP50 protein:protein interaction. LNCaP prostate cancer cells were treated with Compound 17 for 72 hours. Cells were harvested, RNA isolated, and then submitted for RNA-sequencing,

overall_design: Three biological replicates of LNCaP cells were treated with PRMT5:MEP50 PPI inhibitor Compound 17 (also called MP18) or DMSO control. Cells were treated for 72 hours, RNA was isolated, and mRNA was sequenced to identify differentially regulated genes.

first: Mingji

last: Dai

first: Jun

last: Wan

first: Andrew

last: Asberry

first: Xinpei

last: Cai

first: Xuehong

last: Deng

first: Sheng

last: Liu

first: Ulises

last: Santiago

first: Hunter

last: Sims

first: Weida

last: Liang

first: Xueyong

last: Xu

first: Wen

last: Jiang

first: Carlos

last: Camacho


title: Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Single-cell RNA-seq]

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

summary: Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.

overall_design: Single-cell RNA sequencing of vertical, tension, and opposite stem differentiating xylem (SDX) in P. trichocarpa

first: Jo-Wei Allison

last: Hsieh

first: Pin-Chien

last: Liou

first: Chia-Chang

first: Xiufang

first: Chen-Wei

first: I-Fan

last: Wang

first: Jr-Fong

last: Dang

first: Yi-Chi

last: Ho

first: Kai-Wen

last: Cheng

first: Wenjing

first: Shang-Che

last: Kuo

first: Chung-Ting

last: Kao

first: Dian-Xuan

last: Yang

first: Ray

first: Ke

last: Xiao

first: Jeng-Shane

first: Cheng-Chih

last: Hsu

first: Chuan-Chih

first: Te-Lun

last: Mai

first: Yuxiang

first: Mei-Chun

last: Tseng

first: Wei

last: Li

first: Ying-Lan

last: Chen


title: Overcoming resistance to anti-VEGF therapy via epigenetic regulation of BARD1

first: Emine

last: Bayraktar


title: RSK1-driven TRIM28-E2F1 feedback loop promotes castration-resistant prostate cancer progression

city: lexington

first: ka wing

last: Fong

state: KY

address: 760 press ave

institute: University of Kentucky

summary: Castration-resistant prostate cancer (CRPC) marks the advanced and lethal stage of prostate cancer (PCa). TRIM28, also known as KAP1, is a transcriptional regulator recently shown to promote CRPC cell proliferation and xenograft tumor growth. Nonetheless, knowledge gaps persist regarding the mechanisms underlying TRIM28 upregulation in CRPC as well as the genomic targets regulated by TRIM28. Here, we report that TRIM28 is a novel E2F1-target in CRPC. Using an integrated genomic approach, we have demonstrated that TRIM28 forms a positive feedback loop to promote the transcription activation and genomic function of E2F1 independent of Rb status. Furthermore, we identified RSK1 as a kinase that directly phosphorylates TRIM28 at S473, and as such, RSK1 drives the TRIM28-E2F1 feedback loop. Accordingly, pS473-TRIM28 promotes CRPC progression, which is mitigated by RSK inhibition. In summary, our study reveals a critical role of the RSK1–TRIM28–E2F1 axis in CRPC progression, which may be exploited as a vulnerability in treating Rb-deficient CRPC.

overall_design: Examination of the genomic landscape of E2F1 and TRIM28 in human prostate cancer cells LNCaP and C4-2B cells. There are 11 CUT&RUN-seq and 4 ATAC-seq samples.

first: Fong

last: ka wing

first: Jinpeng

last: Liu

first: Ryan

last: Goettl


title: GPC2-Targeted CAR T Cells Engineered with NFAT-Inducible Membrane-Tethered IL15/IL21 Exhibit Enhanced Activity against Neuroblastoma

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

summary: T-cells redirected for antigen-unrestricted cytokine-initiated killing (TRUCKs) are engineered chimeric antigen receptor (CAR) T-cells that constitutively or inducibly release cytokines upon CAR engagement. Their purpose is to enhance the function of effector cells in the immune-suppressive tumor microenvironment (TME) of particularly solid tumors that is often devoid of pro-inflammatory cytokines. We capitalize on the pleiotropic effects of two γc family cytokines, interleukin (IL)-15 and IL-21, and use them synergistically for TRUCK engineering. We demonstrate that TRUCKs with soluble IL-15/IL-21 eradicate CAR T-cell–resistant neuroblastoma, the most common extra-cranial solid tumor of childhood, but are associated with significant toxicities in mice. These toxicities can be delayed when we constitutively tether the cytokines to the surface of T-cells but are abrogated when we engineer CAR T-cells with NFAT-induced membrane-tethered IL-15/IL-21 expression.

overall_design: To investigate the difference in splenocyte population and tumor microenvironment status between GPC2-CAR T cells expressing membrane tethered cytokines constitutively or conditionally (by NFAT system), we inoculated mice orthotopically with neuroblastoma cell line IMR-5 or a PDX; SJNBL013762. Around 3 weeks after the tumor injection, we injected the following GPC2-CAR T cells via tail vein. 1) Untransduced control T cells, 2) CAR T cells, 3) CAR T cells with mteth.IL15.IL21, 4) CAR T cells with NFAT.mteth.IL15.IL21. After 5-6 weeks after the CAR T injection, we harvested spleens and tumors from mice treated with 3) or 4). As for 4), we included samples from good responders and poor responders. After enzymatic dissociation, the cells were analyzed using scRNA seq.

first: Rosa

last: Nguyen

first: Reona

last: Okada


title: Human cytomegalovirus induces neuronal gene expression to promote virion maturation in macroH2A1-dependent manner

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Human cytomegalovirus (HCMV) uniquely remodels host cells, generating a cytoplasmic viral-induced assembly compartment (vIAC) and a kidney-bean-shaped nucleus. How these stark morphology changes take place in the context of host gene regulation is still emerging. Here, we discovered that HCMV titers, but not virus particle numbers, were significantly reduced in the absence of the histone variant macroH2A1, indicating that macroH2A1 is essential for producing infectious progeny. Because virion maturation and cellular remodeling are closely linked processes, we used confocal and electron microscopy to define structural changes in the host cell. We uncovered that HCMV-induced reorganization of the host nucleus, cytoskeleton, and endoplasmic reticulum does not occur in the absence of macroH2A1. Furthermore, we discovered using RNA-seq that while all viral genes were highly expressed in the absence of macroH2A1, many HCMV-induced host genes were not. Hundreds of these HCMV-induced macroH2A1-dependent host genes are associated with neuronal synapse formation and vesicle trafficking. Knock-down during infection of several HCMV-induced neuronal genes resulted in malformed vIACs and smaller plaques, establishing their importance to HCMV infection. Together, our findings demonstrate that HCMV manipulates host gene expression to hijack the dormant neuronal secretory pathway for proper virion maturation.

overall_design: RNA-seq of MRC5 cells expressing dox-incucible IE1, IE1ΔCTD, IE2, or Luciferase (PMID:21533215)  treated for 48 hours with dox. MRC5s with no transgene and no dox treatment included as control.

