first: Liyuan

summary: MASLD, especially its severe form MASH, progresses to liver fibrosis, leading to cirrhosis and liver cancer. The crosstalk between spleen and liver in MASLD/MASH progression remains poorly understood. Here, we find the enlarged spleens in MASLD patients, and the induced TRNP1hiCD8+ T cells in the spleens of MASLD/MASH mouse models and confirmed in MASLD patients, with pro-fibrotic property by secreting INSR-α. Mechanistically, demethylated DNA and H3K27me3, increased H3K27ac, together with bolstered enhancer-promoter contact, synergistically reorganized chromatin topologically associating domains spatially to initiate the expression of transcription factor TRNP1 in splenic CD8+ T cells. TRNP1 then transcriptionally activates the expression of FURIN and CTSD, promoting the maturation and ectodomain shedding of INSR-α thereby facilitating its secretion to activate hepatic stellate cells. In vivo blockade of INSR-α using neutralizing antibodies alleviates MASLD/MASH-induced liver fibrosis. Therefore, this study reveals splenic TRNP1hiCD8+ T cells with pro-fibrotic property and suggests a potential anti-fibrotic strategy.

overall_design: scRNA-seq profiling of splenocyts from ND or MCDHFD (7 weeks) induced MASH mice models.

first: Yahui

last: Wang

first: Kai

last: Wei

first: Wen

last: Nie

first: Yayuan

last: Feng

first: Zhiwen

last: Shi

first: Jin

last: Hou


title: Epigenome analysis of precursor lesions of endometrial endometrioid carcinoma

status: Public on Apr 30 2026

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation For Cancer Research

summary: We performed genome-wide DNA methylation profiling on 126 samples from 59 cases with atypical endometrial hyperplasia, atypical polypoid adenomyoma, and endometrial carcinoma, all of whom had received oral MPA treatment at the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

overall_design: DNA methylation status was analyzed using genomic DNA from each tissue on the Illumina Infinium MethylationEPIC BeadChip Arrays, according to the manufacturer’s instructions.

first: Seiichi

last: Mori


title: Metabolically and epigenetically reprogrammed splenic TRNP1hiCD8+ T cells exacerbate liver fibrosis

city: Shanghai

last: Zhang

state: China

address: Xiangyin road

department: National Key Laboratory of Medical Immunology & Institute of Immunology

country: China

institute: Naval medical university

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K27me3 and H3K27ac CUT&TAG-seq profiling of splenic CD8+ T cells from ND or CDAHFD (7 weeks) induced MASH mice models.


overall_design: Hi-C profiling of splenic CD8+ T cells from ND or MCDHFD (7 weeks) induced MASH mice models.


title: Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [cytoDRIP-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

country: USA

institute: University of Texas M.D. Anderson Cancer Center

summary: R-loops are three-stranded nucleic acids containing DNA-RNA hybrid and a third displaced ssDNA and are widely distributed across the genome. Dysregulation in R-loop dynamics cause DNA damage and genome instability. Although its role has been extensively investigated in various pathological processes, whether R-loops are perturbed during senescence and tissue aging remains unclear. Here we observe a global decline in R-loop stalling across the genome during senescence. While R-loops in nucleus were dramatically decreased, we detected their significant accumulation in the cytoplasm in senescent cells. We identify their source as nuclear R-loops with a specific enrichment in alpha-satellites, a subset of repetitive elements. Notably, these cytoplasmic R-loops localize into cytoplasmic chromatin fragments (CCF) to induce cGAS-STING innate immune response, and this nucleocytoplasmic transport is dependent on exportin 1 (XPO1)/DEAD-Box helicase 1 (DDX1) complex. Targeting R-loop nuclear export by XPO1 inhibitor Selinexor (KPT-330) suppresses the inflammatory response in senescent cells and relieves inflammaging in aged mice. In summary, our findings linked aberrant accumulation of cytoplasmic R-loops to inflammaging, rendering their nucleocytoplasmic transport process an ideal target for suppressing inflammaging.

overall_design: We performed cytoDRIP-seq (cytoplasmic DNA-RNA-hybrid immunoprecipitation-seq) in proliferating and senescent IMR90 cells to identify the origins of cytoplasmic R-loops, and we combined it with NuclearDRIP to confirm their sources as nuclear R-loops. In CytoDRP-seq, we also treated senescent cells with DDX1 knockdown to determine if DDX1 is required for nucleocytoplasmic transport of R-loops.

first: Xue

last: Hao

first: Rugang


overall_design: CUT&TAG-seq profiling of splenic CD8+ T cells from ND or MCDHFD (7 weeks) induced MASH mice models.


title: Eosinophils Orchestrate Intestinal Remodeling and Promote Innate Defense During Reproduction

city: Princeton

first: Yuri

last: Pritykin

state: New Jersey

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Mammalian reproduction requires profound maternal immune adaptations to safeguard reproductive success and ultimately shape the evolutionary trajectories of a species. While systemic and placental immunity is known to shift toward tolerance during pregnancy, how maternal immunity adapts in barrier tissues, sites of frequent infection and inflammation, from pregnancy through the postpartum lactation period remains poorly understood. Here, we discovered a previously unrecognized role for eosinophils, a type of granulocyte typically associated with allergies and helminth infections, in remodeling the intestinal barrier during reproduction. Beginning in pregnancy and peaking during lactation, eosinophils originating from bone marrow accumulate in the small intestine in the absence of infection or inflammation. Using genetic and pharmacological perturbations, organoid cultures, and single-cell and spatial transcriptomics, we show that eosinophils promote goblet cell differentiation in a stem-cell-intrinsic manner, leading to increased mucus production. This adaptation culminates during lactation, limits pathogen entry and dissemination, conferring broad innate protection against enteric bacterial infections. Remarkably, both eosinophil accumulation and goblet cell induction persist after lactation, revealing durable remodeling of the intestinal immune and epithelial landscapes with sustained innate defense. Our findings demonstrate that, despite a general trend toward systemic immunosuppression during reproduction, the maternal intestine undergoes remodeling to strengthen innate defense against enteric pathogens, a mechanism that may have evolved to protect mothers and offspring in pathogen-rich environments. More broadly, our work establishes a framework for studying tissue immune adaptation across the reproductive cycle and highlights that tissue can retain memory of physiological states, with lasting implications for host defense and reproductive health.

overall_design: Xenium spatial transcriptomics of mouse small intestine for nulliparous and lactating mice. The first 10 cm of small intestine were collected, fresh-frozen with isopentane, and embedded in OCT. Tissues cryosectioned at 10 μm were analyzed using the Xenium Prime 5k Mouse Panel. Samples were taken from two nulliparous and two lactating mice, with one nulliparous and one lactating sample placed on the same Xenium slide.

first: Chenyan

last: Huang

first: Amanda

last: Sun

first: Jojo

last: Reyes

first: Jessica

last: Ribeiro de Souza

first: Thomas

middle: R

last: Cafiero

first: Krist

middle: H

last: Antunes Fernandes

first: Fabricio

last: Marcus Silva Oliveira

first: Yujie

last: Qiao

first: Pedro

last: Gazzinelli-Guimaraes

first: Ai Ing

last: Lim


first: Liyuan

type: Expression profiling by high throughput sequencing

overall_design: Splenic CD8+ T cells were isolated and cultured in RPMI 1640 medium or methionine deficient meidum for 8 hours and harvested for RNA-seq.

