title: CRISPR targeting of H3K4me3 activates gene expression and unlocks centromere-proximal crossover recombination in Arabidopsis

city: Cambridge

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: H3K4me3 is a fundamental and highly conserved chromatin mark across eukaryotes, playing a central role in many genome-related processes, including transcription, maintenance of cell identity, DNA damage repair, and meiotic recombination. However, identifying the causal function of H3K4me3 in these diverse pathways remains a challenge, and we lack the tools to manipulate it for agricultural benefit. Here we use the CRISPR-based SunTag system to direct H3K4me3 methyltransferases in the model plant, Arabidopsis thaliana. Targeting of SunTag-SDG2 activates the expression of the endogenous reporter gene, FWA. We show that SunTag-SDG2 can be employed to increase pathogen resistance by targeting the H3K4me3-dependent disease resistance gene, SNC1. Meiotic crossover recombination rates impose a limit on the speed with which new traits can be transferred to elite crop varieties. We demonstrate that targeting of SunTag-SDG2 to low recombining centromeric regions can significantly stimulate crossover formation. Finally, we reveal that the effect is not specific to SDG2 and is likely dependent on the H3K4me3 mark itself, as the orthogonal mammalian-derived H3K4me3 methyltransferase, PRDM9, produces a similar effect on gene expression with reduced off-target potential. Overall, our study supports an instructive role for H3K4me3 in transcription and meiotic recombination and opens the door to precise modulation of important agricultural traits.

overall_design: ChIP-seq and Quant-seq data to evaluate the epigenome engineering lines in Arabidopsis thaliana.


title: Thymic iNKT cells in Prkd2/3 mice (scRNA/TCR-seq, scATAC-seq)

status: Public on Sep 08 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

summary: We have conducted single cell-RNA, -TCR, -ATAC sequencing (10x Genomics) to investigate a difference of gene expression, TCR repertoir and chromatin accesibility of thymic iNKT cells from wild-type and CD4-Cre-mediated T cell-specific Prkd2/3 doubly deficirnt (Prkd2/3ΔCD4) mice. Results demonstrate that Prkd2/3 are required for iNKT cell development and formaion of proper iNKT cell subtypes.

overall_design: Thymus was taken from wild-type and Prkd2/3ΔCD4 mice. Thymic iNKT cells were enriched by CD1d-tetramer using MACS magnetic separators followed by purification by a cell sorter. Cells were applied to scRNA/TCR-seq analysis. For scATAC-seq analysis, nuclei were ioslated from purified cells according to manufacture's protocol (10x Genomics).

first: Eri

last: Ishikawa

first: Yu-Chen

last: Liu

last: Okuzaki

first: Sho

last: Yamasaki


title: TCR a/b profiling of thymic iNKT cells in Prkd2/3 mice (bulk TCR-seq)

summary: We have conducted TCR a/b profiling to compare the usage of TCR a/b chains of thymic iNKT cells from wild-type (WT) and CD4-Cre-mediated T cell-specific Prkd2/3 doubly deficirnt (Prkd2/3ΔCD4) mice. Results demonstrate that top one frequent TCRa chain is identical, whereas usage of TCRb chain is different between WT and Prkd2/3ΔCD4 iNKT cells.

overall_design: Thymus was taken from wild-type and Prkd2/3ΔCD4 mice. Thymic iNKT cells were enriched by CD1d-tetramer using MACS magnetic separators followed by purification by a cell sorter. Cells were applied to bulk TCR-sequencing analysis using SMARTer (Takara).


title: Pan-cancer Myc modulator that targets Myc-α-tubulin interaction to drive selective mitotic catastrophe

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

country: USA

institute: University of Michigan

summary: MYC overexpression is a well-established cancer vulnerability, yet direct therapeutic targeting of Myc remains a challenge. Here, we identify DL78 as a potent antimitotic agent with selective anticancer activity through its regulation of Myc. DL78 demonstrated broad efficacy by inhibiting growth across nine cancer types and significantly reducing tumor burden in an in vivo model of platinum-resistant high-grade serous ovarian cancer, with no overt toxicity. DL78 preferentially targets chromosomally unstable, MYC-overexpressing cancer cells, a hallmark of high-grade serous ovarian cancer. Mechanistically, DL78 exploits Myc’s role in mitotic entry by disrupting its interaction with α-tubulin, leading to sustained mitotic arrest, mitotic catastrophe, and apoptosis while sparing nonmalignant cells. This study establishes a novel paradigm for Myc-targeted therapy by introducing DL78, which induces cancer-selective mitotic catastrophe by disrupting Myc’s interaction with α-tubulin rather than its transcriptional activity

overall_design: RNA extracted from OV81.2 cells treated with DMSO or DL78 10µM for 6 hours to investigate global transcription. The experiment was performed in triplicate and was compared relative to vehicle treated (DMSO).

first: Analisa

last: DiFeo


title: Spontaneous Immortalization of Bovine Fibroblasts through Extended In Vitro Culture

city: Jerusalem

first: Shaun

last: Regenbaum

address: The Hebrew University of Jerusalem Edmond J. Safra Campus - Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

summary: Spontaneous immortalization in large animals like cattle is rare and has previously required genetic manipulation of TP53 or TERT. Here, we demonstrate the spontaneous immortalization of fibroblast lines from Holstein and Simmental cows over 500 days of continuous culture, corresponding to 240 population doublings. Initial senescence was observed at population doubling 60, marked by telomere shortening, γH2AX foci, and an active SASP profile. After 400 days, stable immortalized lines with a doubling time of 45 hours emerged. Transcriptomic and metabolic analyses revealed a reversal of senescence-associated apoptotic processes and mitochondrial stress, with no change in telomerase or p53 activity. Our findings suggest bovine fibroblast immortalization can occur through alternative pathways, with applications in cultivated meat production and aging research.

overall_design: Primary fibroblasts were isolated from Holstein (PBF-15) and Simmental (PBF-13) cows and cultured in vitro over 500 days. Senescence markers, telomere lengths, and doubling times were tracked throughout culture, with immortalization events noted after extended periods.  Transcriptomic analysis (RNA-seq) compared primary, senescent, and immortalized cell stages to characterize the molecular changes associated with spontaneous immortalization. Additional metabolic and chromosomal stability assays were performed to assess telomere maintenance and mitochondrial function.

first: Laura

last: Pasitka

first: Merav

last: Cohen

first: Yaakov

last: Nahmias


title: An interleukin-27 centered cytokine circuit regulates macrophage and T cell interactions in autoimmune diabetes

city: Milwaukee

first: Yi-Guang

last: Chen

state: WI

address: 9200 W. Wisconsin Ave.

department: Pediatrics

institute: Medical College of Wisconsin

summary: In the NOD mouse model of autoimmune diabetes, IL-27 stimulates CD4 and CD8 T cells to enhance their IFNγ production and diabetogenic capacity. Here, single-cell RNA sequencing and T cell adoptive transfer showed that IL-27 intrinsically controlled the differentiation of islet-infiltrating CD4 T cells by driving them toward an IL-21+ Th1 phenotype. Consequently, IL-27 signaling in CD4 T cells was important for BATF and granzyme B expression in islet CD8 T effectors. Complete absence of IL-21 signaling in CD8 T cells additionally impaired their cytokine production. BATF overexpression increased the diabetogenic potential of β-cell autoreactive CD8 T cells lacking help from CD4 T cell-derived IL-21. Macrophages were the main source of IL-27 in islets, whose expression correlated with T cell infiltration. IFNγ and CD40 signaling conferred by activated T cells induced macrophage IL-27 production. Collectively, our findings reveal a role of IL-27 in orchestrating interconnected positive feedback loops involving CD4 T cells, CD8 T cells, and macrophages in autoimmune diabetes.

overall_design: Islet-infiltrating T cells from mixed bone marrow chimera mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence of CD45.1 or CD45.2 expression and analyzed by scRNA-seq.

first: Ashley

middle: E

last: Ciecko

first: Nabi

last: Rabia

first: Amber

last: Drewek

first: Chien-Wei

last: Lin


title: Open Chromatin Guided Interpretable Machine Learning Reveals Cancer-Specific Chromatin Features in Cell-free DNA

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cell-free DNAs (cfDNAs) are DNA fragments found in blood, originating mainly from immune cells in healthy individuals and from both immune and cancer cells in cancer patients. While cancer-derived cfDNAs carry mutations, they also retain epigenetic features such as DNA methylation and nucleosome positioning. In this study, we examine nucleosome enrichment patterns in cfDNAs from breast and pancreatic cancer patients and find significant enrichment at open chromatin regions. Differential enrichment is observed not only at cancer cell type specific ATAC-seq peaks but also at CD4? T cell specific peaks, suggesting both tumor- and immune-derived contributions to the cfDNA signal. To leverage these patterns, we apply an interpretable machine learning model (XGBoost) trained on cell type specific open chromatin regions. This approach improves cancer detection accuracy and highlights key genomic loci associated with the disease state. Our pipeline provides a robust and interpretable framework for cfDNA-based cancer detection.

overall_design: Cell-free DNAs were isolated from patients with breast and pancreatic cancer. Enrichment patterns were analyzed at accessible chromatin regions defined by ATAC-seq. Subsequently, the XGBoost machine learning model was employed to interpret these patterns and identify cancer-specific features. For the Breast_Cancer_cfDNA_2 dataset, additional deep sequencing was performed, and these data have been deposited under the accession Breast_Cancer_cfDNA_2_DeepSeq.

first: Gunarathna

middle: D

last: Sakuntha

first: Nagornyuk

last: Aerica

first: Belabbaci

middle: A

last: Nazim

first: Nguyen

last: Regina

first: Ghosh

last: Bappa

first: Ganai

last: Sabha

first: Lemke

last: Tabatha

first: Garry

last: Cassy

first: Saotome

last: Mika

first: Yu

last: Muhan

first: Takada

last: Mamoru

first: Wang

last: Xusheng

first: Takaku

last: Motoki


title: Sparing effects of FLASH irradiation in patient-derived lung tissue

city: Paris

first: Charles

last: Fouillade

address: 25 rue d'Ulm

country: France

institute: Institut Curie

summary: This study aims to assess the effect of conventional radiotherapy compared to FLASH radiotherapy on healthy human lung tissue. FLASH radiotherapy, characterized by ultra-high dose rates, is hypothesized to spare healthy tissue from radiation-induced damage while maintaining efficacy against tumors. To achieve this goal and better characterize this sparing effect, bulk RNA sequencing analysis was conducted on 3 patients to study the molecular and cellular responses of lung tissue to both types of radiotherapy. The main objectives are to evaluate if FLASH radiotherapy effectively spares healthy lung tissue from radiation-induced damage and to understand the underlying molecular mechanisms behind this potential protective effect.

overall_design: Lung samples from lobectomies (n = 3) were irradiated either with FLASH radiotherapy (FLASH), conventional radiotherapy (CONV) at a dose of 9 Gy or untreated (NI). After 24-hours at 37°C in culture medium, total RNAs were extracted using RNAeasy Mini Kit from Qiagen. Libraries were prepared and sequenced on an Illumina NovaSeq 6000 sequencer. Three biological replicates were performed per condition and per patient.