first: Laurel

last: Kelnhofer-Millevolte

first: Julian

last: Smith

first: Hannah

last: Lewis

first: Lea

last: Wilson

first: Daniel

first: Edward

last: Arnold

first: Mia

last: Brinkley

first: Kihye

last: Shin

first: Jin-Hyun

last: Ahn

first: Eui-Tae

last: Kim

first: Katarzyna

last: Kulej

first: Adam

last: Geballe

first: Daphne

last: Avgousti


title: ATAC-seq analysis of wildtype and ETV2-overexpressing embryoid body-derived progenitor cells

city: Minneapolis

last: Garry

state: Minnesota

address: 2231 6th Street SE, Suite 4-156

department: Lillehei Heart Institute

institute: University of Minnesota

summary: Wild-type (WT) and Etv2-overexpressing (OE) mouse embryonic stem cells (mESC) were cultured and differentated to embryoid bodies (EBs) in mesodermal conditions. Induction of Etv2 in OE EBs was achieved by the addition of doxycycline. Cells were collected at different time points (i.e., D2, D3, D4 for WT and D3, D4 for OE EBs) following FACS sorting based on the presence or absence of two surface markers: Flk1 (F+/-) and Pdgfrα (P+/-). ATAC-seq was performed using 50,000 cells and the Tn5 transposase enzyme. Sequencing of libraries was carried out on the Illumina NextSeq platform (2×50 bp). Chromatin accessibility profiling revealed that Etv2 overexpression during EB differentiation increases accessibility of genes related to the hematoendothelial lineage, while reducing accessibility of genes associated with the cardiac lineage.

overall_design: A total of 13 samples (each with 2 replicates) were used for the analysis. The following list shows the sample with the annoation format as Day_Surface-Marker_Condition:  For WT EBs the samples are D2_P-F-_WT,  D3_P-F-_WT, D3_P+F-_WT, D3_P+F+_WT, D3_P-F+_WT, D4_P-F-_WT, D4_P+F-_WT, D4_P+F+_WT and D4_P-F+_WT. For OE EBs the samples are D3_P-F-_OE, D3_P-F+_OE, D4_P-F-_OE, and D4_P-F+_OE.

first: Kidus

last: Hailemariam

first: Satyabrata

last: Das

first: Xiao

last: Ma


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR

city: Seattle

first: Pete

last: Nelson

state: WA

address: 1100 Eastlake Ave E

department: Human Biology

institute: Fred Hutch Cancer Center

summary: Comprehensively understanding the gene regulatory network that modulates the biology of the Androgen Receptor (AR) oncogene is a central goal of prostate cancer research. To study regulators of AR, we knock-in a split neon green fluorescent protein onto the AR in prostate cancer cells creating an endogenous AR reporter cell line. Using our endogenous AR reporter, we performed a genome-scale fluorescence-activated cell sorting based CRISPRi screen to comprehensively identify genes that modulate AR protein levels. We identify and validate known AR protein regulators including HOXB13, GATA2, GRHL2 as well as unexpected top hits including PTGES3, SAE1 and CSNK2A1. Loss of PTGES3 in multiple models of ARSI-resistant Pca resulted in loss of AR protein and thus AR’s oncogenic activity. Mechanistically, we demonstrate a novel nuclear co-factor function of PTGES3 facilitating AR-mediated transcription aside from its canonical co-chaperone function regulating AR protein levels. Lastly using a disulfide tethering chemical screen, we developed a PTGES3 inhibitor demonstrating PTGES3 is a therapeutically tractable target for the treatment of AR-addicted mCRPC.

overall_design: ChIP-seq of the androgen receptor (AR) in LNCaP-sgCtrl and LNCaP-sgPTGES3 cells grown in complete growth medium (RPMI 1640 medium with 10% FBS).

first: Wanting

last: Han

first: Haolong

last: Li


title: Targeting SUMOylation triggers interferon-beta-dependent activation of patient and allogenic Natural Killer cells in preclinical models of Acute Myeloid Leukemia [CUT&RUN]

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

summary: Natural Killer (NK) cells are critical actors of the anti-tumoral immune response. However, NK cells are often dysfunctional in cancer patients, particularly in hematological malignancies like Acute Myeloid Leukemias (AML), where patients typically exhibit low NK cells numbers and activity. In addition, there is increasing interest in using allogenic NK cells transplantation as cancer immunotherapy. New strategies are however required to both reactivate NK cells in cancer patients and enhance the anti-tumor activity of transplanted NK cells. Here, we demonstrate that targeting SUMOylation, a protein post-translational modification, activates NK cells from both healthy donors and AML patients. Subasumstat (TAK-981), a first-in-class inhibitor of SUMOylation used in phase I/II clinical trials, enhances NK cells degranulation, secretion of inflammatory cytokines (IFN-γ, TNF-α, FasL) and cytotoxicity against AML cells. In vivo, TAK-981 improves the anti-leukemic efficacy of ex-vivo expanded cord-blood NK cells in leukemia-bearing mice. One early effect of TAK-981 is to specifically increase the accessibility and activation of cis-regulatory regions of interferon pathway genes and induce their transcription. TAK-981 induces the secretion of interferon-beta, mostly by NK cells and monocytes, which is required for NK cells activation. Surprisingly, IFNB1 induction is independent of MDA5, cGas, IRF-1, -3 and -7. Altogether, this suggests that targeting SUMOylation activates a non-canonical interferon pathway able to boost NK cells anti-leukemic potential.

overall_design: DNA from NK cells purified from 2 differents healthy donors and treated or not with TAK-981 for 6 h were subjected to CUT&RUN using anti-H3K27acetyl antibodies or rabbit IgG antibodies as a non-specific control. Drosophila melanogaster spike-in DNA was used as downstream analysis normalizer.

first: Rawan

last: Hallal

first: Guillaume

last: Bossis


title: Transcriptomic footprinting following restoration of p53 sequence and function utilising Adenine Base Editing

city: Dresden

first: Frank

last: Buchholz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: The tumor suppressor TP53 is the most frequently mutated gene in human cancer. Here, we utilised a Adenine Base Editing system to efficiently repair the p53-R273H hotspot mutation in four cancer cell lines of different origins followed by transcriptomic analysis at three different timepoints to unveil the molecular network of p53 tumor suppression. Moreover, we were able to repair the p53-R175H hotspot in two cell lines of different origins. Our data demonstrates that recovery of wildtype TP53 leads to restoration of p53 function and suggests a preserved network of p53's tumor-suppressive activities following mutation repair that is irrespective of cell type, mutation profile, and epigenetic cell state. Furthermore, we attempted correcting a nonsense mutation in the tumor suppressor gene SMAD4 in one cell line leading to a progressive depletion of cancer cells, albeit with a milder phenotype compared to the one following TP53 repair. Taken together, our data provide a molecular framework following driver mutations repair, besides providing insights into key players orchestrating transcription leading to cell apoptosis. Our findings demonstrate the utility of this Base Editing system to systematically interrogate the functional consequences of cancer driver mutations and the downstream effects on gene expression.

overall_design: RNA-seq profiling of p53-repaired cells compared to their non-repaired (p53-mutant) counterparts at 36 hours post infection (hpi), 48hpi and 72hpi.

first: Pascal

last: Wang

first: Shady

last: Sayed

first: Rituparno

last: Sen


title: Targeting SUMOylation triggers interferon-beta-dependent activation of patient and allogenic Natural Killer cells in preclinical models of Acute Myeloid Leukemia [ATAC-seq II]

overall_design: DNA from NK cells purified from 2 differents healthy donors and treated or not with TAK-981 for 6 h were tagmented using Tagment DNA Enzyme 1 followed by sequencing.


title: Bulk RNA-Seq of Bone Marrow-Derived Macrophages Exposed to Avirulent Coccidioides posadasii (Δcts2/Δard1/Δcts3)

city: Livermore

first: Dina

last: Weilhammer

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

summary: To verify that Spp1+ macrophage differentiation is contact dependent, macrophages were exposed to Coccidioides in vitro directly, or indirectly via conditioned media (cm), and expression of the gene signature was evaluated by RNA-seq.

overall_design: First, we differentiated macrophages with each cytokine and subsequently exposed them to Coccidioides in vitro. GM-CSF differentiated bone marrow-derived macrophages (GM-BMDM) and M-CSF differentiated macrophages (M-BMDM) were incubated overnight with Coccidioides arthroconidia. Next, to determine if Spp1 induction was contact-dependent, fresh GM-BMDM were exposed to CM collected from control GM-BMDM or GM-BMDM incubated with Coccidioides (GM-BMDM + cocci). RNA-seq was conducted on RNA isolated from the following groups: GM-BMDM, GM-BMDM + CM, GM-BMDM + cocci, and GM-BMDM + cocci CM.