first: Yahui

last: Wang

first: Kai

last: Wei

first: Wen

last: Nie

first: Yayuan

last: Feng

first: Zhiwen

last: Shi

first: Jin

last: Hou


last: Zhang

overall_design: CUT&TAG profiling of splenic CD8+ T cells from ND or MCDHFD (7 weeks) induced MASH mice models.


title: Eosinophils Orchestrate Intestinal Remodeling and Promote Innate Defense During Reproduction [scRNA-seq]

first: Yuri

last: Pritykin

overall_design: scRNA-seq of EPCAM+ intestinal epithelial cells (IECs) from the duodenum of nulliparous, pregnant, and lactating mice.

first: Chenyan

last: Huang


title: Boosting CAR T-cell functionality with oncolytic viruses for the treatment of pediatric diffuse midline gliomas

city: Utrecht

first: Konstantinos

last: Vazaios

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Although the potential of CAR (chimeric antigen receptor) T-cells has been demonstrated in hematological malignancies, their efficacy remains limited in the treatment of solid tumors such as pediatric diffuse midline gliomas (DMGs). Contributing factors hampering the success of CAR T-cells include the immunosuppression induced by the DMGs and the surrounding tumor microenvironment (TME). Oncolytic viruses (OVs) have shown to reverse this immunosuppressive effect, suggesting a potential combinatorial benefit of OV and CAR T-cells. Infection with high concentrations of the Goravir adenovirus and R124 reovirus induced DMG (n=6 cultures) lysis without affecting viability of GD2 or B7H3 directed CAR T-cells. In addition, RNA sequencing of tumor cells showed altered gene expression of cell cycle and antiviral response pathways. When used in combination, cytotoxicity of the CAR T-cells was enhanced and complemented with increased release of pro-inflammatory cytokines and chemokines, especially with R124. Furthermore, CAR T-cells co-cultured with OV-infected DMGs demonstrated a more cytotoxic effector phenotype compared to co-cultures with non-infected DMGs. Finally, these data demonstrate the enhanced benefit of DMG pre-infection with OVs for boosted CAR T-cell activity.

overall_design: RNA profiling of six diffuse midline glioma (DMG) patient-derived cell cultures. The collection included untreated DMG cells at timepoint 0, 24 and 72 hours, DMGs infected with 200 multiplicity of infection Goravir for 24 and 72 hours. As weel as DMG cells infected with 100 multiplicity of infection R124 for 24 and 72 hours

first: Antonio

middle: C

last: Tallon Cobos

first: Louisa

middle: P

last: van Oosterhout

first: Piotr

last: Waranecki

first: Annelisa

middle: M

last: Cornel

first: Noël

last: Dautzenberg

first: Marliek

last: van Hoesel

first: Caitlyn

last: Forbes

first: Stefan

last: Nierkens

first: Vera

last: Kemp

first: Rob

last: Hoeben

first: Jasper

last: van der Lugt

first: Friso

middle: G

last: Calkoen

first: Esther

last: Hulleman


first: Liyuan

last: Zhang

type: Methylation profiling by high throughput sequencing

overall_design: Six-week old C57BL/6 mice were induced by ND, CDAHFD or MCDHFD for 7 weeks. The spleen tissues were harvest for isolating primary CD8+ T cells and perfoming whole-genome bisulfite sequencing (WGBS).

first: Yahui

last: Wang

first: Kai

last: Wei

first: Wen

last: Nie

first: Yayuan

last: Feng

first: Hongmei

last: Xiao

first: Weifen

last: Xie


overall_design: RNA-seq profiling of splenic CD8+ T cells transfected with control or Flag-TRNP1 letiviral packaged vectors.

first: Zhiwen

last: Shi

first: Jin

last: Hou


overall_design: Splenic CD8+ T cells were isolated and cultured in RPMI 1640 control meidum or methionine deficient meidum for 6 hours and harvested for ATAC-seq.


overall_design: RNA-seq profiling of splenic CD8+ T cells from ND or MCDHFD (7 weeks) induced MASH mice models.


overall_design: RNA-seq profiling of splenic CD8+ T cells from ND or CDAHFD (7 weeks) induced MASH mice models.


overall_design: CUT&TAG-seq profiling of splenic CD8+ T cells transfected with control vector or Flag-TRNP1 letiviral packaged vector by anti-Flag antibody.


overall_design: ATAC-seq profiling of splenic CD8+ T cells from ND or MCDHFD (7 weeks) induced MASH mice models.


title: LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair [MeRIP-seq]

city: Beijing

first: Jun

last: Liu

address: Haidian District

department: School of Life Sciences

institute: Peking University

summary: Repression of DNA damage repair by PARP inhibitors (PARPi) has shown great efficacy in cancer treatment. However, therapy resistance remains a significant clinical challenge. Here, we demonstrated that the N6-methyladenosine (m6A) modification of long interspersed nucleotide element-1 (LINE1, or L1) facilitates DNA damage repair in cancer cells, whereas removal of L1 m6A modifications enhances the sensitivity of both BRCA-wild-type and BRCA-mutant cells to PARPi. Specifically, following olaparib treatment, METTL3 accumulates on chromatin, which results in increased chromatin accessibility. Knockdown of METTL3 or removal of m6A on L1 RNAs increases H3K9me3 levels, leading to reduced chromatin accessibility. This, in turn, inhibits DNA end resection at damage sites and prevents PARP1 dissociation, ultimately impairing homologous recombination repair and enhancing tumor sensitivity to PARPi. Our findings unveil a novel regulatory mechanism of L1 m6A that governs the DNA damage repair response, providing a potential strategy of targeting METTL3 in combination with PARPi for cancer therapy.

overall_design:
Chromatin-associated RNA m6A profiles of METTL3 knockdown cells (LOVO and RKO) and its control were generated by deep sequencing, in duplicate.

Chromatin-associated RNA m6A profiles of METTL3 knockdown cells (OVCAR8 and SKOV3) and its control were generated by deep sequencing, in duplicate.

first: Zihong

last: Kang

first: Ruimeng

last: Li


title: Human cerebellar organoids to study medulloblastoma pathogenesis and treatment. [scRNA-Seq]

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Faithful in vivo models of Group 4 medulloblastoma (G4 MB) are currently unavailable and recent studies showed the unique role of human-specific progenitors in the development of G3 and G4 MB. Here, we obtained cerebellar organoid (CbO) from expanded potential stem cells (EPSC) and developed them in vitro as 3D structures. We performed extensive characterisation of the epigenetic and transcriptomic profile of the mature CbO confirming the presence of sub compartment-specific cerebellar lineages linked to MB formation, including populations expressing signature genes reminiscent of the G3 and G4 MB cell-of-origin never described before. In parallel we have established a protocol to co-culture primary MB cells with our CbO to generate CbO-MB models. We confirmed that CbO sustains MB cells proliferation and invasion while preserving their molecular identity, and that CbO-MB recapitulated the efficacy of in vivo anti-tumour therapy, hence representing a suitable model to gain insight into G3/G4 MB pathogenesis and to set up pre-clinical drug screening.