first: Maxime

last: Dubail


title: The multimodal transcriptional response of denervated skeletal muscle involves alterations in cholesterol homeostasis impacting muscle size

city: Cincinnati

first: Douglas

middle: P

last: Millay

state: OH

address: 3333 Burnet Ave Cincinnati, OH 45229

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: The development and maintenance of the neuromuscular junction (NMJ) requires reciprocal signals between the nerve terminals and the multinucleate skeletal muscle fiber (myofiber). This interaction leads to highly specialized transcription in the sub-synaptic or NMJ myonuclei within mature myofibers leading to clustering of acetylcholine receptors  (AChRs). Here we utilized single-nucleus RNA sequencing (snRNA-seq) to delineate the transcriptional response of myonuclei to denervation. Through snRNA-seq on skeletal muscle from two independent mouse models of denervation, sciatic nerve transection and amyotrophic lateral sclerosis, we identify a multimodal transcriptional response of NMJ-enriched genes and an alteration in cholesterol homeostasis in both slow and fast myofibers. Gramd1, a family of genes involved in non-vesicular cholesterol transport, are enriched at the NMJ at baseline and upregulated in both models of denervation by the NMJ and extrasynaptic myonuclei In vivo gain and loss of function studies indicate that NMJ-enriched Gramd1 genes regulate myofiber sizes independent of an obvious impact on AChR clustering. We uncovered a dynamic transcriptional response of myonuclei to denervation and highlight a critical role for cholesterol transport to maintain myofiber sizes.

overall_design: Tibialis anterior (TA) muscles from SOD1G93A or C57BL/6 mice were harvested immediately following euthanasia, minced, and placed in homogenization buffer (0.25 M sucrose and 1% BSA in Mg2+-free, Ca2+-free, RNase-free 1x PBS). Nuclei isolation was done as previously described [20]. After filtration via a 40 μm strainer, nuclei were labeled with Hoechst dye and 0.2 U/μL Protector RNase inhibitor (Roche). All Hoechst stained myonuclei were purified using FACS (BD Aria, 70 μm nozzle) and gathered in sorting buffer containing Protector RNase inhibitor (0.2 U/μL). The nuclei were counted with a hemocytometer, and the concentration was fine-tuned as needed to reach the optimal range for the 10X Chromium chip. The 10X Chromium system was then used to load the nuclei using the Single Cell 3′ Reagent Kit v3.1, following the guidelines provided by the manufacturer. Around 12,000 nuclei were loaded for each operation. Sequencing was performed on an Illumina NovaSeq 6000 System.

first: Cristofer

last: Calvo

first: Casey

middle: O

last: Swoboda

first: Fabian

middle: M

last: Morales

first: Siddhant

last: Nagar

first: Michael

middle: J

last: Petrany

first: Chengyi

last: Sun

first: Hima

middle: B

last: Durumunla

first: Mattia

last: Quattrocelli


title: Effect of heterozygous RhoQ344X/+ mutation on gene expression in postnatal day (P) 35 mouse retina

status: Public on Sep 07 2025

city: Indianapolis

first: Yoshikazu

last: Imanishi

state: Indiana

address: 1160 W Michigan Street

department: Department of Ophthalmology

institute: Indiana University School of Medicine

summary: Class I rhodopsin mutations are known for some of the most severe forms of vision impairments in dominantly inherited rhodopsin retinitis pigmentosa. They disrupt the VxPx transport signal, which is required for the proper localization of rhodopsin to the outer segments. While various studies have focused on the light-dependent toxicity of mutant rhodopsin, it remains unclear whether and how these mutations exert dominant-negative effects. Using the class I RhoQ344X rhodopsin knock-in mouse model, we characterized the expression of rhodopsin and other genes by RNA sequencing and qPCR. Those studies indicated that rhodopsin is the most prominently downregulated photoreceptor-specific gene in RhoQ344X/+ mice. Rhodopsin is downregulated significantly prior to the onset of rod degeneration, whereas downregulation of other phototransduction genes, transducinα, and Pde6α, occur after the onset and correlate with the degree of rod cell loss. Those studies indicated that the mutant rhodopsin gene causes downregulation of wild-type rhodopsin, imposing a mRNA-level dominant negative effect. Moreover, it causes downregulation of the mutant mRNA itself, mitigating the toxicity. The observed dominant effect is likely common among rhodopsin retinitis pigmentosa as we found a similar rhodopsin downregulation in the major class II rhodopsin mutant model, RhoP23H/+ mice, in which mutant rhodopsin is prone to misfold. Potentially due to mitigated toxicity by reduced rhodopsin expression, RhoQ344X/+ mice did not exhibit light-dependent exacerbation of rod degeneration, even after continuous exposure of mice for 5 days at 3000 lux. Thus, this study describes a novel form of dominant negative effect in inherited neurodegenerative disorders.

overall_design: RNA-seq profiling of P35 wild-type and RhoQ344X/+ mutant mice reared under either standard cyclic 200 lux light or dark conditions, and RNA-seq profiling of P35 RhoP23H/+ mutant mice reared under standard cyclic 200 lux light condition.

first: Shimpei

last: Takita


title: RNAseq analysis of Vibrio cholerae A1552 ∆rpoS (∆VC0534) from Smooth and Rugose backgrounds

city: Santa Cruz

first: Giordan

last: Kitts

state: CA

address: 1156 High St.

department: METX

institute: UCSC

summary: RNA-sequencing of Vibrio cholerae A1552 ∆rpoS and parental strains from smooth and rugose backgrounds grown as spots on LB agar

overall_design: Three biological replicates of Vibrio cholerae A1552 strains (Smooth (S), S ∆rpoS (S∆VC0534), Rugose (R), and R ∆rpoS (R∆VC0534)) were grown for 48-hours on LB agar at 30˚C. Spots were then scraped from agar plates and resuspended in TRIzol for subsequent RNA isolation.

first: Trebino

last: Michael

first: Yildiz

middle: H

last: Fitnat

first: Kitts

last: Giordan


title: Effect of Gum Arabic supplement on Zebrafish gut microbiota and reproduction

city: Norwich

first: Alice

last: Godden

state: Not applicable

address: School of Biological Sciences, University of East Anglia, Norwich Research Park

institute: University of East Anglia

summary: A whole-food, plant-based diet rich in fruits and vegetables in addition to whole grains and legumes is highly praised for its positive health benefits. A reason for that is the high content of dietary fibres that are essential for optimal health and well-being. However, most people in the UK do not meet the minimum daily intake of at least 30 g. Gum Arabic (GA), a safe and rich source of soluble fibre, could potentially be incorporated into a typical Western diet as more evidence-based research confers its positive impact on health. To elucidate the mechanisms of action of GA’s role in health improvement, we combined bioinformatics (RNA-seq and 16S rRNA microbiome analysis) with metabolomics in combination with the zebrafish (Danio rerio) model. The results of this study show that a two-week diet consisting of 60% GA can significantly (adjusted p-value < 0.05) alter the expression levels of three genes related to appetite control and neuroprotection in the zebrafish brain. Our analysis also shows that incorporating GA into the diet affects the structure of the microbiota. It induces a variation in richness and bacterial taxa abundance by reducing microbiome alpha diversity and increasing the similarity in the microbial structure of the treated samples which is suggestive of a possible strain-specific selectivity mechanism. Overall, the significance of this report lies in its ability to underscore the importance of dietary fibre on health but specifically the role of GA as a prebiotic and a promising dietary soluble fibre in the context of the gut-microbiota-brain axis.

overall_design: Adult zebrafish were housed in standard conditions and had their diet supplemented with Gum Arabic, at either 6% or 60% doses. They were housed in equal sex-ratios and then out-crossed for breeding to see if there was an impact on fertility.

first: Jean-Charles

last: De Coriolis

first: Justin

last: Assaf

first: Rispah

last: Ng'Ang'A

first: Karina

last: Silova

first: Eve

last: Redhead

first: Zoe

last: Crighton

first: Jamie

last: Bartram

first: Jayme

last: Cohen

first: Gwenaelle

last: Le Gall

first: Saber

last: Sami

first: Simone

last: Immler


title: single-cell RNA sequencing of hepatitis A virus (HAV) infected mouse livers

status: Public on Sep 06 2025

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

summary: we employed single cell RNAseq with the 10XGenome approach to study the transcriptomic changes in liver with a mouse model of HAV infection.

overall_design: hepatocytes and CD45+ leukocytes were isolated from HAV or mock infected mouse livers at 2d post-infection

first: You

last: Li

first: Ichiro

last: Misumi


title: Transcriptional analysis of T cells derived from individuals with neurodevelopmental disorder carrying de novo heterozygous PSMC5 variants.

city: Nantes

first: Frédéric

last: Ebstein

address: IRS-UN - 8 quai Moncousu - BP 70721

department: L'unité de recherche de l'institut du thorax, Inserm UMR 1087

institute: French Institute of Health and Medical Research (Inserm)

summary: Gene expression profiling on T cells to investigate the effects of PSMC5 missense variants on the immune system using the Nanostring nCounter® Human AutoImmune Profiling Panel.

overall_design: Peripheral blood mononuclear cells (PBMC) isolated from blood draws from patients and healthy dnonors were subjected to polyclonal stimulation with phytohemagglutinin (PHA) and interleukin-2 (IL-2) to expand naive T cells. After 3 weeks of culture, total RNA was isolated from resting T cells for gene expression analysis.

first: Maja

last: Studencka-Turski


title: m6A IP sequencing analysis of m6A mRNA methylation regulation by YTHDF2 in keratinocytes

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: The role of m6A RNA methylation of self non-coding RNA remains poorly understood. Here we show that m6A-methylated self U6 snRNA is recognized by YTHDF2 to reduce its stability and prevent its binding to Toll-like receptor 3 (TLR3), leading to decreased inflammatory responses in human and mouse cells and mouse models. At the molecular level, endosomal U6 snRNA binds to the LRR21 domain in TLR3, independent of m6A methylation, to activate inflammatory gene expression, a mechanism that is distinct from that of the best known synthetic TLR3 agonist poly I:C. Both U6 snRNA and YTHDF2 are localized to endosomes via the transmembrane protein SIDT2, where YTHDF2 functions to prevent the U6-TLR3 interaction. We further show that UVB exposure inhibits YTHDF2 by inducing its dephosphorylation and autophagic protein degradation in human keratinocytes and mouse skin. Skin-specific deletion of Ythdf2 in mice enhanced the UVB-induced skin inflammatory response and promoted tumor initiation. Taken together, our findings demonstrate that YTHDF2 plays a crucial role in controlling inflammation by inhibiting m6A U6-mediated TLR3 activation, suggesting that YTHDF2 and m6A U6 are potential therapeutic targets for preventing and treating inflammation and tumorigenesis.