first: Nadia

last: Miranda

first: Oscar

middle: A

last: Davalos

first: Aimy

last: Sebastian

first: Bria

last: Gorman

first: Katrina

last: Hoyer


title: Ataxia-telangiectasia mutated kinase disruption enhances the efficacy of radiation therapy in spatially-directed diffuse midline gliomas

city: Durham

first: Vennesa

last: Valentine

state: NC

address: 308 Research Drive

institute: Duke Univerisity

type: Methylation profiling by high throughput sequencing

summary: Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by p53-inactivating mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress. Using RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce native H3.3K27M mutations in a lineage- and spatially-directed manner, we generated primary mouse tumors that recapitulate human DMG. Disrupting ataxia-telangiectasia mutated kinase (ATM) enhanced the efficacy of radiation therapy in murine and patient-derived DMG models, increasing survival. Microscopy-based in situ sequencing was used to spatially resolve transcriptional profiles in >750,000 single cells with or without ATM disruption and radiation therapy, revealing altered immune-neoplastic and endothelial cell interactions after treatment. An allelic series of primary murine DMG models with different p53 mutations confirmed that transactivation-independent p53 activity is a key mediator of radiosensitivity after ATM disruption. Our findings contribute primary DMG mouse models with deep profiling and reveal the mechanisms of treatment response to an actionable therapeutic strategy.

overall_design: Bisulfite methylation sequencing and data analysis were performed by Novogene. Briefly, K27M mutant (nPH) and matched K27M wildtype (nP) tumor-bearing mice (n = 4 biological replicates per group) were generated, and tumor-bearing brains embedded in FFPE. Tumor regions were identified in the brains on matched H+E slides, and tumor microdissection was performed . Genomic DNA was isolated, spiked with lambda bacteriophage DNA (to serve as an internal negative control), fragmented to 200-400 base pairs, and bisulfite treatment was performed to convert unmethylated cytosines into uracil via deamination. After methylation sequencing adapter ligation, double strand DNA synthesis, and library size selection, PCR amplification was performed followed by Illumina sequencing. FastQC was used for quality control on the raw reads.


title: Genomic and immune profiling of prognostic risk groups in IgM gammopathy reveals novel biomarkers beyond MYD88 L265P

city: Barcelona

first: David

middle: F.

last: Moreno

state: Barcelona

address: Villarroel 170

department: Hematology

institute: IDIBAPS - Hospital Clínic de Barcelona

summary: Bone marrow samples were obtained from each patient and underwent CD19+ enrichment by immunomagnetic beads to obtain a purity of at least 90% to perform targeted next generation sequencing covering 54 lymphoma driver genes. The remaining depleted samples underwent RNA isolation and further quantitative measurement of gene expression by the NanoString nCounter platform using the PanCancer Immune Profiling assay that involved 770 genes.

overall_design: The aim was to analyze transcriptomic signatures in immune cells for each prognostic risk category of IgM gammopathy patients

middle: F

first: Carlos

last: Fernández


title: Unveiling Clonal Cell Fate and Differentiation Dynamics: A Hybrid NeuralODE-Gillespie Approach

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

summary: Recent lineage tracing single-cell techniques (LT-scSeq), e.g., the Lineage And RNA RecoverY (LARRY) barcoding system, have enabled clonally resolved interpretation of differentiation trajectories. However, the heterogeneity of clone-specific kinetics remains understudied, both quantitatively and in terms of interpretability, thus limiting the power of bar-coding systems to unravel how heterogeneous stem cell clones drive overall cell population dynamics. Here, we present CLADES, a NeuralODE-based framework to faithfully estimate clone-specific kinetics of cell states from newly generated and publicly available human cord blood LARRY LT-scSeq data. By incorporating a stochastic simulation algorithm (SSA) and differential expression gene (DEGs) analysis, CLADES yields cell division dynamics across differentiation timecourses and fate bias predictions for the early progenitor cells. Moreover, clone-level quantitative behaviours can be grouped into characteristic types by pooling individual clones into meta-clones. By benchmarking with CoSpar, we found that CLADES improves fate bias prediction accuracy at the meta-clone level. In conclusion, we report a broadly applicable approach to robustly quantify differentiation kinetics using meta-clones while providing valuable insights into the fate bias of cellular populations for any organ system maintained by a pool of heterogeneous stem and progenitor cells.

overall_design: Haematopoietic stem and progenitor cells (CD34+) were isolated via FACS from human umbelical cord blood donors. Cells were cultured in conditions that promote the differentiation of cells towards Megakaryocyte, Erythroid and Myeloid lineages (MEM) with reduced levels of EPO cytokine. For barcode labelling, CD11c− CD34+ cells were seeded. LARRY lentivirus was added directly to the culture. After 24 hours, the virus was diluted. At 3, 10 and 17 days post-transduction, GFP+ and GFP− cells were FACS-sorted and sent for sequencing.

first: Mingze

last: Gao

first: Melania

last: Barile

first: Shirom

last: Chabra

first: Myriam

last: Haltalli

first: Emily

last: Calderbank

first: Yiming

last: Chao

first: Elisa

last: Laurenti

first: Yuanhua

last: Huang


title: Regulation of somatic hypermutation by higher-order chromatin structure [PRO-Seq]

city: Freiburg im Breisgau

first: Maximilian

middle: Christian

last: von der Linde

address: Stefan-Meier-Straße 17

department: Institute for Medical Bioinformatics and Systems Medicine (IBSM)

institute: University Medical Center Freiburg

summary: The generation of protective antibodies by somatic hypermutation (SHM) is essential for antibody maturation and adaptive immunity. SHM involves co-transcriptional mutagenesis of immunoglobulin variable (V) regions regulated by enhancers located hundreds of kilobases away. How 3D chromatin structure affects SHM is poorly understood. Here, we measure higher-order interactions on single alleles of the human immunoglobulin heavy chain locus (IGH) using Tri-C. We find that SHM is underpinned by a multiway hub wherein the V region is proximal to all enhancers. Cohesin-mediated loop extrusion is dispensable for IGH transcription and hub architecture. Transcription and mutagenesis of IGH switch regions, which are necessary for antibody class-switch recombination, creates new chromatin loops that can form without cohesin. However, these additional loops do not compromise hub integrity, V region transcription or SHM. Thus, antibody maturation occurs within a multiway hub accommodating several gene-enhancer loops wherein transcription and mutagenesis of different segments can occur non-competitively.

overall_design: Examination of the multiway-interactome at the IGH locus through the chromatin conformation caputure technique Tri-C.