overall_design: scRNAseq of developing cerebellar organoids (CbOs) and CbO-Medulloblastoma co-cultures

first: Silvia

last: Marino

first: Thomas

last: Willott

first: Yunchen

first: Sara

last: Badodi


title: Human cerebellar organoids to study medulloblastoma pathogenesis and treatment. [methylation]

summary:
Faithful in vivo models of Group 4 medulloblastoma (G4 MB) are currently unavailable and recent studies showed the unique role of human-specific progenitors in the development of G3 and G4 MB. Here, we obtained cerebellar organoid (CbO) from expanded potential stem cells (EPSC) and developed them in vitro as 3D structures. We performed extensive characterisation of the epigenetic and transcriptomic profile of the mature CbO confirming the presence of sub compartment-specific cerebellar lineages linked to MB formation, including populations expressing signature genes reminiscent of the G3 and G4 MB cell-of-origin never described before. In parallel we have established a protocol to co-culture primary MB cells with our CbO to generate CbO-MB models. We confirmed that CbO sustains MB cells proliferation and invasion while preserving their molecular identity, and that CbO-MB recapitulated the efficacy of in vivo anti-tumour therapy, hence representing a suitable model to gain insight into G3/G4 MB pathogenesis and to set up pre-clinical drug screening.
DNAme analysis of cerebellar organoids derived from 2 EPSC lines during development, then comparison of DNAme profiles of cerebellar organoids to human foetal cerebellum during development

overall_design: Silvia Marino


title: Disordered protein LAT encodes relative levels of signaling pathways in T cell activation

status: Public on Apr 29 2026

city: Cambridge

first: Adam

middle: J

last: Rubin

state: Massachusetts

address: 415 Main St.

institute: Broad Institute

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

overall_design: Refer to individual Series

first: Alex

middle: K

last: Shalek


title: LINE1 RNA demethylation represses chromatin accessibility and sensitizes cancer cells to blockage of DNA damage repair ChIP-seq

summary: Repression of DNA damage repair by PARP inhibitors (PARPi) has shown great efficacy in cancer treatment. However, therapy resistance remains a significant clinical challenge. Here, we demonstrated that the N6-methyladenosine (m6A) modification of long interspersed nucleotide element-1 (LINE1, or L1) facilitates DNA damage repair in cancer cells, whereas removal of L1 m6A modifications enhances the sensitivity of both BRCA-wild-type and BRCA-mutant cells to PARPi. Specifically, following olaparib treatment, METTL3 accumulates on chromatin, which results in increased chromatin accessibility. Knockdown of METTL3 or removal of m6A on L1 RNAs increases METTL3 levels, leading to reduced chromatin accessibility. This, in turn, inhibits DNA end resection at damage sites and prevents PARP1 dissociation, ultimately impairing homologous recombination repair and enhancing tumor sensitivity to PARPi. Our findings unveil a novel regulatory mechanism of L1 m6A that governs the DNA damage repair response, providing a potential strategy of targeting METTL3 in combination with PARPi for cancer therapy.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3 in LOVO and RKO cells, with or without METTL3 knockdown.

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for METTL3 in LOVO and RKO cells


title: Unbiased niche labeling maps immune-excluded niche in bone metastasis

status: Public on Apr 28 2026

first: Xiang

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse in different organs. In bone, niche macrophages express estrogen receptor (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of ER in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in metastatic niche and functionally tie ER signaling in macrophages to T cell exclusion during metastatic colonization.

overall_design: For the preparation of mouse tissues from Macrophage-specific Esr1-knockout mice, bone tissues (including bone and tumor) were collected, and live cells were isolated via FACS sorting. The study included both male and female mice, divided into two groups: the control group (LysM-ctrl) and the LysM-cre group (macrophage-specific Esr1 knockout). Each group consisted of three mice, and each mouse had two technical replicates (represented by two barcodes).

first: Xu

last: Zhan

first: Liu

last: Fengshuo

first: Zhang

last: Xiang


title: Vacuolar ATPase subunit Atp6v0c transgene promotes neuroprotection and long-distance axon regeneration in injured retinal ganglion neurons

status: Public on Apr 09 2026

city: Farmington

first: Jacob

last: Brady

state: Connecticut

address: 263 Farmington Avenue

department: Neuroscience

institute: UConn School of Medicine

summary: Central nervous system (CNS) projection neurons’ failure to repair/regenerate injured axons has devastating consequences for those who have sustained CNS injuries. Thus, there is a need for translatable factors capable of promoting long-distance axon regeneration in the CNS. We hypothesized that supporting lysosomes in injured neurons by supplementing their structural factors through gene therapy may foster axon regeneration. To test our hypothesis, we selected Atp6v0c for experimental regulation because it plays roles in lysosomal acidification and degradation of misfolded proteins in response to endoplasmic reticulum (ER) stress in injured neurons. We tested in a rodent optic nerve crush (ONC) model of traumatic optic neuropathy (TON) in which injured prototypical CNS projection neurons, the retinal ganglion cells (RGCs), do not regenerate damaged axons and eventually degenerate. Atp6v0c transgene expression was achieved using intravitreally-injected adeno-associated virus serotype 2 (AAV2), which transduces the RGCs. For benchmarking, we compared efficacy to AAV2-targeting of prominent regulators of axon regeneration, Pten and Klf9. We found that Atp6v0c transgene promoted RGC survival and long-distance axon regeneration, comparable to targeting Pten and Klf9. Thus, Atp6v0c is an axon regeneration-promoting factor with a potential for treating CNS injury and disease.

overall_design: Uninjured and injured (2 weeks post-ONC) RGCs from 12-week old wild-type (129S1/SvImJ (JAX strain 002448)) mice of both sexes were immunopanned and FACS-isolated from the retinal single cell suspension. After sorting, cells were processed by 10X Chromium scRNA-seq.

first: Ephraim

middle: F

last: Trakhtenberg


overall_design: For the preparation of mouse tissue for the SAMENT single-cell experiment, we collected various tissues, including lungs, livers, brains, femurs, and tibias, following an overnight (~10 hr) SAMENT substrate labeling period. Then tissues were processed and went through the cell sorting, to seperate the biotin positive and biotin negative populations. All the sorted cells from each sample were multiplexed following the CellPlex or TotalSeqC instructions, followed by library construction and sequencing.

first: Zhan

last: Xu

first: Fengshuo


title: Resilience to Diabetic Retinopathy (RDR) is Associated with a Pre-Retinopathy Transcriptional Program Induced by Diabetes

city: Chicago

first: Andrius

last: Kazlauskas

state: IL

address: 1905 W Taylor St

department: Department of Ophthalmology and Visual Sciences

institute: University of Illinois at Chicago

summary: The purpose of this project was to define gene expression changes associated with the acquisition and loss of resilience to diabetic retinopathy (RDR) in individual retinal cell types. Diabetes mellitus (DM) was induced with streptozotocin in male C57Bl6J mice. Single-cell RNA sequencing was performed on retinas from mice that experienced DM for 5 or 15 days, along with retinas from age-matched, non-DM mice. The resulting data sets were analyzed to identify DM-associated differentially expressed genes and pathway enrichments after each duration of DM. We observed that acquisition of RDR, shown to occur after 5 days of DM, was linked to altered expression of genes in a subset of retinal cells, mainly Müller cells. Pathway analysis indicated enhancement of numerous modes of protection, including reinforced neurovascular and structural homeostasis through phagocytosis, integrin signaling, and interferon-mediated defense. After 15 days of DM, when RDR is waning, this pro-protection surge in gene expression subsided. We conclude that a duration of DM that is too short to cause diabetic retinopathy (DR) nonetheless evoked a profound change in the gene expression profile within a subset of retinal cell types.  The nature and timing of this molecular shift indicated that it was not the preamble to DM-related damage that eventually develops. Rather, DM engaged numerous defense programs within Müller cells. These observations provide a molecular foundation for the retina's transient ability to remain healthy in the face of DM.