overall_design: m6A IP seq of control and YTHDF2-knockdown HaCaT keratinocytes

first: Jiangbo

last: Wei

first: Seungwon

last: Yang


title: G-Quadruplex structural motifs modulate protein-RNA interactions within the transcriptome

city: Perth

first: Nicole

last: Smith

state: WA

address: 35 Stirling Hwy

country: Australia

institute: The University of Western Australia

summary: RNA secondary structures, including G-quadruplexes (G4s), have emerged as vital players in protein–RNA interactions. The RNA-binding protein Fused in Sarcoma (FUS), which is strongly implicated in both neurodegenerative disease and cancer, is known to interact with RNA molecules through a variety of GU-rich sequences. However, a definitive consensus motif for FUS–RNA recognition and binding has not yet been determined. Here, we hypothesize that G4 structures, which are inherently G-rich, may play a key role in FUS binding. We examine the role of G4s in FUS–RNA binding by developing an RNA immunoprecipitation sequencing (RIP-seq) protocol under G4-stabilising and non-stabilising conditions. We find that G4s regulate the binding of FUS to target RNAs, providing new information on protein–RNA binding motifs, while reinforcing the importance of RNA secondary structures as pivotal regulators of protein interactions. These insights advance our understanding of FUS-RNA binding dynamics and future potential for identifying new therapeutic targets for neurodegenerative disease and other FUS-related pathologies.

overall_design: RNA G4 secondary structures were annealed in RIP buffer containing 150 mM of K+ or Li+, then bound to recombinant C-terminal FUS protein. FUS-bound RNA was purified and next-generation sequencing performed to identify G4-dependent FUS-RNA binding. Input samples were subject to all steps as FUS-RNA samples except for immunoprecipitation and subsequent washes. Each condition was performed in triplicate.

first: Uditi

last: Bhatt

first: Cameron

middle: W

last: Evans

first: Anne

last: Cucchiarini

first: Julien

last: Gros

first: K Swaminathan

last: Iyer

first: Jean-Louis

last: Mergny


title: The immune receptor SLAMF5 Regulates Myeloid-Cell Mediated Neuroinflammation in Multiple Sclerosis

city: Rehovot

first: Laura

last: Bellassen

address: 234 herzl

institute: Weizmann Institute of Science

summary: Multiple sclerosis (MS) is a chronic neurological disorder characterized by demyelination of the central nervous system (CNS), leading to a broad spectrum of physical and cognitive impairments. Myeloid cells within the CNS, including microglia and border-associated macrophages, play a central role in the neuroinflammatory processes associated with MS. Activation of these cells contributes to the local inflammatory response and promotes the recruitment of additional immune cells into the CNS. SLAMF5 is a cell surface receptor that functions as a homophilic adhesion molecule, capable of modulating immune cell activity through both activating and inhibitory signals. In this study, we investigated the expression and function of SLAMF5 in CNS-resident and peripheral myeloid cells using the murine model of MS, experimental autoimmune encephalomyelitis (EAE). Our findings demonstrate that both total and brain-specific SLAMF5 deficiency in myeloid cells leads to decreased expression of activation and costimulatory molecules, including MHC class II (MHCII) and CD80. This downregulation is mediated, at least in part, through the transcription factor BHLHE40 and its regulation of CD52, resulting in delayed onset and reduced progression of the disease. Furthermore, pharmacological blockade of SLAMF5 in the brain halted disease progression and reduced the expression of myeloid activation markers. In human studies, SLAMF5 blockade in peripheral monocytes from MS patients and in induced pluripotent stem cell (iPSC)-derived microglia reduced the expression of HLA-DR, CD80, and CD52. Together, these results identify SLAMF5 as a key regulator of myeloid cell activation in neuroinflammation and suggest that it may represent a promising therapeutic target for autoimmune disorders such as MS.

overall_design: Bulk RNA sequencing of brain myeloid cells CD45+ CD11b+ of WT and KO of SLAMF5 in  EAE induced mice.

first: Avital

last: Sarusi-Portuguez

first: Idit

last: Shachar


title: Pan-Cancer MLL3 Mutational Landscape and Its Association with Immunotherapy

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

country: China

institute: Hangzhou Normal University

summary: Translocation-linked Mixed Lineage Leukemia (MLL) genes were discovered ~ 30 years ago and are homologs of Trithorax in Drosophila. MLL3 is a histone methyltransferase catalyzing the monomethylation of histone H3 lysine 4 (H3K4me1), a hallmark for gene enhancers. Although recurrent mutations of MLL3 are reported across a broad spectrum of cancers and MLL3 represents one of the most commonly mutated cancer genes, a pan-cancer-wide portrait of this high-frequency mutational event is still lacking. We report here a comprehensive analysis of MLL3 mutation and its association with molecular, cellular, and clinical features in 33 cancer types. The genetic alterations of MLL3 are primarily driven by point mutations or small INDELs rather than large-scale chromosomal perturbations and exhibit lineage-specific variations, which spontaneously yet heterogeneously impinge on the clinical behaviors of cancers and are intrinsically linked to hot tumor microenvironments, especially in uterine corpus endometrial carcinoma (UCEC) and colon adenocarcinoma (COAD), where MLL3 aberrances surprisingly predict better overall survivals and favorable responses to immunochemotherapy. Concurrent mutation of MLL3 and POLE in UCEC is associated with high immune cell infiltration and immune checkpoint gene expression, endowing the applicability of immune checkpoint inhibitors in these patients. Mouse models with Mll3-ablated colon cancer validate the immunostimulatory trait of Mll3 aberration. Our study provides a pan-cancer spectrum of the MLL3 mutational event and will contribute to the understanding of the genetic evolution and disease management of cancers, especially COAD and UCEC.

overall_design: Mll3WT and Mll3KO CT26 cells for RNA-seq and CUT&Tag, and tumor tissues for single-cell RNA-seq

first: Yongfeng

last: Shang


title: Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation [Feces]

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

summary: A cohoused condition with Tg mice alteration in fecal microbiota was linked to the emergence of intraepithelial bacteria and a unique transcriptome profile in the mouse colon during IBD development.

overall_design: The gut microbiota in fecal  samples was analyzed.

first: Yu-Chen

last: Pai

first: Yi-Hsuan

last: Li

middle: C


title: ZNF296 drives immune evasion in epithelial cancer cells [ChIP-seq]

city: Beijing

first: Deng

last: Pan

address: Tsinghua University Medical Science Building

department: School of Basic Medical Sciences

institute: Tsinghua University

summary: Using a genome-wide CRISPR activation screen, we identified ZNF296, a transcription factor highly expressed in epithelial cancers, as a key regulator of tumor resistance to NK cell-mediated cytotoxicity. To uncover its direct targets, we performed ChIP-seq in A549 cells overexpressing ZNF296-Flag, revealing its preferential binding to specific genomic regions. IP-MS further demonstrated that ZNF296 interacts with the NuRD complex, which suppresses gene expression via histone deacetylase activity.To test whether ZNF296 mediates transcriptional repression through the NuRD complex, we conducted ChIP-seq for HDAC1, a core component of the complex, in ZNF296-overexpressing (ZNF296-OE) and control A549 cells. These analyses revealed genomic targets co-regulated by ZNF296 and the NuRD complex, providing insights into its mechanism of transcriptional regulation.

overall_design: ChIP-seq was performed in A549 cells overexpressing ZNF296-Flag using anti-Flag antibodies to identify direct genomic targets of ZNF296. ChIP-seq for HDAC1 was also conducted in ZNF296-OE and control A549 cells to determine co-regulation by ZNF296 and the NuRD complex.


title: Effect of depletion NEDD4 on gene expression on 4T1 and EMT6 tumor cells

city: Xiamen

last: Su

state: Fujian

address: No. 4221 Xiang'an South Road

institute: Xiamen university

summary: Tumor immune microenvironment greatly influences triple-negative breast cancer (TNBC) progression. Identifying novel targets to convert “cold” tumors into “hot” tumors holds promise for improving treatment outcomes. Here, we show that high expression of NEDD4, a HECT-type E3 ubiquitin ligase, correlates with poor prognosis and reduced CD8+ T cell infiltration in TNBC patients. NEDD4 depletion in TNBC cells significantly inhibits tumor growth through enhancing CD8+ T cell-mediated cytotoxicity in immunocompetent hosts. Mechanistically, NEDD4 depletion stabilizes β-TrCP, leading to YAP ubiquitination and degradation. Downregulated YAP reprograms the immunosuppressive tumor extracellular matrix (ECM) to increase CD8+ T cell infiltration. Furthermore, a small-molecule inhibitor of NEDD4, XMU-MP-10, exhibits significant in vivo efficacy in inhibiting TNBC tumor growth by enhancing CD8+ T cell infiltration in mouse models. Collectively, our findings suggest that the genetic depletion or pharmacological inhibition of NEDD4 enhances antitumor immune responses via the β-TrCP/YAP/ECM cascades, offering a promising therapeutic strategy for TNBC treatment.

overall_design: Conparative gene expression profiling analysis of RNA-seq for 4T1 and EMT6 cells and its KO derivatives (sgNEDD4)


title: ZNF296 drives immune evasion in epithelial cancer cells [RNA-seq]

summary: Using a genome-wide CRISPR activation screen,  we identified ZNF296, a transcription factor prominently expressed in epithelial cancers, as a key regulator of tumor resistance to NK cell-mediated cytotoxicity. To systematically investigate the mechanisms by which ZNF296 suppresses NK cell-mediated killing, RNA-seq analysis was performed on A549 cells overexpressing ZNF296 (ZNF296-OE), and 4T1 cells with knockdown of its murine homolog Zfp296 (Zfp296KD). By analyzing differential gene expression and signaling pathways, we aimed to understand the influence of ZNF296/Zfp296 on tumor-intrinsic mechanisms.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To identify ZNF296-dependent transcriptional changes, bulk RNA-seq was conducted on cells with both ectopic and inhibited ZNF296 expression. ZNF296-overexpressing A549 cells were generated using a lentiviral expression system, while Zfp296 inhibition was achieved in 4T1 cells via the CRISPRi system.


title: Combining brigatinib with mTOR inhibition to effectively treat NF2-SWN-associated and sporadic NF2-deficient meningiomas

status: Public on Sep 05 2025

city: Columbus

first: Long-Sheng

last: Chang

address: 575 Children's Crossroad

institute: Abigail Wexner Institute at Nationwide Children's Hospital

summary: We previously generated an orthotopic, NF2-deficient meningioma model using the luciferase-expressing Ben-Men-1 cell line established from a sporadic tumor and identified the multi-kinase inhibitor brigatinib and the mTOR kinase inhibitor INK128 to potently impede tumor growth. Here, we describe generation of the telomerase-immortalized AG-NF2-Men cell line from a grade-1 meningioma of an NF2-related schwannomatosis (NF2-SWN) patient. We showed that like Ben-Men-1 cells, AG-NF2-Men cells were NF2-null, expressed several NF2-regulated receptor tyrosine kinases, and responded to their cognate ligands. We also found that brigatinib and INK128 alone inhibited AG-NF2-Men cell proliferation at IC50 values similar to those in Ben-Men-1 cells. Combining brigatinib with INK128 exhibited growth-inhibitory synergy. Mechanistically, the combination not only completely abrogated p-AKT(S473) and its downstream signaling compared to either drug alone but also prevented INK128-mediated re-phosphorylation of AKT on T308. Also, the combination more-effectively blocked ligand-mediated phosphorylation of EGFR, ErbB3, and IGF-1R and elicited major changes in the expression of genes including the upstream regulators of several signaling networks important for meningioma growth. Further, we generated luciferase-expressing AG-NF2-Men cells that readily grew as intracranial xenografts. Importantly, combining brigatinib with INK128 enhanced tumor regression in both the orthotopic AG-NF2-Men and Ben-Men-1 xenograft models. As the first NF2-SWN-related meningioma cell line, AG-NF2-Men is a unique reagent for investigating meningioma biology and therapeutics. A clinical trial to evaluate the combination of brigatinib with an mTOR inhibitor in NF2-deficient meningiomas is warranted.