first: Ursula

last: E. Schoeberl

first: Johanna

last: Fitz

first: Renan

last: Valieris

first: Bernd

last: Bauer

first: Daniel

last: Malzl

first: Kimon

last: Froussios

first: Julia

last: Costea

first: Franziska

last: Schmidt

first: Jeremy

last: Pflaum

first: Bianca

last: Bartl

last: Albrecht

first: Eva-Maria

last: Wiedemann

first: Adriana

last: Cantoran Garcia

first: Mihaela

last: Peycheva

first: Marta

last: Rizzi

first: Anton

last: Goloborodko

first: Israel

last: Tojal da Silva

first: Rushad

last: Pavri


title: Gene expression profile at single cell level of murine bone marrow derived CD71 positive cells

city: London

first: Antal

last: Rot

state: England

address: Charterhouse Square

department: Center of Microvascular Research

institute: Queen Mary University London

summary: We used single cell RNA sequencing to define the different stages of erythroid differentiation

overall_design: CD71 positive cells were FACS sorted from bone marrow of 3 different mice (wild-type C57 BL6J, UBC-Cre-ERT2, CXCR4 flox/flox UBC-Cre-ERT2)

last: Gutjahr

first: Esteban

last: Gomez


title: Rapid Epigenomic Classification of Acute Leukemia

city: Boston

first: Salvatore

last: Benfatto

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Acute leukemias (AL) are aggressive blood cancers that require precise molecular classification and urgent treatment. However, standard-of-care diagnostic tests are time and resource intensive and do not capture the full spectrum of AL heterogeneity. Here, we developed a machine learning framework to classify AL using genome-wide DNA methylation profiling. We first assembled a large reference cohort (n=2,540 samples) and defined 38 distinct methylation classes across AL lineages and age groups. A subset of methylation classes mirrored established AL categories defined by genetics, such as AML with CBFB::MYH11 and B-ALL with ETV6::RUNX1, while others revealed epigenetic heterogeneity not captured by standard-of-care testing alone, including four methylation classes associated with NPM1-mutant AML (HOXA/B-activated) and four with KMT2A-rearranged AML (HOXA-activated). Using this reference, we next developed a deep neural network model (MARLIN) for methylation-based AL classification from extremely sparse data, and applied this for rapid analysis of clinical samples profiled by nanopore sequencing. In a retrospective AL cohort, MARLIN-based classifications were concordant with standard-of-care diagnoses in 25/26 (96.2%) cases with high-confidence prediction scores, including samples of diverse lineages and molecular subtypes. In five additional patients presenting with suspected AL, we performed nanopore sequencing and MARLIN classification of clinical blood and bone marrow samples in real-time, typically achieving an accurate methylation class prediction in less than two hours from sample receipt and less than one hour of sequencing time. In summary, we present a DNA methylation-based machine learning framework for rapid AL classification in the clinic that can complement and enhance standard-of-care diagnostics.

overall_design:
We sequenced 19 retrospective acute leukemia samples on individual MinION runs with flow cell reloading to maximize read output and 15 retrospective acute leukemia samples profiled using sample barcoding and multiplexed sequencing with the PromethION platform. 5 prospective acute leukemia samples on individual MinION flow cells. We then perfomed DNA methylation profiling analysis.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Til

last: Steinicke

first: Maria de los Reyes

middle: R

last: Capilla Guerra

first: Andre

last: Monteleone

first: Evan

last: Chen

first: Gabriel

middle: K

last: Griffin

first: Volker

last: Hovestadt


title: A single-cell multiomics approach for simultaneous analysis of replication timing and gene expression

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

summary: Replication timing (RT) allows us to analyze temporal patterns of genome-wide replication, that is, if genes replicate early or late during the S-phase of the cell cycle. RT has been linked to gene expression in normal and diseased states such as cancer. However, studies done to date were on bulk cell populations that required tens of thousands of cells for RT analysis. Here, we developed an affordable novel single cell (sc)-multiomics approach to simultaneously analyze RT and gene expression from cells or nuclei. We used this approach to generate sc-RT profiles and sc-gene expression data from the well-established human liver cancer cell line, HepG2. We demonstrated that as few as 17 mid S-phase cells were sufficient to produce cell-type specific pseudo bulk RT profiles, that had a high correlation to previously published HepG2 bulk RT profiles. The sc-RT profiles allowed us to visualize how individual cells progressed through genome replication. We were also able to demonstrate high-resolution correlations between RT and gene expression within each individual cell, which to our knowledge, has not been done before. We observed trends conserved between individual cells, as well as cell-to-cell variations, which has not been possible so far with the bulk RT studies.

overall_design: gDNA and mRNA were simultaneoulsy extracted from single HepG2 nuclei. gDNA was processed using the sc-Repiseq and Kronos computational pipelines for Replication Timing (RT). mRNA was processed for gene expression analysis. RT and gene expression were analysed per cell and compared to bulk datasets. Correlations between RT and gene expression were drawn within each cell and across the HepG2 population.

first: Anala

middle: V

last: Shetty

first: Clifford

last: Steer

first: Walter

last: Low


title: Regulation of somatic hypermutation by higher-order chromatin structure [ChIP-Seq]

first: Maximilian

last: von der Linde

first: Ursula

last: E. Schoeberl

first: Johanna

last: Fitz

first: Renan

last: Valieris

first: Bernd

last: Bauer

first: Daniel

last: Malzl

first: Kimon

last: Froussios

first: Julia

last: Costea

first: Franziska

last: Schmidt

first: Jeremy

last: Pflaum

first: Bianca

last: Bartl

last: Albrecht

first: Eva-Maria

last: Wiedemann

first: Adriana

last: Cantoran Garcia

first: Mihaela

last: Peycheva

first: Marta

last: Rizzi

last: Goloborodko


title: IRF4 promotes immune-evasion and shapes the Tumor Microenvironment in Follicular Lymphoma

first: Geoffrey

last: Nelson

address: 45 Shattuck St

department: BCMP

institute: Harvard Medical School

summary: Twenty percent of follicular lymphoma (FL) patients relapse early with poor outcomes; however, the molecular mechanisms underlying this aggressive feature are unknown. Using a multiomics approach, we show that FL patients with elevated IRF4 expression (IRF4hi) have poor prognosis, dysregulated immune signaling, and a suppressive tumor microenvironment. Loss- and gain-of-function experiments in IRF4hi lymphoma cells, along with chromatin profiling, demonstrate that IRF4 impairs their interaction with T cells by repressing antigen presentation and co-receptor gene modules, while promoting the expression of cytokines that antagonize TFH and Treg functions. Additionally, IRF4 rewires tumor metabolism which restricts glucose availability to immune cells. Silencing of IRF4 inhibits tumor cell growth, and restores immune surveillance mechanisms, thus representing a promising target for therapy. Our data suggest that IRF4hi lymphoma cells co-opt a developmental mechanism used to exit the germinal center response in promoting a more aggressive cancer via engagement of multiple immune-evasive mechanisms.

overall_design: CUT&Tag profiling of H3K4me3, H3K4me1, H3K27ac, H3K27me3 in TMD8 cells with (IRF4 siRNA) and without (control) knockdown of IRF4.

first: Patrizia

last: Mondello

first: Stephen

last: Ansell

first: Karen

last: Adelman


title: Regulation of somatic hypermutation by higher-order chromatin structure

first: Maximilian

last: von der Linde

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Homeostatic pockets of interferon lambda-stimulated gene production in the intestine are associated with localized exposure to bacterial microbiota

city: Portland

first: Timothy

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary: Tolerance of enteric microbiota and clearance of potential pathogens is critical for gut homeostasis. We previously found that the healthy small intestine of mice contains discrete pockets of antiviral gene expression that depend on bacterial microbiota colonization and interferon lambda (IFN-λ) receptor expression by intestinal epithelial cells. We now use spatial transcriptomic profiling of homeostatic interferon response pockets to show that they contain a broader cytokine signature that is consistent with activation of innate immune sensors, including toll-like receptors (TLRs). Additionally, we find that these homeostatic innate immune responses are associated with increased local abundance of luminal bacteria, but not with particular bacterial species or defects in the epithelial barrier. We find that deficiency of the TLR adaptor MyD88 in hematopoietic cells significantly reduces the abundance of homeostatic innate immune pockets, and stimulation with the bacterial product lipopolysaccharide preferentially stimulates IFN-λ production by intestinal immune cells. We propose that localized and transient increases in bacterial microbiota proximity result in increased homeostatic uptake of TLR ligands, which stimulate resident immune cells to produce cytokines, including IFN-λ. These localized innate immune responses enhance the immunological barrier, maintaining homeostasis with beneficial microbes and protecting against potential occult pathogens that may be present among the luminal microflora.