overall_design: Diabetes was induced in eight-week-old male C57BL/6J mice by five consecutive daily intraperitoneal injections of streptozotocin  prepared in citrate buffer. Age-matched non-diabetic control mice received an equivalent volume of citrate buffer. Retinal tissues were collected at two time points following diabetes induction: 5 days and 15 days. Four experimental groups were analyzed: Control 5D, DM 5D, Control 15D, and DM 15D. For each condition, retinas from three mice were pooled to generate a single-cell suspension (n = 3 pooled per sample). Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the 10× Chromium Single Cell platform (10× Genomics).

first: Janani

last: Rajasekar

first: Maria

last: Paula Zappia

first: Maximilian

middle: A

last: McCann

first: Maxim

middle: V

last: Frolov


title: Behavioral and transcriptomic markers of susceptibility to escalate fentanyl intake.

status: Public on Mar 31 2026

city: Lexington

first: Jack

middle: Vicent

last: Keady

state: KY

address: 789 S Limestone

department: Pharmaceutical Sciences

institute: University of Kentucky

summary: Background: The “loss of control” over drug consumption, known as escalation of intake in opioid use disorder (OUD), is well-established in preclinical rodent models. However, little is known about how antecedent behavioral characteristics, such as valuation of hedonic reinforcers prior to drug use, influence fentanyl intake trajectories. Moreover, it is unclear if distinct escalation phenotypes are driven by genetic markers predictive of OUD susceptibility. Methods: Male and female Sprague-Dawley rats (n=72) were trained in a sucrose reinforcement task using a progressive ratio schedule. Individual differences in responsivity to sucrose were hypothesized to predict escalation of fentanyl intake. Rats underwent daily 1-h acquisition sessions for i.v. fentanyl self-administration (2.5 µg/kg; FR1) for 7 days, followed by 21 6-h escalation sessions, then tissue from prefrontal cortex was collected for RNA sequencing and qPCR. Latent growth curve and group-based trajectory modeling were used, respectively, to evaluate the association between sucrose reinforcement and fentanyl self-administration and to identify whether distinct escalation phenotypes can be linked to gene expression patterns. Results: Sucrose breakpoints did not predict fentanyl acquisition nor change during escalation, but did predict fentanyl intake on the first day of extended access. Permutation analyses found no associations between behavior and single gene expression, either overall or within our ascertained phenotypes. However, weighted genome correlation network analysis (WGCNA) and gene set enrichment analysis (GSEA) determined several gene modules linked to escalated fentanyl intake, including genes coding for voltage-gated potassium channels, calcium channels, and excitatory synaptic signaling. Transcription factor analyses identified EZH2 and JARID2 as potential transcriptional regulators associated with escalated fentanyl intake. Further, genome-wide association study (GWAS) term categories positively associated with terms relating to substance use disorders. Discussion: Escalation of opioid intake largely differs from motivation for natural rewards like sucrose. Further, the gene networks associated with fentanyl escalation suggest that engagement of select molecular pathways were associated with “addiction prone” behavioral endophenotypes, potentially representing druggable targets for OUD. Our extended in silico identification of SNPs and transcription factors associated with the “addiction prone” high escalating rats highlights the importance of integrating findings from translational preclinical models, supporting patient-centered treatment options for OUD.

overall_design: RNA-seq profiling of the PFC of phenotypically distinct fentynal escalating rats.

first: Richard

last: Charnigo

first: Jakob

last: Shaykin

first: Emily

last: Prantzalos

first: Mengfan

last: Xia

last: Denehy

first: Cody

last: Bumgardner

first: Justin

last: Miller

first: Pavel

last: Ortinski

first: Michael

last: Bardo

first: Jill

last: Turner


title: Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation [Smart-seq2]

status: Public on Apr 27 2026

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

summary: The progression of IDH-mutant gliomas (IDH-G) from slow-growing tumors to fatal disease is associated with transcriptional and DNA methylation changes that remain poorly understood. Here, we profiled a longitudinal cohort of 36 IDH-G samples from 19 patients by joint-capture multi-omic single-nucleus (sn) DNA methylation and snRNA-seq. We show that IDH-G progression is associated with increase in malignant stem-like states, decreased differentiation and with methylation loss, which marks tumors with worse clinical outcome. Methylation loss was uniformly observed across malignant cells within individual tumors, suggesting that it may underlie rather than result from the increase in stem-like states. Analysis of cell state heritability and plasticity based on high-resolution phylogenetic trees connects DNA methylation loss to alterations in glioma cell states encoding and heritability. Our study offers insights on how DNA methylation loss reshapes cellular transitions and how it may mark clinically more aggressive tumors across IDH-G subsets.

overall_design:
Nuclei from frozen tumor tissue were isolated. Nucleus suspensions were inspected by microscope, counted using a hemocytometer, and sorted into 96 well plates by FACS. The single nucleus plates were processed by dual Smart-seq2 and DNA methylation protocol.

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

first: Ramya

last: Ravirum

first: Joshua S.

last: Schiffman

first: Dan A.

last: Landau

first: Mario L.

last: Suvà


title: Single-cell analysis of human kidney biopsy tissue reveals epithelial and immune cell responses to BK polyomavirus infection

status: Public on Feb 10 2026

city: Ann Arbor

first: Phillip

middle: John

last: McCown

state: MI

address: 1500 E. Medical Center Drive

department: Internal Medicine - Nephrology

institute: University of Michigan Medicine

summary: BK polyomavirus (BKV) infection is associated with injury and subsequent graft loss due to the extent of injury or rejection. However, the molecular mechanisms driving injury and subsequent adverse outcomes remain poorly understood. In a cross-sectional study, single-cell RNA sequencing from kidney allograft biopsies was used to assess cell type-specific responses between uninfected controls and two distinct phases of BKV infection: peaking (increasing viral blood titers) and resolving (decreasing viral titers following immunosuppression reduction). Genes upregulated in BK viral nephropathy (BKVN) were enriched for polyomavirus infection hallmarks, including ribosome biogenesis, translation, and energy restructuring. Additionally enriched pathways included wound healing, cellular stress, antigen presentation and immune signaling. Even without BKVN (peaking BK viremia alone), epithelial cells expressed signatures for wound healing, cellular stress, and extracellular matrix remodeling. In vivo tubular cell responses at single-cell resolution were validated against single cell transcriptomic data of BKV infected cells in a cell culture model. Despite similarities, in vivo tubular cells underwent metabolic adaptation favoring fatty acid oxidation and proinflammatory responses not observed in culture models likely from an absent innate and adaptive immune system. Despite lymphopenia and immunosuppressive therapies, the proportion of recipient derived intrarenal adaptive immune cells was expanded in biopsies associated with peaking viremia alongside activation of innate immune responses. Adaptive immune cells continued to have persistent inflammatory signaling and remodeling of energy metabolism during the resolving phase of infection. These novel insights into BKV-associated injury could have implications for clinical management and improved allograft outcomes

overall_design: Kidney biopsies post transplantation were collected from allografts at time of transplant, 3 months post transplantation, and 12 months post transplantation. If a patient developed BK infection, additional kidney biopsies were collected during the course of infection. Due to the rarity of kidney transplants and to respect the confidentiality of patients' sequencing data, raw data is not deposited.