overall_design: RNA-sequencing of AG-NF2-Men telomerase-immortalized neurofibromatosis-2 schwannomatosis (NF2-SWN) benign meningioma cell line after a 24-hour incubation with DMSO or 1x growth-inhibitory IC50 of the multi-kinase inhibitor brigatinib, the mTOR kinase inhibitor INK128, or their combination. Experiments were conducted as as three biological replicates.

first: Janet

middle: L

last: Oblinger

first: Lai-Man Natalie

last: Wu

first: Cecelia

last: Miller

first: Sarah

middle: S

last: Burns


title: ZNF296 drives immune evasion in epithelial cancer cells [ATAC-seq]

summary: Using a genome-wide CRISPR activation screen, we identified ZNF296, a transcription factor prominently expressed in epithelial cancers, as a key regulator of tumor resistance to NK cell-mediated cytotoxicity. To investigate the role of ZNF296 in regulating chromatin accessibility and its effects on gene transcription, we performed ATAC-seq on ZNF296-overexpressing (ZNF296-OE) and control A549 cells. These data provide insights into the epigenetic mechanisms underlying ZNF296-mediated tumor immune evasion.

overall_design: To identify ZNF296-dependent chromatin accessibility, ATAC-seq was performed on A549 cells with control and ZNF296 overexpression. ZNF296-overexpressing A549 cells were generated by introducing ZNF296 ORF.


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [in vivo Tuba-seqUltra Saturation]

city: Stanford

first: Yuning

last: Tang

address: 279 Campus Drive, Beckman Center

institute: Stanford University

summary: Epigenomic dysregulation is widespread in cancer. However, the specific epigenomic regulators and the processes they control to drive cancer phenotypes are poorly understood. We employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of >250 epigenomic regulators within autochthonous oncogenic KRAS-driven lung tumors. We identified many previously unappreciated epigenomic tumor-suppressor and tumor-dependency genes. We show that a specific HBO1 complex and MLL1 complex are robust tumor suppressors in lung cancer. Histone modifications generated by HBO1 complex are frequently diminshed in human lung adenocarcinomas and is associated with worse clinical features. HBO1 and MLL1 complexes co-occupy shared genomic regions, impacting chromatin accessibility, expression of canonical tumor suppressor genes and lineage fidelity. The HBO1 complex is epistatic with the MLL1 complex and other tumor suppressor genes in lung adenocarcinoma development. Collectively, these results uncover HBO1 and MLL1 complexes as critical functional modules restraining lung adenocarcinoma development and provide a in vivo phenotypic roadmap of epigenomic regulators in lung tumorigenesis.

overall_design: In vivo Tuba-seqUltra analysis was conducted on KrasG12D; R26LSL-TdTomato; H11LSL-Cas9 (KTC) mice and KrasG12D; R26LSL-TdTomato (KT) mice to study MLL and MYST family genes.


title: Mitochondrial complex III-derived ROS amplify immunometabolic changes in astrocytes and promote dementia pathology

city: New York

first: Adam

middle: L.

last: Orr

state: NY

address: 413 East 69th St

department: Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute

institute: Weill Cornell Medicine

summary: Neurodegenerative disorders alter mitochondrial functions, including the production of reactive oxygen species (ROS). Mitochondrial complex III (CIII) generates ROS implicated in redox signaling, but its triggers, temporal dynamics, targets, and disease relevance are not clear. Using site-selective suppressors and genetic manipulations together with live mitochondrial ROS imaging and multiomic profiling, we found that CIII is a dominant source of ROS production in astrocytes exposed to neuropathology-related stimuli. Astrocytic CIII-ROS production was dependent on nuclear factor-κB (NF-κB) and the mitochondrial sodium-calcium exchanger (NCLX) and caused oxidation of select cysteines within immune- and metabolism-associated proteins linked to neurological disease. CIII-ROS amplified metabolomic and pathology-associated transcriptional changes in astrocytes, with STAT3 activity as a major mediator, and facilitated neuronal toxicity. Therapeutic suppression of CIII-ROS in mice decreased dementia-linked tauopathy and neuroimmune cascades and extended lifespan. Our findings establish CIII-ROS as an important immunometabolic signal transducer and tractable therapeutic target in neurodegenerative disease.

overall_design: Bulk RNA sequencing of RNA isolated from primary mouse astrocytes after treatment for 6 hours with Vehicle, S1QEL2.2, S3QEL1.2, Interleukin-1alpha (IL-1ɑ), IL-1ɑ + S1QEL2.2, or IL-1ɑ + S3QEL1.2

first: Daniel

last: Barnett

first: Till

last: Zimmer

first: Caroline

last: Booraem

first: Fernando

last: Palaguachi

first: Samantha

last: Meadows

first: Haopeng

last: Xiao

first: Man Ying

last: Wong

first: Wenjie

last: Luo

first: Li

last: Gan

first: Edward

middle: T

last: Chouchani

first: Anna

middle: G


title: Single-cell Transcriptomic Profile of Brain Immune Cells From Alzheimer’s Disease Mouse Models With or Without CD8+ T Cell–Specific Nr4a Deletion

city: Noda

first: Masaki

last: Ohyagi

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

institute: Tokyo University of Science

summary: We performed single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (scTCR-seq) using the 10x Genomics platform to characterize brain-infiltrating CD8+ T cells and their interactions with brain immune cells in the App^NL-G-F Alzheimer’s disease mouse model, with or without CD8⁺ T cell–specific deletion of Nr4a. This dataset provides comprehensive transcriptional profiles of brain immune cells and insights into CD8+ T cell clonal expansion in the context of amyloid pathology.

overall_design: CD45+ immune cells were isolated from the brains of sex-matched 8-month-old AppNL-G-F control mice (AppNL-G-F; Cd8a-WT; Nr4a^flox_flox) and CD8+ T cell-specific Nr4a-deficient mice (AppNL-G-F; Cd8a-Cre; Nr4a^flox/flox) (n = 5 per genotype) using fluorescence-activated cell sorting (FACS) technique.

first: Minako

last: Ito

first: Mana

last: Iizuka-Koga

first: Setsuko

last: Mise-Omata

first: Akihiko

last: Yoshimura


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [KP787]

first: Yuning

last: Tang

overall_design: CUT&RUN experiments for murine KrasG12D;p53-/- mouse lung adenocarcinoma cell line treated with 1 uM of KAT7 catalytic inhibitor WM3835 or 0.02% DMSO as vehicle control. IgG is used as negative control and H3K27me3 is used as positive control.


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [in vivo Tuba-seqUltra Epigenomics]

overall_design: In vivo Tuba-seqUltra analysis was conducted on KrasG12D; R26LSL-TdTomato; H11LSL-Cas9 (KTC) mice and KrasG12D; R26LSL-TdTomato (KT) mice to epigenomic regulators in lung tumorigenesis. Experiment is performed in two batches.


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [802T4]

overall_design: CUT&RUN experiments for murine KrasG12D;p53-/- mouse lung adenocarcinoma cell line for KAT7, MLL1, H3K14ac and H3K4me3. IgG is used as negative control and CTCF is used as positive control.


title: Unraveling Enteroendocrine Cell lineage dynamics and associated gene regulatory networks during intestinal development

city: ILLKIRCH

first: Adèle

last: DE ARCANGELIS

address: 1 rue Laurent Fries

department: Development & Stem Cells

institute: IGBMC, CNRS UMR 7104, Inserm U 1258

summary: Enteroendocrine cells (EECs) are rare intestinal epithelial cells producing multiple hormones that regulate essential aspects of digestion and energy. EEC subtypes, their hormone repertoire and differentiation mechanisms from intestinal stem cells have been characterized in the adult intestine. However, the mechanisms underlying EEC subtype specification during development are largely unknown. We characterized EEC lineages and their dynamics during development using both genetically modified mouse and human models (i.e. human intestinal organoids, HIOs, derived from induced pluripotent stem cells and transplanted HIOs, tHIOs), which we analyzed by single-cell RNA sequencing using plate-based SORT-seq technology. Our findings demonstrate that in both mice and humans, the majority of EECs are specified during development through similar differentiation trajectories as observed in the adult intestine. This suggests that EEC subtypes specification occurs independently of fully organized crypt-villus structures and stimulation by diet or microbiota. However, the emergence of certain EEC subtypes depends on tissue maturation. Finally, our integrative approach infers lineage-specific regulators dynamically, identifying new candidates controlling EEC differentiation in the developing human gut.

overall_design:
Characterization of EEC diversity in the mouse embryonic and post-natal intestine by single cell transcriptomics To dissect the mechanisms governing EEC differentiation during development, we used the Neurog3eYFP mouse model which allows the tracing and purification of all eYFP+ EECs from Neurog3-expressing enteroendocrine progenitors to various differentiated EEC subtypes (Blot et al., 2023; Mellitzer et al., 2004; Piccand et al., 2019). We used a plate-based scRNA-seq technology (Sorting and Robot assisted Transcriptome sequencing, SORT-seq (Muraro et al., 2016)) to profile eYFP+ EECs isolated from small intestine at embryonic day 15.5 (E15.5); at E18.5; and at postnatal day 12 (P12). We analyzed the transcriptional profile of a total 1138 cells, comprising 384 from E15.5 small intestine, 514 from E18.5, and 240 from P12 retaining 14495 genes.
Characterization of EEC diversity in the developing human small intestine (SI) using in vitro avatars, human intestinal organoids (HIOs) and transplanted HIOs (tHIOs). HIOs mimicking the developing SI were generated from human induced pluripotent stem cells (hiPSCs) of the NEUROG3-HA-P2A-Venus line, enabling EECs to be isolated and traced (Schreiber et al., 2021). The EEC differentiation process was analyzed in HIOs and tHIOs, a model known to induce tissue maturation after transplantation of HIOs under the kidney capsule of immunocompetent mice. Venus-positive EECs were sorted from HIOs or tHIOs and sequenced using plate-based scRNA-seq, SORT-seq. For HIOs, 633 cells and 16513 genes were kept; for tHIOs, 556 cells and 17511 genes were kept.