overall_design: Regions of interest (ROI) from mouse small intestine sections were selected by RNAscope staining of tissue sections for Ifit1. ROI were isolated by laser capture microdissection on an Arcturus LCM instrument from unstained serial sections mounted on RNAse free membrane slides (Molecular Machines & Industries, #50102) using CapSure Macro LCM caps (ThermoFisher Scientific, #LCM0211). Positive regions and negative regions were separately captured and pooled from each mouse in RNA lysis buffer (Quick-RNA FFPE Miniprep, Zymo Research, cat#R1008).

first: David

last: Constant

first: Jacob

last: Van Winkle


title: Human cytomegalovirusinduces neuronal geneexpression to promote virionmaturationin macroH2A1-dependent manner

first: Srinivas

last: Ramachandran

overall_design: RNA-seq of WT and macroH2A1 KO HFF-t cells from 3 separate infections with Towne CMV at an MOI of 1 and harvested at 4,16,24,48,72 hours post infection. Uninfected aka "mock" cells included as control.

first: Laurel

last: Kelnhofer-Millevolte

first: Julian

last: Smith

first: Hannah

last: Lewis

first: Lea

last: Wilson

first: Daniel

last: Nguyen

first: Edward

last: Arnold

first: Mia

last: Brinkley

first: Adam

last: Geballe

first: Daphne

last: Avgousti


title: Characterizing dynamics and lineage of bihormonal cell in mammalian pancreatic islets [10X Genomics]

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

summary: The precise roles and prevalence of bihormonal cells within pancreatic islets are not fully understood. Here, we utilized genetically engineered mouse strains with specific fluorescent markers for pancreatic endocrine cells and advanced imaging flow cytometry to investigate the presence of bihormonal cells in adult mouse islets. Our results revealed a marginal presence of such cells, contradicting the hypothesis that transdifferentiation contributes significantly to β-cell restoration in diabetic mice or during pregnancy-induced β-cell proliferation. Employing single-cell RNA sequencing (scRNA-seq), we observed that Gcg+Ppy+ bihormonal cells closely resemble either α- or PP-cells, lacking distinct gene expression profiles. This finding suggests bihormonal cells may not represent a unique lineage but could be transitional states in cellular differentiation. Furthermore, a dual-genetic tracing approach revealed that embryonic Ins+Gcg+ cells differentiate into α-cells postnatally. By integrating gene co-expression network analysis with 10x Genomics scRNA-seq data, we established a hierarchical classification of endocrine cells in mouse and human islets, identifying distinct populations with minimal overlap in conserved genes between species. This study not only refines our understanding of bihormonal cells in islet function and development but also highlights the complexities in translating murine model findings to human applications, emphasizing the need for species-specific considerations in diabetes research and therapy development.

overall_design: scRNA-seq of mouse pancreatic bihormonal cells.

first: Cheng-Ran

first: Mao-Yang

last: He

first: Shuang

first: Xin-Xin

last: Yu

first: Peng

last: Peng

first: Yi-Ning

last: Wang


first: Maximilian

last: von der Linde

first: Ursula

last: E. Schoeberl

first: Johanna

last: Fitz

first: Renan

last: Valieris

first: Bernd

last: Bauer

last: Malzl

first: Kimon

last: Froussios

first: Julia

last: Costea

first: Franziska

last: Schmidt

first: Jeremy

last: Pflaum

first: Bianca

last: Bartl

last: Albrecht

first: Eva-Maria

last: Wiedemann

first: Adriana

last: Cantoran Garcia

first: Mihaela

last: Peycheva

first: Marta

last: Rizzi

first: Anton

last: Goloborodko

first: Israel

last: Tojal da Silva

first: Rushad

last: Pavri


title: Overcoming resistance to anti-VEGF therapy via epigenetic regulation of BARD1 [OVCAR8ip1 BARD1 overexpression]

city: Houston

first: Emine

last: Bayraktar

address: 1881 East Road

institute: MD Anderson Cancer Center

summary: Despite widespread use of anti-vascular endothelial growth factor (VEGF) antibody (AVA) for cancer therapy, most patients develop progressive disease after initial response. Therefore, novel strategies are needed to understand and overcome AVA resistance. Here, we identify an unexpected role of BRCA1-associated RING domain 1 (BARD1) in overcoming adaptive resistance to AVA. We investigated the effects of epigenetic modulation on cellular response to AVA; in particular, the molecular effects of both global and targeted DNA methylation. Using in vitro assays, BARD1 was identified as being specifically involved in angiogenesis. Sequential treatment with azacytidine overcame AVA therapy resistance in cancer models in vivo. We further demonstrated that specifically targeting BARD1 with either small-interfering RNA or CpG-targeted demethylation reduced tumor growth when combined with AVA therapy (compared with AVA alone) in mouse models of ovarian cancer. These results identify a previously unrecognized role for BARD1 in tumor angiogenesis and show that targeted restoration of BARD1 can enhance the efficacy of AVA therapy in cancer models.

overall_design: To understand the effect of BARD1 expression on tumor angiogenesis pathways, we performed RNA sequencing of BARD1-expressed OVCAR8ip1 cells. A BARD1-expressing OVCAR8 cell line was generated by transduction with a BARD1 plasmid (EX-Q0613-Lv122, GeneCopoeia, Inc). Lentivirus particles containing BARD1 open reading frames were produced using the Lenti-Pac HIV Expression Packaging Kit protocol (HPK-LvTR-20; GeneCopoeia) and transduced into OVCAR8 cells

first: Cristian

last: Rodriguez-Aguayo

first: Elaine

last: Stur

first: Sudhir

last: Kumar

first: Lingegowda

last: Mangala

first: Nicholas

last: Jennings

first: Nazende

last: Bayram

first: Sara

last: Corvigno

first: Mark

last: Kim

first: Thanh

middle: C

last: Vu

first: Pahul

last: Hanjra

first: Adrian

middle: L

last: Ahumada

first: Sanghoon

last: Lee

first: Anna

last: Szymanowska

first: Hulya

last: Oztatlici

first: Abhinav

last: Jain

first: John

last: Hagan

first: Stephen

last: Baylin

first: Jinsong

last: Liu

first: Gabriel

last: Lopez-Berestein

first: Sunila

last: Pradeep

first: Anil

last: Sood


title: ACOD1 regulates microglial arginine metabolism and inflammatory responses

status: Public on Jun 15 2025

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

summary: Itaconate is produced by inflammatory macrophages and negatively feedbacks on inflammation. It is synthesized by aconitate decarboxylase 1 (ACOD1) from cis-aconitate, a metabolite of the tricarboxylic acid cycle. Here, we studied the role of ACOD1 in the inflammatory response of microglia, the resident macrophage-like cells of the brain. Similarly to macrophages, ACOD1 deficient microglia displayed a stronger inflammatory response to lipopolysaccharide (LPS) compared to their wild type counterparts. ACOD1 deficiency reprogramed arginine metabolism by enhancing argininosuccinate synthesis in the expense of polyamine synthesis in an ACLY-dependent manner. These findings provide new insights in the immunometabolic role of ACOD1 in inflammatory microglia.

overall_design:
LPS versus PBS (in-vitro): Primary murine microglia were treated with 100 ng/ml LPS or carrier (PBS) for 4 h. Transcriptional changes were analyzed by bulk RNAseq.
LPS versus PBS (in-vivo): C57BL/6J mice were treated interaperitoneally with 3 mg/kg LPS or PBS and 4 h later whole brain  microglia (CD45intermCD11b+Ly6G-) were FACS sorted and analyzed by bulk RNAseq.
Acod1-/- versus Wt: Acod1-/- and Wt mice were treated interaperitoneally with 3 mg/kg LPS or PBS and 16 h later whole brain  microglia (CD45intermCD11b+Ly6G-) were FACS sorted and analyzed by bulk RNAseq.