first: Tess

last: Marvin

first: Rachel

last: Sealfon

first: Olga

last: Troyanskaya

first: Matthias

last: Kretzler

first: Chandra

middle: L

last: Theesfeld

first: Abhijit

middle: S

last: Naik


title: Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation

status: Public on Apr 14 2026

city: Oxford

first: Felice

middle: Hoching

last: Tsang

state: Oxfordshire

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

first: Rosa

last: Stolper


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

city: Geneva

first: Hanrong

last: Hu

address: B1 0 266.045 (Campus Biotech bâtiment B1)

department: Brain Mind Institute

country: Switzerland

institute: EPFL

summary: Why mammals cannot regenerate limbs, unlike amphibians, presents a longstanding puzzle in biology. We show that exposing ex vivo amputated embryonic mouse limbs to subatmospheric oxygen environment, or stabilizing oxygen-sensitive HIF1A enables not only rapid wound healing, but alters cellular mechanics, and reshapes the histone landscape to prime regenerative fates. Conversely, regenerative Xenopus tadpole limbs display low oxygen-sensing capacity, robust wound healing, a regenerative histone landscape, and glycolytic programs even under high oxygen. This reduced oxygen-sensing capacity, in stark contrast to mammals, associates with decreased HIF1A-regulating gene expressions. Our findings thus uncover species-specific oxygen sensing as a unifying mechanism for limb regeneration initiation across vertebrates, reveal how aquatic subatmospheric habitats may enhance regenerative capabilities, and identify targetable barriers to unlock latent limb regenerative programs in adult mammals.

sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus

overall_design: CUT&Tag of mouse and xenopus limb explants cultured at hypoxic or atmospheric oxygen levels

first: Kelly

first: Aztekin

last: Can


title: Metabolically and epigenetically reprogrammed splenic TRNP1hiCD8+ T cells exacerbate liver fibrosis

first: Liyuan

last: Zhang

summary: MASLD, especially its severe form MASH, progresses to liver fibrosis, leading to cirrhosis and liver cancer. The crosstalk between spleen and liver in MASLD/MASH progression remains poorly understood. Here, we find the enlarged spleens in MASLD patients, and the induced TRNP1hiCD8+ T cells in the spleens of MASLD/MASH mouse models and confirmed in MASLD patients, with pro-fibrotic property by secreting INSR-α. Mechanistically, demethylated DNA and H3K27me3, increased H3K27ac, together with bolstered enhancer-promoter contact, synergistically reorganized chromatin topologically associating domains spatially to initiate the expression of transcription factor TRNP1 in splenic CD8+ T cells. TRNP1 then transcriptionally activates the expression of FURIN and CTSD, promoting the maturation and ectodomain shedding of INSR-α thereby facilitating its secretion to activate hepatic stellate cells. In vivo blockade of INSR-α using neutralizing antibodies alleviates MASLD/MASH-induced liver fibrosis. Therefore, this study reveals splenic TRNP1hiCD8+ T cells with pro-fibrotic property and suggests a potential anti-fibrotic strategy.

overall_design: Splenic CD8+ T cells were isolated and clutured in RPMI 1640 control medium or methionine deficient medium for 6 hours and harvested for H3K27me3 CUT&TAG-seq.

first: Yahui

last: Wang

first: Kai

last: Wei

first: Wen

last: Nie

first: Yayuan

last: Feng

first: Zhiwen

last: Shi

first: Jin

last: Hou


title: Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [mono-colonized_RNA-seq]

status: Public on Feb 03 2026

city: Atlanta

first: Timothy

last: Sampson

state: Georgia

address: 615 Michael St

institute: Emory University

summary: The native microbiome influences a plethora of host processes, including neuroimmune function. However, the consequences of individual gut microbes on neuroinflammatory tone remain largely unexplored. In the present dataset, we investigated the consequences of four bacterial type strains representing prevalent genera within the mammalian gut microbiome (Bacteroides thetaiotaomicron (B. theta), Clostridium celatum, Lactobacillus johnsonii, and Escherichia coli) on the transcriptional profile of CD11b+ brain myeloid cells. After 2 weeks of mono-colonization with the bacteria species of interest, it was found that each bacterial type had distinct effects on brain myeloid cell gene expression, highlighting the bacterial dependent consequences of the microbiome for neuroinflammatory outcomes.

overall_design: Germ-free DBA/2NTac were either maintained as germ-free or mono-colonized with Bacteroides thetaiotaomicron, Clostridium celatum, Lactobacillus johnsonii, or Escherichia coli for 2 weeks. Brains were then perfused with PBS and CD11b+ cells were isolated by magnetic activated cell sorting for bulk RNA-seq.

first: Lisa

last: Blackmer-Raynolds

first: Lyndsey

middle: D

last: Lipson

first: Anna

last: Kozlov

first: Aimee

last: Yang

first: Emily

last: Hill

first: Maureen

first: Adam

last: Hamilton

first: Isabel

last: Fraccaroli

first: Sean

last: Kelly

first: Pankaj

last: Chopra

first: Jianjun

last: Chang

first: Steven

last: Sloan


title: Hierarchical regulation of oxygen-sensing through coupled transducers in Arabidopsis thaliana

status: Public on Apr 16 2026

city: Loughborough

first: Michael

last: Holdsworth

address: Sutton Bonington

department: Biosciences

institute: Univesrity of Nottingham

summary: The sensing of molecular oxygen is an essential component of development and environmental response in both animals and plants. Few substrates of the plant oxygen-sensing PLANT CYSTEINE OXIDASE (PCO) N-degron pathway have been identified. Here we show that HYPOXIA TRANSDUCER (HYT)1, an angiosperm-specific tail anchored-domain protein, is a substrate of this pathway through a Cys-2 dependent N-degron. HYT1 is stabilised in response to acute hypoxia in root tissues and present throughout the cytoplasm and nucleus. Genetic evidence shows that HYT1 is an important component in the transduction of oxygen-sensing, required for tolerance to acute hypoxia and other stress responses. Expression of HYT1 is directly activated by group VII ETHYLENE RESPONSE FACTOR transcription factors (ERFVIIs), that are also pathway substrates. The relationship between ERFVIIs and HYT1 has properties of a coherent feed-forward loop initiated and maintained by hypoxia, providing a mechanism to ensure robust response to reduced oxygen.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for prt6-1hyt1-1 mutant lines with our published datasets of Col-0, prt6-1, prt6-1erfvII lines grown for 7 days in continuous light (Zubrycka, A., Dambire, C., Dalle Carbonare, L. et al. ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana. Nat Commun 14, 4665 (2023). https://doi.org/10.1038/s41467-023-40366-y)

first: Gunjan

last: Sharma


title: Effects of mutation of the SUMO protease Ulp1 on chromatin-associated sumoylation genome-wide in budding yeast