first: Sara

last: Jiménez

first: Florence

last: Blot

first: Aline

last: Meunier

first: Rishabh

last: Kapoor

first: Valérie

last: Schreiber

first: Colette

last: Giethlen

first: Sabitri

last: Ghimire

first: Maxime

last: Mahe

first: Nacho

last: Molina

last: De Arcangelis

first: Gérard

last: Gradwohl


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [In vivo Tuba-seqUltra]

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: In vivo Tuba-seqUltra analysis was performed in KrasG12D;R26LSL-TdTomato;H11LSL-Cas9 (KTC), KrasG12D;R26LSL-TdTomato;H11LSL-Cas9;Kat7fl/fl (KTC;Kat7fl/fl), and KrasG12D;R26LSL-TdTomato mice to investigate epistatic interactions with Kat7.


title: Differential gene expression analysis of Kat7 inhibitor-treated versus control-treated lung adenocarcinoma cells [bulk RNA-seq]

summary: Epigenomic dysregulation is widespread in cancer. However, the specific epigenomic regulators and the processes they control to drive cancer phenotypes are poorly understood. We employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of >250 epigenomic regulators within autochthonous oncogenic KRAS-driven lung tumors. We identified many previously unappreciated epigenomic tumor-suppressor and tumor-dependency genes. We show that a specific HBO1 complex and MLL1 complex are robust tumor suppressors in lung cancer. Histone modifications generated by HBO1 complex are frequently reduced in human lung adenocarcinomas and is associated with worse clinical features. HBO1 and MLL1 complexes co-occupy shared genomic regions, impacting chromatin accessibility, expression of canonical tumor suppressor genes and lineage fidelity. The HBO1 complex is epistatic with the MLL1 complex and other tumor suppressor genes in lung adenocarcinoma development. Together, these results uncover the HBO1 and MLL1 complexes as critical functional modules in restraining lung adenocarcinoma development and provide a in vivo phenotypic roadmap of epigenomic regulators in lung tumorigenesis.

overall_design: Murine KrasG12D; p53-/- lung adenocarcinoma cells were cultured in 6-well plates in DMEM supplemented with 10% FBS and 1% Pen/Strep. The cells were treated with either 1 µM WM3835 or 0.02% DMSO (vehicle control) for 5 consecutive days. Each technical replicate is a from an separate well. Total RNA was extracted for bulk RNA-sequencing.


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [KPTC CUT&RUN]


title: Building a Bovine Blood DNA Methylation EpiMap Related to disease Phenotypes

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

type: Methylation profiling by high throughput sequencing

summary:
Background
Epigenetic variations, particularly in response to environmental factors, play a crucial role in shaping immune identity and function in hematopoietic cells. This study investigates interindividual differences in DNA methylation among dairy cows, with the aim of enhancing our understanding of the adaptive capacity essential for sustainable animal production. We conducted whole-genome sequencing and DNA methylation analysis using enzymatic methyl-seq on whole blood from 60 Holstein cows. The study included five phenotype groups: mastitis, lameness, infertility, metabolic disorders and healthy controls.
Results
Among the 50 million CpG sites, 5.1% were identified as variable methylated cytosines (VMCs) and 94.9% as conserved methylated cytosines (CMCs). VMCs displayed variability in distal promoter regions, suggesting potential plasticity in the associated genes, while CMCs exhibited a bimodal methylation pattern near the transcription start site, indicative of tissue-specific functions. Notably, we identified motif enrichments related to genes potentially expressed in blood. An age-related analysis revealed a 1.4% faster decline in CMCs methylation compared to VMCs. Additionally, disease risk assessment may be achievable using as few as 586 methylation biomarkers, which could be used to select which cows to keep in the herd for additional lactation.
Conclusion
Our results suggest a dual role for VMCs and CMCs: while the stability of conserved sites is potentially associated with essential functions in cell development and homeostasis, variable sites may be involved in dynamically regulating gene transcription in response to internal or external stimuli. These insights underscore the epigenome’s role in immune regulation and adaptive resilience in cattle.

overall_design:
Blood samples were collected from cows at a Vancouver farm between November 2020 and January 2021. A year later, we selected 30 cows that had been culled during the year due to complications related to infertility (BFR, n=6), mastitis (BMS, n=6), lameness (BFL, n=12), or metabolic disorders (BMT, n=6), which were not identified at the time of sampling. This culling reason was recorded in farm management logs and represented the primary cause for culling. These cows formed the “diseased group.” For comparison, we selected a second group of 30 cows that remained in the herd without any health issues. This second group represented the “control group.” The ages of the cows in both groups ranged from 1 to 9 years.
The pairing of each subgroup with controls (6 vs. 6, 12 vs. 12, or 30 vs. 30) for the comparison analyses was performed by selecting individuals as close in age as possible, even though age was excluded as a covariate in the differential analyses. This allowed us to minimize age-related effects while focusing the analysis on disease-associated methylation differences.

first: Lotfi

last: Bouzeraa

first: Helene

last: Martin

first: Jessica

last: Marques

first: Ronaldo

last: Cerri

first: Marc-Andre


title: Unraveling the regulatory development and molecular mechanisms of identical sea urchin twins

city: Chiba

first: Koki

last: Tsuyuzaki

address: 1-8-1, Inohana, Chuo-ku, Chiba-shi

institute: Chiba University

summary: Since Hans Driesch’s pioneering work in 1891, it has been known that animal embryos can develop into complete individuals even when divided1–6. However, the developmental processes and molecular mechanisms enabling this self-organization remain poorly understood. In this study, we revisit Driesch’s experiments by examining the development of isolated 2-cell stage blastomeres in the sea urchin, Hemicentrotus pulcherrimus. Contrary to intact embryos, these isolated blastomeres initially form a flat, single layer of dividing cells that eventually round up to be a blastula. Live imaging and knockdown experiments reveal that actomyosin activity at the basal side of the cells and septate junctions drive this process. Intriguingly, we observed temporal disorganization of the anterior-posterior (A-P) and dorsal-ventral (D-V) axes, where the original A-P poles come into contact after sphere shape formation. The disrupted A-P axis is subsequently corrected as the embryos employ the Wnt/β-catenin signaling mechanisms assumed to be used in intact embryos to re-establish a normal axis. These findings suggest that axis re-organization through pre-existing developmental mechanisms is essential for the successful regulative development of divided embryos.

overall_design: In the process of elucidating the ability of the sea urchin Hemicentrotus pulcherrimus to develop into normal larvae even when blastomeres are separated at the 2-cell stage, we compared mRNA expression between embryos separated at the 2-cell stage and normal embryos using bulk RNA-seq. The comparisons were conducted at 11, 14, 18, and 24 hours post-fertilization, with the 2-cell stage prior to separation also analyzed. RNA-seq was performed in three batches for each condition.

first: Haruka

last: Suzuki

first: Junko

last: Yaguchi

first: Shunsuke


title: Stage-specific roles of clonally expanded CD8+ T cells in regulating amyloid pathology in Alzheimer's disease models

first: Masaki

last: Ohyagi

summary: Clonally expanded CD8+ T cells may contribute to Alzheimer's disease (AD) pathology through interactions with brain-resident cells. However, the functional impact of AD-specific T cell receptor (TCR) clonotypes remains unclear. Here, we demonstrate that CD8+ T cells undergo clonal expansion in early-stage AD mouse models, AppNL-G-F and 5xFAD, and that their depletion reduces amyloid plaque accumulation. Expanded TCR-expressing CD8+ T cells preferentially infiltrate the brain, exacerbating plaque deposition. Moreover, brain-infiltrating CD8+ T cells impair microglial transition into disease-associated states, suppressing amyloid clearance via CCL5-CCR5 signaling. Pharmacological blockade of CCL5 attenuates amyloid deposition, whereas CCL5 administration aggravates pathology. Notably, T cell depletion at later disease stages exacerbates amyloid pathology, suggesting a temporal shift in their function. Early-stage CD8+ T cells exhibit cytotoxic and effector profiles, whereas late-stage cells acquire tissue-resident and exhausted phenotypes. This temporal switch-from pathogenic to protective roles-highlights the stage-specific contribution of CD8+ T cells to AD and their potential as therapeutic targets.

overall_design: CD45-expressing cells were isolated from sex-matched 3-month-old wild-type, AppNL-G-F, and T cell-deficient AppNl-G-F mouse brains (n = 3 per genotype) using FACS sorting technique.

first: Minako

last: Ito

first: Mana

last: Iizuka-Koga

first: Setsuko

last: Mise-Omata

first: Akihiko

last: Yoshimura


title: PHASE IB STUDY OF AVELUMAB WITH RADIOTHERAPY IN PATIENTS WITH LEPTOMENINGEAL DISEASE

city: Tampa

first: Kieran

last: Smalley

state: Fl

address: 12902 USF Magnolia Drive,

institute: Moffitt cancer Center

summary: A phase IB, single-arm, non-randomized study to establish the safety of the PDL-1 inhibitor Avelumab with radiotherapy in patients with leptomeningeal disease (LMDz) from metastatic melanoma, lung cancer, and breast  cancer. We hypothesize 1) systemic Avelumab will activate peripheral T cells and, with whole-brain radiotherapy (to induce blood-brain-barrier breakdown and stimulate antigen expression), significantly increase the number and activation status of T cells that migrate into the cerebrospinal fluid (CSF), with an Inflammatory CSF cytokine profile, in patients with LMDz; 2) this treatment regime is safe and tolerated without significant toxicities and will improve overall survival compared to historical controls; and 3) point estimates (with confidence intervals) can be derived using CSF measurements, toxicities, and clinical benefit to estimate sample sizes/schedules for an expanded Recommended Phase II Study.

overall_design: A maximum of 15 individuals with any cancer that is not hematologic and leptomeningeal disease, being treated at Moffitt Cancer Center, Tampa, Florida. This is a Phase 1b study with safety evaluated continuously. I = initial sample. E = endpoint sample.

first: Peter

last: Forsyth

first: Michael

last: Yu

first: Ann

last: Chen

first: Robert

last: Macaulay

first: John

last: Arrington

first: Keiran

first: Nikhil

last: Khushalani

first: Yolanda

last: Pina

first: Solmaz

last: Sahebjam

first: Inna


title: Differential gene expression analysis upon Kat7 deletion in mouse lung AT2 cells [bulk RNA-seq]

first: Yuning

last: Tang

overall_design: R26LSL-tdTomato; H11LSL-Cas9; Kat7f/f  and R26LSL-tdTomato; H11LSL-Cas9 mice were intratrachially transduced with SPC-Cre adenovirus. TdTomato+ cells were FACS isolated from the transduced lungs after 4 days, and used for bulk RNA-seq.


title: Preclinical Evaluation of the Efficacy of a Cyclin-dependent Kinase Inhibitor Ribociclib in Combination with Letrozole Against Patient-Derived Glioblastoma Cells

city: Cincinnati

first: Pankaj

middle: B.