first: V

middle: I

first: A

last: Sinha


title: Droplet-based RNA sequencing and chromatin accessibility of muscles from young and aged mice

city: Stanford

first: Yu Xin

last: Wang

state: California

address: 269 Campus Dr

institute: Stanford University School of Medicine

first: Helen

middle: M

last: Blau

first: Thach

last: Mai

first: Chris

last: Still


title: Overcoming resistance to anti-VEGF therapy via epigenetic regulation of BARD1 [BeadChip expression]

first: Emine

last: Bayraktar

summary: Despite widespread use of anti-vascular endothelial growth factor (VEGF) antibody (AVA) for cancer therapy, most patients develop progressive disease after initial response. Therefore, novel strategies are needed to understand and overcome AVA resistance. Here, we identify an unexpected role of BRCA1-associated RING domain 1 (BARD1) in overcoming adaptive resistance to AVA. We investigated the effects of epigenetic modulation on cellular response to AVA; in particular, the molecular effects of both global and targeted DNA methylation. Using in vitro assays, BARD1 was identified as being specifically involved in angiogenesis. Sequential treatment with azacytidine overcame AVA therapy resistance in cancer models in vivo. We further demonstrated that specifically targeting BARD1 with either small-interfering RNA or CpG-targeted demethylation reduced tumor growth when combined with AVA therapy (compared with AVA alone) in mouse models of ovarian cancer. These results identify a previously unrecognized role for BARD1 in tumor angiogenesis and show that targeted restoration of BARD1 can enhance the efficacy of AVA therapy in cancer models. (Microarray was used to investigate altered genes that have signature of anti-VEGF therapy resistance.)

overall_design: Total RNA was extracted and purified with RNeasy Mini Kit (#79104 QIAGEN). Concentrations were measured with NanoDrop (Thermo Scientific, Wilmington, DE, USA) and samples were run on the Illumina microarray Human HT-12_v4 Bead Chip gene expression array.

first: Cristian

last: Rodriguez-Aguayo

first: Elaine

last: Stur

first: Sudhir

last: Kumar

first: Lingegowda

middle: S

last: Mangala

first: Nicholas

middle: B

last: Jennings

first: Nazende

middle: N

last: Bayram

first: Sara

last: Corvigno

first: Mark

last: Kim

first: Thanh

last: Vu

first: Pahul

last: Hanjra

first: Adrian

last: Ahumada

first: Sanghoon

middle: P


title: Nucleosomes gate cofactor access to the transcription factor p53 [CUT&Run]

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

summary: The transcription factor p53 regulates cell cycle progression, apoptosis, and the DNA damage response. A large fraction of p53 resides in inaccessible chromatin, where it is unclear how nucleosomes impact p53’s ability to engage cofactors. We examined the interaction of p53 with the members of the ubiquitin proteasome system (UPS) on chromatin. At two distinct motif locations (SHL-5.7, +5.9), the viral E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. The corresponding cryo-EM structure finds USP7 intricately engaged with p53 and nucleosomes, with the TRAF domain contacting the nucleosome at SHL-5.7 sandwiched between the p53 tetramerisation and DNA-binding domains. The structures of p53 bound to USP7/nucleosomes and E6AP illustrate how chromatin imposes a barrier for some, albeit not all p53 interactors. Our work suggests a conceptual framework for how nucleosomes govern TF/cofactor interactions.

overall_design: Examination of p53 and USP7 in mouse embryonic stem cells. Includes p53 Cut and Run in p53-degron tagged mouse ESC lines under p53untreated/p53-activated conditions (duplicates), GFP Cut and Run  in constitutive GFP-expressing mouse ESC lines (duplicates).  Conditions to activate p53 performed for 4 hours.


title: Droplet-based RNA sequencing of single cells from injured and regenerating skeletal muscles of young and aged mice

first: Yu Xin

last: Wang

summary: Single-cell RNA sequencing of cells from healthy and notexin injured muscles in a time course. To ensure we capture a wide variety of cell types and myogenic states, cells from uninjured and injured timepoints were mixed for each droplet-generation and sequencing run.

overall_design: Examination of transcriptomes of single cells and myogenic cell states of cells found in healthy and regenerating muscles of young and aged mice.

first: Helen


title: Characterizing dynamics and lineage of bihormonal cell in mammalian pancreatic islets [Smart-seq3xpress]

first: Cheng-ran

last: Xu

first: Cheng-Ran

first: Mao-Yang

last: He

first: Shuang

first: Xin-Xin

last: Yu

first: Peng

last: Peng

first: Yi-Ning


title: Chromatin accessibility of young and aged muscle stem cells in response to prostaglandin E2

summary: Assessment of openly accessible chromatin regions in young and aged muscle stem cells and short term epigenetic response to prostaglandin E2 treatment.

overall_design: Examination of chromatin accessibility of muscle stem cell changes that occur with aging and how these cells respond to prostaglandin E2 (PGE2).

last: Blau

first: Glenn

last: Markov

first: Meenakshi

last: Ravichandran


title: APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition [bulk RNA-seq]

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: The Christchurch mutation (R136S) on the APOE3 (E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high levels of amyloid beta pathology in the carrier. However, the specific molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse ApoE with wild-type human E3 or E3S/S on a tauopathy background. The R136S mutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, the R136S mutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-type E3 with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by the R136S mutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects of R136S against tauopathy.

overall_design: bulk RNAseq of primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau

first: Sarah

last: Naguib

first: Chloe

last: Lopez-Lee

first: Eileen

last: Torres

first: Se-In

last: Lee

first: Jingjie

last: Zhu

first: Daphne

first: Pearly

last: Ye

first: Kendra

last: Norman

first: Mingrui

last: Zhao

first: Man Ying

last: Wong

first: Yohannes

middle: A

last: Ambaw

first: Rodrigo

last: Castaneda

first: Wei

first: Tark

last: Patel

first: Maitreyee

last: Bhagwat

first: Rada

last: Norinsky

first: Sue-Ann

last: Mok

first: Tobias

last: Walther

first: Robert

last: Farese

first: Wenjie

last: Luo

first: Subhash

last: Sinha

first: Zhuhao

last: Wu

last: Fan

first: Shiaoching

last: Gong


title: APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition

first: Li

last: Gan

overall_design: snRNAseq of hippocampi to determine the effect of the APOE3 R136S mutation on tau pathology

first: Sarah

last: Naguib

first: Chloe

last: Lopez-Lee

first: Eileen

last: Torres

first: Se-In

last: Lee

first: Jingjie

last: Zhu

first: Daphne

first: Pearly

last: Ye

last: Wang


title: Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

first: Luke

last: Isbel

overall_design: Examination of p53 and USP7 in mouse embryonic stem cells. Includes Usp7 ChIPseq in mouse ESC lines under p53untreated/p53-activated conditions (duplicates), IgG control ChIPseq in wildtype mouse ESC lines (duplicates).  Conditions to activate p53 performed for 4 hours.


title: Nfkb1 removal from proximal tubule cells improves renal tubular outcomes following ischemia reperfusion injury

city: Los Angeles

first: Shun-Yang

last: Cheng

state: CA

address: 1425 San Pablo St

department: USC Stem cell - Eli and Edythe Broad Center for Regenerative Medicine

institute: University of Southern California

summary: Chronic kidney disease (CKD) is a significant global health burden. Acute kidney injury (AKI) is a risk factor for progression to CKD. Recent studies have linked a failure in proximal tubule repair as a potential contributing factor to CKD in mouse and human studies. Failed repair proximal tubule cells (FR-PTCs), initially present at the site of maximal sensitivity to ischemia reperfusion injury and spreading to more cortical regions over time, adopt a senescence-associated secretory phenotype (SASP) linked to activation of the NF-kB pathway. Several transcriptional regulatory factors mediate NF-kB pathway action. Of these, Nfkb1 is prominent within FR-PTCs and chromatin studies predict Nfkb1 interactions with pathology-associated gene targets. To examine the role of NF-kB in nephron injury outcomes, we removed Nfkb1 activity within the nephron lineage of the mouse kidney and examined the kidney’s response to bilateral ischemia reperfusion injury (Bi-IRI).