city: Toronto

first: Emanuel

last: Rosonina

state: ON

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

summary: Steady-state levels of SUMO post-translational modifications are determined by the balance between sumoylation and desumoylation machineries. Eukaryotic cells can modulate cellular levels of SUMO conjugation by regulating the enzymes involved in these processes. In budding yeast, for example, heat shock induces a global increase in SUMO conjugation, at least in part by triggering the degradation of the major SUMO protease, Ulp1. ChIP-seq analyses by our group and others have identified hundreds of sites across the yeast genome that contain sumoylated proteins, including the promoter regions of 265 protein-coding genes, consistent with a role for sumoylation in regulating transcription widely. Paradoxically, despite the overall increase in SUMO conjugation upon heat shock, chromatin-associated sumoylation decreases at most of these loci when temperatures rise. Here, we show that a similar pattern is observed in a strain expressing a partially defective form of Ulp1, which exhibits constitutively elevated SUMO conjugation yet reduced sumoylation at sites across the genome. One possible explanation is that reduced Ulp1 activity, whether through heat shock-mediated degradation or mutation, indeed elevates sumoylation of chromatin-bound proteins, but this then promotes their rapid dissociation from chromatin. This model aligns with our previous findings that sumoylation triggers the release of the Gcn4 and Sko1 transcription factors from their genomic binding sites.

overall_design: SUMO ChIP-seq was performed in wild-type and ulp1-mt SUMO protease-deficient yeast strains.

first: Moallem

last: Marjan


title: MHC Class I on Target Cells Regulates CD4+ T cell-mediated Immunity

status: Public on Feb 02 2026

first: Akira

last: Yamamoto

state: Texas

summary: The central tenet of T cell immune surveillance is that MHC class I and class II molecules present antigens to CD8+ and CD4+ T cells, respectively. Here, we uncover a surprising and previously unrecognized role for MHC class I in modulating CD4+ T cell-mediated immunity. Using multiple in vivo models of allogeneic graft-versus-host disease (GVHD) and tumor immunity, we demonstrate that the absence of MHC class I on target cells significantly increases their susceptibility to CD4+ T cell cytotoxicity. Transcriptomic and functional studies indicate this heightened sensitivity to enhanced ferroptosis of the target cells without affecting the degree of CD4+ T cell activation or inflammatory responses. The experimental results are corroborated utilizing multiple large human transcriptomic and sequencing datasets that suggest a role for CD4+ T cells in enhancing immune checkpoint blocker-mediated responses in patients with melanoma and mismatch repair-deficient (MMRd) colon cancers that have downregulated MHC class I. These findings revise and expand the known role of MHC class I in CD8+ T cell and NK cell immunity and demonstrate a previously unrecognized role in CD4+ T cell-mediated cancer and alloimmunity.

overall_design: Libraries were prepared from a single cell suspension of intestinal epithelial cells using 10x Chromium Next GEM Single Cell 3' GEM v3.1 Library Prep. Libraries were sequenced on NovaSeq X Plus 25B 2x150. At day 6 post-transplant, four biological replicates each of Cre– and Cre+ mice were collected for analysis.

first: Emma

last: Lauder

first: Pavan

last: Reddy


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [APCM_Screen_CLCG4I]

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

institute: Yale University School of Medicine

summary: The hostile tumor microenvironment (TME) is major challenge for cancer immunotherapies. Here, we design and perform TME-targeted in vivo CRISPR activation (CRISPRa) screens to uncover factors that promote anti-tumor immunity, culminating in rationally designed immune gene therapy combinations. Through adeno-associated virus (AAV) delivery, we find that multiplexed activation of pooled immunoregulatory genes encoding antigen presentation, cytokine, and co-stimulation molecules (APCM) leads to enhanced anti-tumor immunity. A CRISPRa screen targeting APCM genes in metastatic tumors identifies CD80, TNFSF14, CXCL10, TNFSF18, TNFSF9, and IFNG as the top immunostimulatory candidates. Further optimization pinpoints 4-1BBL(TNFSF9) + IFNG + IL12B (4II) as a potent streamlined therapeutic combination. AAV delivered 4II has potent in vivo anti-tumor efficacy in multiple tumor models, by enhancing tumor antigen presentation while simultaneously promoting the infiltration, activation, and expansion of anti-tumor T cells. We further demonstrate that APCM therapy synergizes with CAR-T therapy against human solid tumors in vivo. CRISPRa screens and gene activation systems targeting APCM factors thus represent a powerful approach for rapid development of off-the-shelf immune gene therapies against solid tumors.

overall_design:
To generate metastatic lung tumors and perform in vivo screening under immune pressure, E0771-CLCG4I library cells were injected into 8-12 weeks old female C57BL/6J mice intravenously.
E0771-1 and E0771-2 are cells before selection, E0771-Lung1-5 are lung tumors after selection; 6 sgRNA to profile

first: Feifei

last: Zhang

first: Ryan D

last: Chow

first: Shan

last: Xin

last: He

first: Lvyun

last: Zhu

first: Daniyal

last: Mirza

first: Yanzhi

last: Feng

first: Xinyu

last: Ling

first: Qin

last: Han

first: Guangchuan

last: Wang

first: Sidi

last: Chen


title: Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [5xFAD_CD11b+_Bulk_RNA-seq]

first: Timothy

middle: R

last: Sampson

summary: The native microbiome influences a plethora of host processes, including neurological function. We have shown that colonization by Escherichia coli induces a distinct adaptive immune and neurogenerative disease-associated cell state in wildtype mice, suggesting increased disease susceptibility. Further, E. coli exposure in the 5xFAD mouse model results in exacerbated cognitive decline and amyloid pathology, demonstrating its sufficiency to worsen Alzheimer’s disease-relevant outcomes. Here, we performed bulk RNA-seq of CD11b+ brain myeloid cells from E. coli or vehicle treated 5xFAD mice to understand how E. coli modulates neuroimmune responses in the context of amyloid pathology. We demonstrate that E. coli exposed animals have a subtle decrease in genes associated with the disease associated microglia phenotype after 1 month of enrichment, perhaps helping to explain why these animals displayed worsened outcomes.

overall_design: The present dataset consists of bulk RNA-seq samples from CD11b+ brain myeloid cells of 5xFAD mice either treated with 10^8 cfu of E. coli or vehicle control 3x a week for either 2 weeks or one month.

first: Lisa

last: Blackmer-Raynolds

first: Lyndsey

last: Lipson

first: Anna

last: Kozlov

first: Aimee

last: Yang

first: Emily

last: Hill

first: Maureen

first: Adam

last: Hamilton

first: Pankaj

last: Chopra

first: Jianjun

last: Chang

first: Steven

last: Sloan


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [APCM_scRNASeq_mouseCD45]

first: Chuanpeng

last: Dong

overall_design: B16F10‑OVA cells were injected intravenously to establish lung metastases. Mice received intravenous AAV‑4II (IFNG, IL12B, and 4‑1BBL) or AAV‑Vector control on day 26 post‑tumor inoculation. OT‑I T cells were infused intravenously 10 days. Five days after OT‑I transfer, CD45⁺ cells were sorted for downstream single‑cell RNA‑sequencing (scRNA‑seq).