last: Desai

address: 231 Albert Sabin Way, Medical Science Building Suite 3303 (Desai Lab)

department: Pharmaceutical Sceinces

institute: University Of Cincinnati

summary: Ongoing studies suggest that letrozole (LTZ), a drug used in the treatment of breast cancer, can potentially be repurposed as a novel therapeutic for Glioblastoma (GBM). In a phase 0/1 trial in recurrent GBM patients we observed that LTZ permeates into the GBM tissue and triggers dose-dependent changes in the expression of genes regulating cell cycle (e.g. CDKN2A/N2B, CDK4). Based on these observations, we hypothesized that a combination of cyclin dependent kinase (CDK) 4/6 inhibitors with LTZ may result in synergistic anti-GBM activity. Therefore, we assessed the anti-tumor effects of LTZ in combination with ribociclib, a third-generation CDK4/6 inhibitor and the brain pharmacokinetics of ribociclib. Using cell viability and neurosphere growth assay against a panel of patient-derived GBM lines both compounds were found to be cytotoxic when used as single agents and were strongly synergistic when used in combination. We then assessed the DNA damaging effects (ɣH2AX induction), cell cycle arrest and the induction of apoptosis (Annexin V-FITC/PI) of both compounds as single agents and when used in combination. LTZ potentiated ribociclib-induced DNA damage and cell cycle arrest leading to apoptosis. Systemic and brain pharmacokinetics analysis of ribociclib in Sprague-Dawley (SD) rats by serial blood and brain extracellular fluid (ECF) sampling showed that ribociclib penetrates the blood-brain barrier with a partitioning coefficient (Kpu, u, brain) of about 10%. Overall, our studies suggest that a combination of ribociclib with LTZ is likely to be strongly synergistic against GBM at concentrations of the drugs that can be achieved in the brain

overall_design: RNAseq analysis of tumor samples from recurrent GBM patients treated with LTZ in a phase 0/1 clinical study (NCT03122197). Formalin-Fixed, Paraffin-Embedded (FFPE) tumor samples LTZ dose cohorts (n = 3 each) in the 2.5 mg (Group 1), 5 mg (Group 2), 10 mg (Group 3) and in the 12.5 mg (Group 4), and (n = 6) in the 15 mg (Group 5) were processed for mRNA isolation via depletion RNA purification.

first: Sidharth

middle: N

last: Gadgil

first: Aniruddha

last: Karve

first: Gary

last: Gudelsky

first: Bhavesh

last: Gabani

first: Mario

last: Medvedovic

first: Shravani

last: Kulkarni

first: Timothy

last: Phoenix

first: David

middle: R

last: Plas

first: Trisha

last: Wise-Draper

first: Soma

last: Sengupta

first: Biplab

last: Dasgupta

first: Lalanthica

middle: V

last: Yogendran


title: Platelets impair the resolution of inflammation in atherosclerotic plaques in insulin-resistant mice after lipid-lowering

first: Sofie

last: Delbare

address: 435 East 30th Street

institute: NYU Langone

summary: Insulin resistance reduces the benefits of lipid-lowering, as evidenced by higher cardiovascular risk in type 2 diabetes despite LDL-cholesterol reduction. Platelet activation, a key feature in insulin resistance, may hinder inflammation resolution in atherosclerosis. Using an obese, insulin-resistant mouse model, we induced atherosclerosis and treated mice with an apoprotein B oligonucleotide for lipid-lowering, with or without platelet depletion. Platelet depletion increased Fcgr4+ macrophages, reduced necrotic cores, and dampened inflammatory gene expression. Platelets hinder inflammation resolution in insulin resistance during lipid-lowering. Targeting platelet activity may enhance atherosclerosis regression and reduce cardiovascular risk.

overall_design: Atherosclerosis, obesity and impaired glucose tolerance were induced in 8-12 weeks old male Ldlr-/- mice by high-fat high-cholesterol diet feeding  for progression period (20 weeks, Basline group) and regression period (3 weeks). Atherosclerosis regression was achieved by reversal of hypercholesterolemia using an apolipoprotein B antisense oligonucleotide. During this period, mice received injections of IgG control or anti-CD42b antibody to deplete platelets. Mice were assigned to baseline (BL) or regression groups: ApoB-ASO + IgG or ApoB-ASO + aCD42.

first: Maria

last: Laskou

first: Michael

last: Gildea

first: Vitor

last: de Moura Virginio

first: Ada

last: Weinstock

first: Maxwell

last: La Forest

first: Franziska

last: Krautter

first: Letizia

last: Amadori

first: Casey

last: Donahoe

first: Tessa

last: Barrett

first: Chiara

last: Giannarelli

first: Jeffrey

last: Berger

first: Edward

middle: A

last: Fisher


title: Performing RNA sequencing on wild-type and Arrb2 knockout mouse primary astrocytes within the MPP+ model

city: Nanjing

first: Lei

last: Cao

address: 101 Longmian Avenue

institute: Nanjing Medical University

summary: We aimed to investigate the potential mechanism underlying the phenotypic transformation of astrocytes mediated by β-arrestin2. Primary astrocytes were isolated and cultured from the midbrain of neonatal WT and Arrb2 KO mice. RNA sequencing (RNA-Seq) was performed to compare the transcriptome of astrocytes in the context of MPP+ treatment.

overall_design: Wild-type and Arrb2 knockout primary astrocytes were treated with PBS or MPP+ for 24 hours followed by RNA sequencing.

first: Xin

last: Sun

first: Yueping

last: Wang

first: Yajie

last: Zhang

first: Ruixue

last: Han

first: Min

first: Jing

first: Ting

first: Yang

last: Liu

first: Gang

last: Hu

first: Ming

last: Lu


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [bullk ATAC-seq]

first: Yuning

last: Tang

summary: Epigenetic dysregulation is widespread in cancer. However, the specific epigenetic regulators and the processes they control to drive cancer phenotypes are poorly understood. We employed a novel, scalable and high-throughput in vivo method to perform iterative functional screens of >250 epigenetic regulators within autochthonous oncogenic KRAS-driven lung tumors. We identified many previously unappreciated epigenetic tumor-suppressor and tumor-dependency genes. We show that a specific HBO1 complex and MLL1 complex are the most impactful tumor suppressive epigenetic regulators in lung cancer. Histone modifications generated by HBO1 complex are frequently reduced in human lung adenocarcinomas. HBO1 and MLL1 complexes regulate chromatin accessibility at shared genomic regions, lineage fidelity and expression of canonical tumor suppressor genes. The HBO1 and MLL1 complexes are epistatic during lung tumorigenesis, and their functional correlation is conserved in human cancer cell lines. Together, these results provide a phenotypic roadmap of epigenetic regulators in lung tumorigenesis in vivo.

overall_design: To investigate the role of HBO1 and MLL1 complexes in regulating the chromatin accessibility landscape in KRAS-driven lung tumor cells, we conducted bulk ATAC-seq on FACS-sorted lung tumor cells from Kras-driven mouse models, where members of these complexes were individually inactivated using lentiviruses expressing sgRNA.

first: Tang

last: Yuning


title: Angel Wing: a class of alternative splicing regulators in animals

city: Hengyang City

first: Zhang

last: Ting

address: 28, West Changsheng Road Hengyang City,. Hunan Province, 421001, China.

institute: University of south China

summary: We have discovered a novel splicing regulatory factor. When this gene is knocked out in Drosophila, the flies exhibit drooping wings, disrupted muscle structure, and numerous aberrant splicing events in the neuromuscular system. Based on the wing phenotype observed in Drosophila, we have named this gene anw (angle wing).Our research focuses on investigating the mechanism of how Anw regulates alternative splicing.

overall_design: RNA-seq profiling of wildtype drosophila and anw knockout drosophila

first: YiKang

last: Rong

first: KaiLi

last: Li

first: Ying

last: Xiao


title: Functional mapping of epigenomic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes [scRNA-seq]

overall_design: To investigate the role of HBO1 and MLL1 complexes in regulating the transcriptional landscape and cellular states in lung cancer, we performed single-cell RNA sequencing (scRNA-seq) on tumor cells sorted by flow cytometry from genetically engineered KRAS-driven mouse lung tumors that were transduced with different sgRNAs targeting these two complexes. The scRNA-seq method employed is based on Split-Seq (PMID: 29545511), in which each sub-library contains all the sgRNAs, which are then computationally deconvoluted by Split-Pipe.


title: Systematic discovery of subcellular RNA patterns in the gut epithelium

city: Basel

first: Ilhan

middle: E

last: Acar

address: Klingelbergstrasse 48

department: BSSE

country: Switzerland

institute: ETH Zurich

summary: Subcellular RNA localization is crucial for the spatio-temporal control of protein synthesis and underlies key processes during development, homeostasis and disease. In epithelial cells, RNA can localize asymmetrically along the apico-basal axis. Yet, we ignore the localization of most transcripts as well as the diversity of patterns that they adopt. Here, we utilized proximity labeling (APEX-seq) and spatial transcriptomics (MERFISH) to map subcellular transcript localization in intestinal organoids and adult mice tissue. Many transcripts presented localization bias, often localizing in granular structures. We described the intrinsic and environmental factors that influence the formation of these patterns. We identified translation-dependent and -independent localization patterns and pintointed the role of 3’ UTRs and RNA-binding proteins. This subcellular RNA atlas can be referenced to extract new biological insights and provide hypothesis-free observation on spatial transcriptomics.

overall_design: In order to capture RNA in its cognate cellular environment, we utilized APEX2. DPP4 gene was fused with APEX2 to investigate apical localization in small intestinal organoids from mouse. As controls, GFP and ACTB genes were fused with APEX2. 4 samples of each fusion were sequenced for their RNA abundance and DPP4 samples were compared against GFP and ACTB samples separately to test for apically enriched RNAs.

first: Minkyoung

last: Lee

first: Davide

last: Eletto

first: Srivathsan

last: Adivarahan

first: Farah

last: Mhamedi

first: Kristina

last: Handler

first: Jihyun

first: Elena

last: Guido Vinzoni

first: Gustavo

last: Aguilar

first: Andreas

last: Moor


title: Single-cell activation screen identifies hepatic maturation regulators with zonal resolution

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: The maturation of lineage-committed embryonic hepatocytes requires both the timed activation of metabolic gene regulatory networks (GRNs) and silencing of embryonic programs to achieve adult hepatic functions. However, in vitro derivation of mature hepatocytes remains imperfect, and key transcriptional regulators governing GRN rewiring during late development are still insufficiently defined. To address this, we generated a developmental reference atlas and employed a dCas9 activation screen with single-cell transcriptomics on primary mouse embryonic hepatocytes, enabling effect ranking among late-onset transcription regulators. We identify Nr1i3 as a potent inducer of pericentrally expressed metabolic genes and Nfix as a critical suppressor of embryonic and periportal signatures. Supplementing liver zonation patterning signals with these regulators further enhanced the expression of pericentrally zonated metabolic genes, emphasizing the importance of a microenvironment-targeted approach. Our screening and analysis therefore highlight regulatory mechanisms underlying organ maturation and offer general strategies for improving the functionality of in vitro-derived cells.