overall_design: In total 7 samples from Six2CreTGC/+;Nfkb1Null/c and Nfkb1c/c  mice were processed for snRNA-seq+snATAC-seq: three mice of Nfkb1c/c  at 4 weeks post-IRI; four mice of Six2CreTGC/+;Nfkb1Null/c at 4 weeks post-IRI.

first: Kari

last: Koppitch

first: Jinjin

last: Guo

first: Nathan

last: Moy

first: Taylo

last: Simonian

first: Parker

last: Wilson

first: Andrew

last: McMahon


title: Evaluation of phage-based treatments for combating Staphylococcus aureus biofilms on dairy surfaces

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

summary: The ability of Staphylococcus aureus to establish strong biofilms in milk poses a significant threat to the consumer’s health and a challenge for the dairy industry. Here, we have evaluated the efficacy of phage-based treatments (phage Kayvirus rodi and lytic protein LysRODI∆Ami) for combating biofilm formation on polystyrene and stainless steel surfaces submerged in UHT skim milk compared to growth medium. An adaptive transcriptional response was observed in cells intended to metabolize lactose and to increase biofilm formation. Also, biofilms grown in milk exhibited a denser and more complex matrix, mainly composed of proteins, presumably casein. These changes in matrix composition and structure offered a high resistance to both LysRODI∆Ami (4 µM) and phage Kayvirus rodi (108 PFU/ml) individual treatments, although combination of the two led to some reduction in the number of attached cells. Both antimicrobials were more successful at biofilm inhibition, exhibiting a synergistic interaction when used together. Unexpectedly, the bacteriophage treatment exhibited enhanced efficacy to prevent biofilm development in milk compared to fresh medium. The shift in matrix composition and pH modulation might be behind these differences. This research contributes to the development of innovative strategies for ensuring milk quality and safety. Moreover, our results demonstrate the importance of testing antimicrobials under conditions that reflect the real-life application as much as possible.

overall_design: 6 samples were analyzed, correponding to 3 biological replicates of 24 hours biofilms formed by S. aureus 15981 in MILK ºC or TSBg

first: Seila

last: Agún

first: Lucía

last: Fernández

first: Ana

last: Rodríguez

first: Pilar

last: García


title: Embryonic motor neuron programming factors reactivate immature gene expression and suppress ALS pathologies in postnatal motor neurons

city: Piscataway

first: Tulsi

last: Patel

state: New Jersey

address: 683 Hoes Lane West

department: Neuroscience and Cell Biology

institute: Rutgers University

summary: Aging is a major risk factor in amyotrophic lateral sclerosis (ALS) and other adult-onset neurodegenerative disorders. Whereas young neurons are capable of buffering disease-causing stresses, mature neurons lose this ability and degenerate over time. We hypothesized that the resilience of young motor neurons could be restored by re-expression of the embryonic motor neuron selector transcription factors ISL1 and LHX3. We found that viral re-expression of ISL1 and LHX3 reactivates aspects of the youthful gene expression program in mature motor neurons and alleviates key disease-relevant phenotypes in the SOD1G93A mouse model of ALS. Our results suggest that redeployment of lineage-specific neuronal selector transcription factors can be an effective strategy to attenuate age-dependent phenotypes in neurodegenerative disease.

overall_design: Sun1-sfGFP-Myc mice were either injected with AAV-Isl1+AAV-Lhx3 at P1 (6 mice, Treatment group) or left untreated (8 mice, Control group). At P21 GFP+ nuclei were separately FAC sorted from treatment and control mice. Brachial and lumbar regions of the spinal cord were dissection and nuclei were isolated and sorted following the exact protocol detailed in Patel et al. 2022, Nature Communications. All nuclei collected (~60,000 from six treatment mice and ~80,000 from eight control mice) were taken to the Genome Center at Columbia University, where they were counted, and processed using 10x multiome kit and 10x Chromium. Data was pre-processed using CellRanger by the Genomics Core. Alignment of sequencing reads were performed using both the standard mm10 genome and a custom genome that included 4 extra genes present in the AAV driven mRNA- the hIsl1 and hLhx3 coding sequences, chimeric-intron, and WPRE.

first: Patel

last: Tulsi

first: Lowry

last: Emily

first: Wichterle

last: Hynek


title: PIK3CA and KRAS codon-specific mutations differentially toggle pathway activity and alter sensitivity to inavolisib (GDC-0077)

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: To explore the single and combinatorial effect of MEK and PI3KCA inhibitors in CRC lines with PIK3CA/KRAS mutations, we used the MULTI-seq CMOs to perform a highly multiplexed single-cell RNA-seq.

overall_design:
Four different CRC lines, GP2d, LS174T, T84 and HCT116 were treated with either with single drug or the combinations. We harvested the cells at 24 hours and 96 hours after the treatment. Two biological duplicates were collected for each condition, and in total there are 64 samples. Upon harvesting, we trypsinized all the cells and labelled each sample with a unique CMO tag. After that, every 32 samples from the same biological duplicate were combined into one cell pool (two pools in total) and a FACS was performed on each pool to get rid of the dead cells. Eventually, we loaded each cell pool on 3 10X Genomics 3' scRNA-seq lanes and a total of 6 runs were performed. In this project, there are 6 transcriptome libraries and 6 corresponding CMO libraries. The results from T84 cell lines showed that they were of low quality and they were removed from CountMatrix.mtx and Metadata.txt
Please note that each sample represents mixed sample, multiplexed experiment and that the barcode labels for demultiplexing are included as a supplemental file along with the cell assignment.

first: Russell

last: Xie

first: Michal

last: Kabza


title: The high-throughput shRNA cleavage assays on 46,000 variants

status: Public on Jun 14 2025

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: DICER-LIKE1 (DCL1), a plant-specific RNase III enzyme, is fundamental to post-transcriptional gene regulation mediated by microRNAs (miRNAs). DCL1 processes precursor miRNAs into mature miRNAs, typically 20–22 nucleotides in length. Despite its crucial role, the RNA elements that guide DCL1's cleavage site selection have remained largely uncharacterized. In this study, we employed a high-throughput sequencing approach to analyze Arabidopsis thaliana DCL1 cleavage patterns on over 46,000 short-hairpin RNA (shRNA) sequences previously studied with human DICER. Our analyses revealed that DCL1 cleavage preferences are governed by specific secondary RNA structures and sequence motifs, among which a particular RNA element, designated the GHR motif, emerged as pivotal. This motif significantly influences cleavage site selection independently of the dsRBD and helicase domains of DCL1, operating primarily through the RNase IIIDa domain. Notably, the GHR motif is evolutionarily conserved across plant species and is essential for the precise cleavage of various plant pre-miRNAs. Our findings also suggest a novel role for the GHR motif in the biogenesis of non-canonical 22-nt miRNAs, expanding its functional impact. These insights deepen our understanding of the molecular mechanisms underlying DCL1's specificity and highlight its integral role in miRNA maturation and gene regulatory networks in plants.

overall_design: 46,000 shRNA variants were processed by plant DCL1 in vitro. The original substrates and cleaved products were cloned and sequenced.

first: Tuan Anh

first: Trung Duc

first: Thi Nhu Y

last: Le


title: Transmission of Maternal Oral Pathobionts to the Infant Gut Predisposes Offspring to Exacerbated Enteritis.