first: Feifei

last: Zhang

first: Ryan D

last: Chow

first: Shan

last: Xin

last: He

first: Lvyun

last: Zhu

first: Daniyal


title: Rational design of immune gene therapy combinations via in vivo CRISPR activation screening of tumor microenvironment modulators [APCM_BulkRNASeq_OT1]

overall_design: B16F10‑OVA cells were injected subcutaneously. On day 14, established tumors received an intratumoral injection of AAV-IFNG, IL12B, 4‑1BBL, andAAV‑4II or empty vector control. On day 21, mice received OT‑I T cells by intravenous infusion. Five days after T cell transfer (day 26), OT‑I T cells were identified from the tumor and sorted as CD45⁺ TCR Vα2⁺ Vβ5⁺.

last: Mirza

first: Yanzhi

last: Feng

first: Xinyu

last: Ling

first: Qin

last: Han

first: Guangchuan

last: Wang

first: Sidi

last: Chen


title: Cis-regulation of IL-22 gene in type 3 immune cells [Chip-seq]

city: Columbus

first: Ankita

last: Saini

state: Ohio

address: 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University Wexner Medical Center

summary: IL-22 is a signature cytokine of type 3 immune cells which include ILC3s and Th17/22. Despite its critical role in barrier tissue integrity, the field lacks the understanding of cis mechanisms regulating IL-22. We took initiative to study and reveal the regulatory mechanisms controlling IL-22 expression in ILC3s and Th17/22 cells.

overall_design: Mnk3 cells were either treated for ~16 hours with IL-1b+IL-23 or left untreated.

first: Eugene

last: Oltz


title: Cis-regulation of IL-22 gene in type 3 immune cells [RNA-Seq]


title: Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [snRNA-seq]

first: Timothy

last: Sampson

summary: The native microbiome influences a plethora of host processes, including neurological function. However, its impacts on diverse brain cell types remains poorly understood. Here, we performed single nucleus RNA sequencing on hippocampi from wildtype, germ-free mice and reveal the microbiome-dependent transcriptional landscape across all major neural cell types. We found conserved impacts on key adaptive immune and neurodegenerative transcriptional pathways, underscoring the microbiome’s contributions to disease-relevant processes. In addition, mono-colonization with Escherichia coli was found to induce a distinct adaptive immune and neurogenerative disease-associated cell state, suggesting increased disease susceptibility.

overall_design: This study consists single nucleus RNA-seq data from the hippocampus of female wildtype mice with a conventional microbiome, germ-free mice without any previous exposure to microbes, and ex-germ-free mice that were mono-colonized with Escherichia coli for either 2 or 4 weeks

first: Lisa

last: Blackmer-Raynolds

first: Lyndsey

last: Lipson

first: Anna

last: Kozlov

first: Aimee

last: Yang

first: Emily

last: Hill

first: Maureen

first: Adam

last: Hamilton

first: Isabel

last: Fraccaroli

first: Sean

last: Kelly

last: Chopra


title: Cis-regulation of IL-22 gene in type 3 immune cells [ATAC-seq_Mnk3]


title: CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock  [RNA-seq]

status: Public on Feb 04 2026

city: Boulder

first: Kaitlyn

last: Walsh

state: CO

address: 3415 Colorado Ave

institute: CU Boulder

summary: Multiple types of cellular stress induce RNA polymerase II (Pol II) to read through normal termination sites at mRNA genes, causing long downstream regions to be transcribed. We observed strong read-through transcription downstream of thousands of genes after heat shock. Additionally, the 3’ Pol II pause that normally occurs during termination was globally lost. Heat shock also increased phosphorylation of Tyr1 and Ser2 residues in the Pol II C-terminal domain (CTD) at the 3’ ends of genes, with smaller increases observed at genes with read-through transcription. We found that 3’ RNA cleavage, a key step of transcription termination, was defective at read-through genes after heat shock; however, the CPSF73 endonuclease responsible for cleavage remained at the 3’ ends of genes. Over-expressing an activator of CPSF73 activity, RBBP6, during heat shock rescued the loss of cleavage and attenuated read-through transcription. Our data suggest that heat shock alters Pol II speed, CTD phosphorylation, and CPSF73 activity via RBBP6, contributing to a multifaceted mechanism that enables transcription to continue far downstream of normal termination sites during cellular stress.

overall_design: 4sU RNA-seq, ctl and heat shocked HEK293 cells, basal and N-RBBP6 expressing cell line

middle: E

first: James

last: Goodrich

first: Jennifer

last: Kugel


title: CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock  [ChIP-seq]

overall_design: ChIP-seq, ctl and heat shocked HEK293 cells, ChIP for total RNA Pol II, Tyr1P RNA Pol II, Ser2P RNA Pol II


title: Cis-regulation of IL-22 gene in type 3 immune cells

overall_design: Mnk3 cells (a mouse ILC3 cell line model) were treated for ~16 hours with IL-1b+IL-23 or left untreated. The cells were then harvested and CUT&RUN was performed using following antibodies: Runx3 (Clone 2B3; Invitrogen, MA5-17169), mouse IgG control (Diagenode, C15400001-100), RORγt (Abcam, ab207082), and rabbit IgG control (Diagenode, C15410206). The CUTANA™ ChIC/CUT&RUN (EpiCypher, 14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001) were used for the experiments. The libraries were sequenced on Illumina NovaSeq X Plus platform to obtain > 10 million paired-end reads per sample.


title: Cis-regulation of IL-22 gene in type 3 immune cells [ATAC-seq]

overall_design: E22-1 or E22-2 cis-elements were deleted from Mnk3 cells using Cas9-RNP system. Single-cell-derived subclones lacking either E22-1 or E22-2 were obtained, along with their corresponding sister subclones. The cells were treated for ~16 hours with IL-1b+IL-23 or left untreated.


title: Genome-wide profiling of histone modification H3K27ac and CTCF transcription factor binding in Rett syndrome iPS cells

city: Tokyo

first: Yutaka

last: Saito

department: Artificial Intelligence Research Center (AIRC)

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: Rett syndrome (RTT) is a rare neurodevelopmental disorder that primarily affects females. It is caused by mutations in the MECP2 gene located on the X chromosome, which plays a critical role in normal brain development and function. The mutation induces epigenetic changes and chromatin re-arrangement which lead to alteration to H3K27ac and CTCF binding in the genome. To determine the epigenetic changes in RTT cells, we performed ChIP-seq on healthy and Rett syndrome iPS cells. RTT increased the H3K27ac marks and reduce CTCF binding, which supports the evidence of MeCP2 role in chromatin alterations.

overall_design: We performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac and transcription factor CCCTC-binding factor (CTCF) in both wild-type and MeCP2-mutated (RTT) iPS cells. Two biological replicates were used and the experiments were performed at most three replicates. Peak calling and differential ChIP-seq peak analysis was performed to elucidate the genomic changes occurred in RTT cells.

first: Wang

last: Yicheng

first: Ab Ghani

last: Nur Syatila

first: Dutta

last: Munmee

first: Adachi

last: Shungo

first: Katoh

last: Kaoru

first: Namihira

last: Masakazu

first: Mitsuyama

last: Toutai

first: Saito

last: Yutaka


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration [scRNA-seq]

city: Tübingen

first: Can

last: Aztekin

address: Max-Planck-Ring 9

department: TheFriedrich Miescher Laboratory

country: Germany

institute: The Max Planck Society for Biology

overall_design: RNA-seq profiling of mouse and Xenopus cells extracted from limb explants cultured under different conditions at 1 or 3 dpa (days post-amputation).