overall_design: We generated a hepatocyte transcriptome dataset covering embryonic to adult stages using bulk RNA-seq of purified hepatocytes and scRNA-seq of liver cells. This dataset provided insights into the kinetics of gene expression, enabling the identification of suitable marker genes for assessing hepatic maturation with zonal resolution, as well as 61 transcriptional regulators activated during late development. In addition, we established a scalable, multi-parallel gain-of-function perturbation dataset through pooled single-cell dCas9-activation screening. This experimental validation of late-onset transcriptional regulators allowed us to identify suppressors of embryonic genes and activators of metabolic genes during liver maturation.

last: P Magalhaes

first: Atsuhiro

last: Taguchi

first: Alexander

last: Meissner


title: KRAS inhibition activates an actionable CD24 "Don't eat me" signal in pancreatic cancer [RNA-seq]

status: Public on Sep 04 2025

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: KRASG12C inhibitors (G12Ci) have produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the function of KRASG12C and possible G12Ci bypass mechanisms, we developed an autochthonous KRASG12C-driven PDAC model. Compared to the classical KRASG12D PDAC model, the G12C model exhibits slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRASG12C tumors produced modest impact despite stimulating a ‘hot’ tumor immune microenvironment. Immunoprofiling revealed that CD24, a ‘don’t eat me’ signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRASG12D-driven PDAC. Together, this study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC.

overall_design: To compare the transcriptomic features between KRAS G12C and KRAS G12D-derived tumor cell lines, bulk RNA-seq was conducted in KRAS G12C and KRAS G12D mouse pancreatic cancer cell lines.

first: Yongkun

last: Wei

first: Jun

last: Yao

first: Wantong


title: Elevated PKA activity at synapses and broad molecular disturbances in the striatum of Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder [bulk RNA-Seq]

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

summary: Loss-of-function mutations in Akap11 (a protein kinase A (PKA)-binding protein) greatly increase the risk of bipolar disorder and schizophrenia. We conducted multi-omic analysis of Akap11 mutant mouse brains, and report that AKAP11 interacts with multiple proteins involved in signaling and proteostasis. In Akap11+/- and Akap11-/- synapses, PKA protein levels were markedly elevated, and many proteins (eg GluA1) were hyperphosphorylated at PKA sites. Akap11 mutant brains showed extensive transcriptomic changes, prominently in synapse-related gene-sets and most profoundly in neurons of the striatum, a brain region implicated in motivation, cognition and psychiatric disorders. Widespread misexpression and differential phosphorylation of neuromodulation-related genes indicated perturbed function and altered organization of the striatum. Our work reveals the molecular mechanism and a potential circuit basis of brain dysfunction in a genetically valid model of psychotic disorder.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from prefrontal cortex (PFC), somatosensory cortex (SSC), hippocampus (HP), striatum (ST), Thalamus (TH) and substantia nigra (SN) at 4, and12 weeks of age in Akap11 mutant mice.

first: Bryan

last: Song


title: KRAS inhibition activates an actionable CD24 "Don't eat me" signal in pancreatic cancer

overall_design: Mouse PDAC tumor tissues were disected from mice pancreas with  KRAS G12C and KRAS G12D mutation and single cells were obtained for scRNAseq analysis.


title: Preventing light-induced toxicity in a new mouse model of sector retinitis pigmentosa caused by Rhodopsin M39R variant

city: London

first: Rosellina

last: Guarascio

address: 11-43 Bath street

institute: UCL Institute of Ophthalmology

summary: Retinitis Pigmentosa (RP) is an inherited retinal dystrophy characterized by the progressive loss of rod photoreceptors. Sector RP is a form of RP, where degeneration originates in the inferior retina, mainly influenced by light exposure. Over 200 RHO variants are pathogenic and associated with autosomal dominant RP. RHOM39R is one of the most common RHO variants linked to sector RP in the UK. A knock-in (KI) mouse model expressing RhoM39R was generated and characterized to investigate the mechanisms of degeneration associated with this variant and explore novel therapeutic strategies for rhodopsin sector RP. Under cyclic ambient light, RhoM39R/+ KI mice exhibited impaired retinal function by ERG, with some defects in OS ultrastructure, but retained normal outer nuclear layer (ONL) thickness. Repeated exposure to bright light led to photoreceptor loss. In contrast, RhoM39R/M39R KI mice in cyclic ambient light displayed severe retinal dysfunction, ONL thinning, and grossly abnormal OS ultra structure. In homozygous mice, a single bright light exposure significantly reduced ONL thickness within 48 h. The rescue of these models was achieved through reduced light exposure and pharmacological intervention. Rearing in dim red light (red cage condition) restored ERG responses in RhoM39R/+ KI mice and improved ONL thickness in RhoM39R/M39R KI mice. Transcriptomic analysis in RhoM39R/M39R KI mice revealed upregulation of Sphingosine 1-P Receptor (S1pr) transcripts. Treatment with the S1PR agonist Fingolimod (FTY720) before bright light exposure significantly reduced degeneration, demonstrating a protective effect in both heterozygous and homozygous models and suggesting potential a therapeutic approach for sector RP patients.

overall_design: We compared gene expression of 3 weeks old Rho+/+ and RhoM39R/M39R mice

first: Kalliopi

last: Ziaka

first: Michael

last: Cheetham


title: Intestinal organoid expression data from patients with MASLD-cirrhosis versus non-fibrotic MASLD

city: Catania

first: Grete Francesca

last: Privitera

address: Via Santa Sofia

department: Department of Clinical and Experimental Medicine

country: Italy

institute: University of Catania

summary:
This study aimed to establish and characterize an in vitro model of human intestinal organoids isolated from duodenal samples of patients with non-fibrotic MASLD and those with MASLD-cirrhosis. Whole transcriptome analysis and the energetic and redox status of the organoids were assessed to characterize intestinal functional impairment in the context of MASLD.
We used microarrays to detail the whole transcriptome dysregulation underlying intestinal dysfunction in organoids isolated from chirrotic versus non-fibrotic MASLD patients.

overall_design: Total RNA was isolated from intestinal organoids derived from duodenal samples of patients with non-fibrotic MASLD and those with MASLD-cirrhosis. High-throughput transcript profiling in organoids from five subjects with non-fibrotic MASLD and five subjects with MASLD-cirrhosis was conducted using microarray methodology (Clariom D Assay, Thermo Fisher Scientific).

first: Agnese

last: Filippello

first: Salvatore

last: Piro


title: The one-carbon metabolism enzyme Ahcy is a redox sensor that modulates gene expression to protect against light stress-induced retinal degeneration

city: WEST LAFAYETTE

first: Weake

middle: Marie

last: Vikki

state: IN

address: 175 S University st

department: Biochemistry

institute: Purdue University

summary: One-carbon metabolism influences the response to oxidative stress through antioxidant biosynthesis and the transcriptional status of the cell via epigenetic mechanisms. One-carbon metabolism is responsible for the production of the universal methyl donor, S-adenosylmethionine (SAM), which generates the potent methyltransferase inhibitor, S-adenosylhomocysteine (SAH). The essential metabolic enzyme, S-adenosylhomocysteinase (AHCY), functions within one-carbon metabolism and is the sole enzyme to catabolize the metabolite S-adenosylhomocysteine (SAH). Under oxidative stress conditions, AHCY becomes oxidized at a critical residue for its activity correlating with increased SAH abundance in the Drosophila head. Here, we profiled the photoreceptor transcriptome at a single time point after 3-hour blue light exposure relative to untreated controls in the Drosophila eye. We used RNAi expressed in all cells of the eye under longGMR-Gal4 to knockdown Ahcy and examined photoreceptor cells enriched using nuclei-immunoenrichment. As a control, we expressed non-specific RNAi against mCherry.

overall_design: To knockdown Ahcy in the Drosophila eye, we crossed longGMR-Gal4, Rh1-KASHGFP flies to UAS-RNAi flies targeting either Ahcy (y[1] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.HMC03222}attP40/CyO, Bloomington Stock #51477) or mCherry (control) in a cnbw background. We then collected male progeny, which were raised in 12-hour light: 12-hour dark conditions at 25C until 5 days post-eclosion. Flies treated with blue light were secured in a blacked-out box with strip LED lights surrounding the samples and were exposed to continuous blue light for three hours relative to untreated controls. 150 male flies were collected per sample (3 replicates). We affinity enriched photoreceptor nuclei for DNA isolation as previously described (Jauregui-Lozano et al., 2021, Genetics). CUT&RUN was performed on bead-bound nuclei as described in (Meers et al. 2019) using pAG-MNase fusion protein (Addgene plasmid #123461) purified using the Pierce cobalt kit (ThermoFisher, PierceTM His Protein Interaction Pull-Down Kit, Cat. #21227). The following antibodies were used for CUT&RUN with a 20-minute pAG-MNase activation time: anti-H3K4me3 (EpiCypher, 13-0060), anti-H3K27me3 (EpiCypher, 13-0055) and IgG (EpiCypher, 13-0042). CUT&RUN libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina®. Libraries were sequenced on the Illumina NovaSeq X Plus platform. We removed three of samples (mCherryRNAi untreated H3K4me3 replicate 2, mCherryRNAi untreated H3K27me3 replicate 1, and AhcyRNAi untreated H3K4me3 replicate 2) after preliminary analysis due to poor data quality. Pair-ended reads were processed similarly as RNA-seq data, except we used bowtie2 (Langmead and Salzberg 2012) for alignment with the dovetail argument. Data is shown as CPM-normalized and subtracted for respective IgG control. Metaplots were generated using deepTools (Ramírez et al. 2016) based on custom GTF files represented unique used transcripts.

first: Sarah

last: Stanhope

first: Makayla

last: Marlin

first: Vikki

middle: M

last: Weake


title: Downregulation of Ahcy with and without blue light exposure significantly alters global gene expression in the Drosophila eye

overall_design: To knockdown Ahcy in the Drosophila eye, we crossed longGMR-Gal4, Rh1-KASHGFP flies to UAS-RNAi flies targeting either Ahcy (y[1] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.HMC03222}attP40/CyO, Bloomington Stock #51477) or mCherry (control) in a cnbw background. We then collected male progeny, which were raised in 12-hour light: 12-hour dark conditions at 25C until 5 days post-eclosion. 150 male flies were collected per sample (3 replicates). We affinity enriched photoreceptor nuclei for RNA isolation as previously described (Jauregui-Lozano et al., 2021, Genetics). Nuclear RNA was purified using ZYMO Direct-zol RNA Microprep Kits (#R2061). RNA library were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760S). rRNA was depleted using NEBNext® RNA Depletion Core Reagent Set with RNA Sample Purification Beads (E7870L). Libraries were sequenced using NovaSeq X Plus.