status: Public on Jun 13 2025

city: Ann Arbor

first: Yeji

last: Kim

state: Michigan

address: 1150 W Medical Center Dr

institute: University of Michigan

summary: The goal of this study was to understand the link between maternal oral dysbiosis and the gut health of offspring. We demonstrate that maternal oral dysbiosis can have lasting health impacts on offspring. Ligature-induced periodontitis in mothers promotes the expansion of oral pathobionts in the mouth, which are transmitted to the infant gut, rendering offspring more susceptible to enteritis. Notably, although these maternal oral pathobionts are eradicated as the microbiota matures, the imprinted susceptibility to enteritis persists into adulthood.

overall_design: To compare gene expression in small intestine tissues from pups born to control dams and dams with periodontitis, we performed the bulk RNA-sequencing. Four groups of pups, 5 samples per group. Group 1: pups at 7 weeks born to dams with periodontitis. Group 2: control pups at 7 weeks. Group 3: pups at 2 weeks born to dams with periodontitis. Group 4: control pups at 2 weeks.

first: Masafumi

last: Haraguchi

first: Natsuru

last: Watanabe

first: Kyoko

last: Yamazaki

first: Kira

last: Newman

first: Merritt

middle: G

last: Gillilland III

first: Yijie

last: Guo

first: Daisuke

first: Ingrid

last: Bergin

first: Takehiro

last: Suzuki

last: Motooka

first: Kohei

last: Sugihara

first: Sho

last: Kitamoto

first: Hiroko

last: Nagao-Kitamoto

first: Nobuhiko

last: Kamamda


title: Hydrolysis of 2-Arachidonoglycerol by Pig Liver Esterase Enhances Inflammation Induced by Porcine Reproductive and Respiratory Syndrome Virus Infection

city: Wuhan

first: Deshi

last: shi

address: hongshanqu

institute: Huazhong Agriculture University Department of Veterinary Medicine

summary: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection induces a robust inflammation in pigs, characterized primarily by severe interstitial pneumonia. It is crucial to elucidate the mechanism of dysregulation of inflammatory mediators during PRRSV infection. This study investigated the function and molecular mechanisms of porcine liver esterase (PLE) in modulating the inflammation induced by PRRSV. Firstly, it was determined that PLE exhibits high expression levels in porcine alveolar macrophages (PAMs), mainly expressing the PLE6 which has high hydrolytic activity. Subsequent experimental investigations demonstrated that the inhibition of PLE activity or PLE knockdown significantly attenuated PRRSV-induced pro-inflammatory cytokines production. At the same time, it was found that the hydrolysis substrate of PLE, endocannabinoid-2-arachidonoglycerol (2-AG), could inhibit the expression of pro-inflammatory cytokines induced by PRRSV. Notably, this anti-inflammatory effect was abolished upon 2-AG hydrolysis, which exacerbated the inflammation. Subsequently, in vivo studies were performed to validate that the inhibition of PLE activity effectively weakened the hydrolysis of 2-AG and mitigated PRRSV-induced inflammation, alleviated lung tissue damage. Transcriptomic analysis identified the PI3K-Akt signaling pathway is important for PLE to modulate PRRSV-mediated inflammatory processes. Finally, mechanistic validation in PAMs demonstrated that both inhibition of PLE activity and 2-AG administration effectively suppressed the activating of the PI3K-Akt-NF-κB signaling cascade by PRRSV, particularly by inhibiting phosphorylation of Akt and p65. In conclusion, our findings demonstrate that PLE exacerbates PRRSV-induced inflammation through the hydrolysis of 2-AG. This study finds a novel mechanism of inflammation pathology caused by PRRSV, and can provide theoretical basis for PRRS control.

overall_design: To investigate the effects of BNPP treatments on PRRSV infected pigs , we randomly divided experimental piglets into three groups (n=5 per group). Following treatment administration, PAMs were isolated from each group using standard bronchoalveolar lavage . Subsequently, total RNA was extracted from PAMs and subjected to high-throughput transcriptome sequencing  . The resulting sequencing data were processed through quality control, alignment to the porcine reference genome (Sus scrofa 11.1), and quantification of gene expression levels. Differential gene expression analysis was performed using DESeq2 (|log2FC| > 1, adjusted p-value < 0.05), followed by functional enrichment analysis (GO and KEGG) to identify significantly altered biological pathways.

first: Yuelin

last: Fu

first: Huiwen

last: Zhu

first: Qiling

last: Xiao

first: Qi

last: Chen

first: Qiongqiong

last: Zhou

first: Xiliang

last: Wang

last: Shi


title: Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish [Spatial Transcriptomics]

city: Durham

first: Liuyang

address: 213 Research Drive

institute: Duke University

summary: Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. We conducted spatial and single-cell RNA sequencing of clinical granuloma biopsy specimens from tuberculosis patients. We found that granulomas consist of concentric transcriptional laminae surrounding areas of central necrosis. Gene expression programs associated with regional architecture were conserved among samples. We identified distinct populations of granuloma-associated stromal cells, fibroblasts, lymphocytes, mast cells, dendritic cells, neutrophils and macrophages. Populations further differentiate into multiple granuloma-specific states that correlate with location. We used inferential analysis to predict dominant granuloma cell-cell interactions, the activity of major signaling pathways, and differential transcription factor activities. Using spatial deconvolution, we mapped a conserved pattern of cellular organization dominated by macrophages rich in osteopontin/SPP1 expression. Trajectory analysis of macrophage subtypes mapped their differentiation and supported the importance of SPP1 to granuloma macrophage polarization.  Cumulatively, we have identified a dominant macrophage granuloma population as well as its central regulatory gene in human samples and confirmed its importance to granuloma biology in vivo.

overall_design: To examine the interdependence of lesional architecture and gene expression, we evaluated the whole spatial transcriptomes of 4 samples from four different patients at 55 µM resolution (~5-10 cells) using the 10x Genomics Visium v2 with CytAssist assay.

first: Charlie

middle: J

last: Pyle

first: David

last: Tobin


title: Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish [scRNA-Seq]

overall_design: We processed tissue sections immediately adjacent to the Visium-imaged sections. We used these closely paired dissociated cells to determine at a single-cell level the transcriptional signature and cellular heterogeneity in human M. tb granulomas and then comprehensively mapped these transcriptional profiles onto the spatial analysis using deconvolution algorithms. To focus more deeply on granulomas in pulmonary tissue, the predominant site of TB disease, we processed 4 M. tb granuloma biopsy specimens resected from 3 patients with pulmonary TB.


title: Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation

summary: Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum-zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA-seq on flow-sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.

first: Rebecca

middle: W

last: Beerman


title: The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing

city: Cambridge

first: Colin

middle: Emory

last: Fowler

state: MA

address: 500 Main Street

department: Biology

institute: Massachusetts Institute of Technology

summary: Protein arginine methyltransferase 5 (PRMT5) is a promising cancer target, yet it is unclear which PRMT5 roles underlie this vulnerability. Here, we establish that PRMT5 inhibition induces a special class of unspliced introns, called detained introns (DIs). We used depletion of  CLNS1A, a PRMT5 cofactor that specifically enables Sm protein methylation to interrogate the impact of DIs. We found that disruption of Sm protein methylation is sufficient to induce DI upregulation, cell cycle defects, and loss of viability. Finally, we discovered that PRMT5-regulated DIs, and the impacted genes, are highly conserved across human, and also mouse, cell lines but display little interspecies conservation. Despite this, human and mouse DIs have convergent impacts on proliferation by affecting essential components of proliferation-regulating complexes. Together, these data argue that the PRMT5-splicing axis, and particularly appropriate DI splicing, underlies cancer’s vulnerability to PRMT5 inhibitors.

overall_design: RNA-seq profiling of established human or mouse cell lines, either WT or dTag-CLNS1A knock-in,  after treatment with PRMT5 inhibitors, dTag-13, or vehicle control.

middle: E

first: Natalie

last: O'Hearn

first: Griffin

last: Salus

first: Arundeep

last: Singh

first: Paul

last: Boutz

first: Jacqueline

last: Lees