first: Gaoya

last: Meng


title: CD47 Expression in Solid Tumors Correlates with Phagocytic Tumor-Associated Macrophage Gene Signature

city: Foster City

first: Mengshu

last: Xu

state: California

address: 300 Lakeside Drive

institute: Gilead Sciences

summary: CD47 is a “don’t eat me” signal that is frequently overexpressed in tumors to evade phagocytosis by tumor associated macrophages (TAM). Investigational agents targeting CD47, such as magrolimab, aim to induce phagocytosis of tumor cells by TAMs. Previously, two functionally defined key TAM subsets have been identified: complement C1q C chain positive (C1QC) TAMs, which display pro-phagocytic activity, and secreted phosphoprotein 1 positive (SPP1) TAMs that express pro-angiogenic markers. Here we characterize CD47 expression and its relationship with tumor macrophages in solid tumor samples.

overall_design: Resectable tumors from patients with head and neck squamous cell carcinoma (HNSCC), breast cancer (BC), and colorectal cancer (CRC) were profiled by RNA sequencing. FFPE samples were procured from commercial sources. Whole slide FFPE samples of tumor biopsies were used without further microdissection. RNA was extracted from all samples and subjected to mRNA sequencing

first: Nicholas

last: van Buuren

first: Min

last: Wang


title: Human microglia reduce alpha-synuclein aggregation and are neuroprotective in adult mouse brain

city: Kuopio

first: Katrina

last: Albert

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: Microglia, brain-resident immune cells, are involved in pathophysiology of several neurodegenerative diseases, including Parkinson’s disease. Given significant species-specific differences in microglia gene expression, particularly in disease-risk genes, as well as the highly reactive nature of these cells, studying human microglia in a whole brain environment is essential. Here, we established a humanized mouse model by transplanting human induced pluripotent stem cell-derived hematopoietic progenitor cells into the striatum of immunodeficient adult mice and injected human alpha-synuclein preformed fibrils to model Parkinson’s disease pathology. We aimed to create a novel model of Parkinson's disease and studied the response of the human microglia and mouse cells to the preformed fibrils.

overall_design: iPSC-derived human microglia transplanted to the striatum of immunodeficient mice, and mouse cells, treated with alpha-synuclein preformed fibrils or saline (vehicle), or no treatment.

first: Sara

last: Kälvälä

first: Šárka

last: Lehtonen


title: Exploring fibroblast activation protein as an early biomarker in chronic lung allograft dysfunction

city: Chicago

first: Yudai

last: Miyashita

address: Simpson Querrey 5-402-C 303 E Superior Street

department: Thoracic Surgery

institute: Northwestern Univesity

summary: This dataset contains single-cell RNA sequencing (scRNA-seq) data from human lung transplant recipients.Lung tissue samples were collected from both CLAD patients and donor  to assess cellular heterogeneity and gene expression dynamics.

overall_design:
Lung tissue samples were obtained from human lung transplant recipients diagnosed with chronic lung allograft dysfunction (CLAD) and from donor. Single-cell suspensions were prepared from these tissues and processed using the 10x Genomics Chromium platform. Raw sequencing data were processed with Cell Ranger, followed by clustering, UMAP visualization, and differential gene expression analysis using Seurat. This experimental design allows for comparative analysis of gene expression profiles between CLAD and control groups.

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

first: Taisuke

last: Kaihou

first: Hideki

last: Nagata

first: Takashi

last: Hiroshima

first: Yusuke

last: Sugiura

first: Kaijie

last: Zhang

first: Yuanqing

last: Yan

first: Alicia

last: Steffens

last: Kanou

first: Toru

last: Kimura

first: Bowen

first: Ankit

last: Bharat

first: Yasushi

last: Shintani

first: Chitaru

last: Kurihara


title: Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation [Cep]

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

institute: National Taiwan University

summary: A time-series alteration in intestine epithelial microbiota was linked to the emergence of intraepithelial bacteria and a unique transcriptome profile in the mouse colon during IBD development.

overall_design: The gut microbiota in epithelial samples was analyzed in a time-series mode.

first: Yu-Chen

last: Pai

first: Yi-Hsuan

last: Li


title: T cell phenotype changes associated with oncolytic virotherapy combined with Nivolumab

first: Roger

state: FL

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: There is a critical unmet need for safe and efficacious neoadjuvant treatment for cisplatin-ineligible patients with muscle invasive bladder cancer. We launched a Phase 1b study using the combination of intravesical cretostimogene grenadenorepvec (oncolytic serotype 5 adenovirus encoding granulocyte-macrophage colony stimulating factor) with systemic nivolumab in cisplatin-ineligible patients with cT2-4aN0-1M0 muscle invasive bladder cancer. The primary objective was to measure safety and the secondary objective to assess the antitumor efficacy of the combination. No dose limiting toxicity was encountered in 21 patients enrolled and treated. Combination treatment achieved a pathologic complete response rate of 42.1%, which was associated with baseline free E2F activity and tumor mutational burden, but not PD-L1 status. Although T cell infiltration was broadly induced following intravesical oncolytic virotherapy, the formation, enlargement and maturation of tertiary lymphoid structures (TLS) was specifically associated with complete response, supporting the importance of coordinated humoral and cellular immune responses. Together, these results highlight the potential of this combination regimen to enhance therapeutic efficacy in cisplatin-ineligible patients with muscle invasive bladder cancer, warranting its additional study as a neoadjuvant therapeutic option.

overall_design: To investigate changes of T cell phenotypes in response to oncolytic virotherapy combined with Nivolumab, we performed RNAseq of pre- and post-treatment tumors from 22 patients.

first: Nancy

last: Villa

first: Xiaoqing


title: The hepatitis E virus capsid protein ORF2 counteracts cell-intrinsic antiviral responses to enable persistence in hepatocytes

city: Heidelberg

first: CARL

last: HERRMANN

state: Baden-Wurtemberg

address: INF 364

department: Institut für Pharmazie und Molekulare Biotechnologie

institute: CRomLab

summary: We used scRNA-seq to study the cell-intrinsic antiviral response to hepatitis E virus infection in the immunocompetent hepatoma cell line HepG2/C3A. In this study, we identified a replication-limiting bottleneck at approximately 56 h post-infection at which the presence of the viral capsid protein ORF2 is decisive for establishment of an equilibrium between viral replication and the antiviral response. ORF2 antagonizes antiviral signaling downstream of pattern recognition receptors, at least partly through direct interaction with the central adaptor protein TBK1. By scRNA-seq, we confirmed that ORF2 dampens the antiviral response directly within infected cells, thereby also affecting the antiviral response in uninfected bystanders. In the presence of ORF2, the antiviral response was globally dampened at the early, replication-limiting bottleneck. This further substantiated that the equlibirium between viral replication and the antiviral response is a crucial mechanism of HEV persistence in hepatocytes.

overall_design: We infected HepG2/C3A cells with HEV-3 Kernow/C1-p6 wild-type (WT) virus particles or derived ΔORF2 virus particles, which do not encode the ORF2 protein and were produced by trans-complementation. Virus particles were bound at 4 °C for 2 h, internalized for 8 h, and harvested for scRNA-seq analysis by microfluidics-based 3’-targeted 10x Genomics 56 h and 7 days post-internalization. Uninfected samples and WT infection were analyzed at both time points, while ΔORF2 infection was only analyzed at 56 h post-internalization.

first: Ann-Kathrin

last: Mehnert

first: Sebastian

last: Stegmaie

first: Carlos

last: Ramirez Alvarez

first: Vladimir

last: Gonçalves Magalhães

first: Carla

last: Siebenkotten

first: Jun-Gen

last: Hu

first: Daniel

last: Kirrmaie

first: Michael

last: Knop

first: Xianfang

last: Wu

first: Carl

last: Herrmann

first: Marco

last: Binder

first: Viet Loan

last: Dao Thi

first: Thibault

last: Tubiana

first: Elif

last: Toprak


title: Adult human subventricular zone microglia promote a protective niche for neuronal progenitors in Parkinson’s Disease

city: Amsterdam

first: Vanessa

last: Donega

address: Boelelaan 1108

department: Anatomy and Neuroscience

country: Netherlands

institute: Amsterdam UMC

summary: Neural stem cells (NSCs) of the subventricular zone (SVZ) of the mammalian brain become increasingly quiescent with aging, which correlates to increased inflammatory signals in the SVZ. Therefore, targeting cells that secrete inflammatory signals, such as microglia cells, could potentially re-activate NSCs. In this study we characterized CD11b‑positive microglia isolated from fresh post-mortem SVZ tissue from non-demented control (Aged), Alzheimer’s disease (AD), and Parkinson’s disease (PD) donors by single-cell RNA sequencing and bulk RNA sequencing. Our transcriptome data revealed changes in gene signature of microglia from the SVZ of PD and AD patients, highlighting a dynamic and disease-dependent response. To determine how these differences in gene signature translated into microglia function, iPSC-derived NSCs were cultured with supernatant from SVZ microglia isolated from Aged, PD, and AD donors. Our data showed a significant increase in proliferation and neuronal differentiation in the PD condition. Furthermore, we identified NR4A2, which encodes for a transcription factor that promotes an anti-inflammatory phenotype in microglia, as a potential molecular mechanism that promotes a more neuroprotective phenotype in microglia. Altogether, our work identified a neuroprotective subpopulation of SVZ microglia that could be a novel target to promote repair in neurodegenerative diseases.

overall_design: Single-cell transcriptome data from the SVZ of PD patients. Progenitors, astrocytes, and microglia were isolated by FACS. Sort-seq was run on single-cells as described in Muraro et al., 2016.

first: Sara

last: Pecoraro

first: Marloes

last: Verkerke

first: Jacqueline

last: A Sluijs

first: Bert

last: van het Hof

first: Miriam

last: van Strien

first: Carlie

last: de Vries

first: H. Elga

first: Wilma

last: D J. van de Berg

first: Elly

last: M Hol


title: Epigenetic and Transcriptional Programming of Esophageal Eosinophils by the Local Tissue Environment [scRNA-seq]

first: Jennifer

last: Felton

state: Ohio

address: 3333 Burnet Ave, ML7028

department: Department of Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

summary: Tissue eosinophilia is a hallmark feature of allergic diseases. Eosinophils resident in different tissues have unique properties, and whether that heterogeneity is stochastic or regulated by cell-intrinsic or extrinsic factors has not been established. We profiled tissue eosinophils in the esophagus during allergic inflammation using single-cell sequencing, epigenomic mapping, and flow cytometry. Human and murine esophageal eosinophils exhibited a specialized transcriptional and epigenetic landscape, composed of metabolic, extracellular sensing, and immunomodulatory genes, and enriched for AP-1 transcription factor binding sites.  Additionally, human esophageal eosinophils were enriched for genes present within allergic disease risk loci and genes that correlated with the degree of esophageal eosinophilia. Furthermore, the esophageal eosinophil molecular signature was regulated by interactions between eosinophils and esophageal epithelial cells.  Taken together, we determined that esophageal eosinophils are programmed through interactions with epithelial cells by interplay of local tissue extrinsic factors that operate through a transcription factor complex containing AP-1.

overall_design: We performed scRNA-seq on esophageal tissue from CC10-iIL13Tg and CD2-IL5Tg mice. Cells were pooled from 4 mice per replicate.

first: Marc

last: Rothenberg