first: Georgios

last: Tsissios

first: Marion

last: Leleu


title: DNA damage burden causes selective CUX2 neuron loss in neuroinflammation

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Neurodegeneration shows regional and cell-type-specific patterns in ageing and disease1, but the underlying mechanisms for cell type-specific neuronal losses remain poorly understood. Previous studies have shown upper cortical layer thinning in progressive human multiple sclerosis (MS) and that cortical layer 2/3 excitatory neurons (L2/3 ENs) that express CUT like homeobox 2 (CUX2) are selectively vulnerable to degeneration2. Here, we report that L2/3 ENs within MS cortical lesions have elevated DNA damage. DNA damage and selective loss of L2/3 ENs was recapitulated in diverse mouse models of demyelination and pan-cortical inflammation, confirming their intrinsic vulnerability. Functions of Cux2 and Activating transcription factor 4 (Atf4) were essential for resilience of L2/3 ENs during postnatal neuroinflammation, acting in neurons to enhance DNA double strand break repair. Interferon-γ, a cytokine implicated in MS pathogenesis3,4, was sufficient to elevate reactive oxygen species leading to DNA damage-mediated neuronal death in vitro and caused selective depletion of L2/3 neurons in mice. These findings indicate that DNA damage burden and inadequate repair in CUX2+ L2/3 ENs contributes to selective vulnerability in neuroinflammatory injury.

overall_design: We collected E18.5 Wildtype, Cux2-Cre/Cre, Cux2-Cre/Wt;Atf4 fl/fl, Cux2-Cre/Cre;Atf4 fl/fl whole cortex to do the snRNA sequencing to compare the gene expression changes in between the different genotypes


title: Expansion of outer cortical layer Cux2+ neurons required selective adaptations for DNA repair

summary: During mammalian evolution, upper cortical layer 2/3 excitatory neurons have shown a disproportionate expansion compared to other layers. Replicative expansion of cortical neural progenitors is associated with significant oxidative DNA damage. Here we show that Activating Transcription Factor 4 (Atf4) has new roles as a critical regulator of the DNA Damage Response, directly activating components of double stranded DNA repair, including CIRBP, Uba52 and Ebf1. Strikingly, pan-cortical knockout (Emx1cre, Atf4fl/fl) demonstrates that Atf4 is specifically required for development of upper layer 2/3 neurons, marked by expression of CUT-homeodomain protein, Cux2.  Atf4 functions to repair DNA damage and attenuate cell death of embryonic radial glial progenitors in a p53-dependent manner.  In particular, we show that Cold-Inducible RNA-Binding Protein (Cirbp) is a transcriptional target of Atf4 that is required for the normal phosphorylation of the key double strand DNA repair factor Ataxia-Telangiectasia Mutated (ATM). These findings establish that Atf4 is an essential regulator of the DNA Damage Response. They further indicate extraordinary requirements for DNA repair post-replicative stress in Cux2+ neurons during mammalian brain development.

overall_design: We collected the E11.5 embryonic cortex from timed-pregnant mice, and after the genotyping been done, three same genotype cortex been pool together as one to get enough sample for snRNA sequencing, Atf4 fl/fl as control and Emx1-Cre, Atf4 fl/fl as knockout group


title: PTP1B inhibition promotes microglial phagocytosis in Alzheimer's disease models by enhancing SYK signaling

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: Amyloid-β (Aβ) accumulation is a hallmark of Alzheimer’s disease (AD). Emerging evidence suggests that impaired microglial Aβ phagocytosis is a key feature in AD, highlighting the therapeutic potential of enhancing this innate immune function. Here, we demonstrate that genetic deletion or pharmacological inhibition of protein tyrosine phosphatase 1B (PTP1B) ameliorated memory deficits and reduced Aβ burden in APP/PS1 mice. Moreover, we show that PTP1B was highly expressed in microglia, and its deficiency promoted a transcriptional shift toward immune activation and phagocytosis. Consistently, PTP1B deletion in microglia enhanced phagocytosis and metabolic fitness, supported by increased AKT-mTOR signaling, a pathway essential for meeting the energy demands of activation. Mechanistically, we identified spleen tyrosine kinase (SYK), a key regulator of microglial phagocytosis, as a direct substrate of PTP1B. Inhibition of SYK showed that PTP1B modulates microglial activation in a SYK-dependent manner. These findings established PTP1B as a critical modulator of microglial activation and a potential therapeutic target for AD.

overall_design: 13-month-old female mice from APP/PS1;PTP1B+/+ and APP/PS1;PTP1B-/- groups were sacrificed for the sample preparation. Mice were perfused with cold HBSS, and hippocampal tissues were dissociated in dissection buffer (DPBS Gibco, 14-287-080). Tissues dissociation was performed using the Adult Brain Dissociation Kit (Miltenyi Biotech, 130-107-677) according to the manufacturer’s instructions, with manual trituration. Briefly, the chopped tissues were incubated in digestion buffer at 37 °C in a water bath for 15 min, with gently tapping of the tubes 3-4 times during the digestion. Following digestion, the tissues were triturated with fire-polished glass pipettes to obtain a single cell preparation, which was then filtered through a 70 μm cell strainer. To minimize ex vivo microglial activation, transcriptional and translational inhibitors were added in perfusion, dissection and digestion buffer as described (Marsh et al, doi: 10.1038/s41593-022-01022-8). In each sample, cells from two animals were pooled together.

first: Yuxin

last: Cen

first: Steven

last: Alves

first: Christy

last: Felice

first: Dongyan

last: Song

first: Linda

last: Van Aelst

first: Nicholas

last: Tonks


title: ZFP148 is a transcriptional regulator of effector CD8+ T cell differentiation [single-cell_multiome]

first: Tong

last: Xiao

state: OH

address: 2255 Kenny Rd, Room 3130

institute: Pelotonia Institute for Immuno-oncology

summary: Chronic antigen exposure, as seen in persistent viral infections and cancer, drives CD8⁺ T cells to differentiate into diverse subsets: progenitor/stem-like, effector, and exhausted/dysfunctional cells. While genetic and epigenetic factors influencing these subsets are known, the mechanisms regulating their dynamic balance remain unclear. We identified Zinc-Finger Protein 148 (ZFP148) as a novel transcriptional checkpoint in CD8⁺ T cell effector differentiation. Using a genetic approach that deletes ZFP148 specifically in CD8+ T cells, we performed matched single cell RNA-seq and ATAC-seq on antigen-specific CD8+ T cells.

overall_design: CD44High GP33-41 tetramer+ CD8+ T cells were FACs-sorted from the spleens of control or ZFP148 KO mice 21 days-post lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl13) infection. After sorting, cells were washed with PBS containing 0.04% BSA, then approximately 10,000 nuclei of either control or ZFP148 KO sample were isolated and processed with the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit following manufacture’s manual (10x genomics). Two separate sets of libraries, Gene expression (GEX) and ATAC, were generated from each sample according to manufacturer’s instructions. Pre-sequencing quality control was performed using an Agilent Tapestation. GEX libraries and ATAC libraries were sequenced on an Illumina Novaseq X plus platform by Azenta Life Sciences.

first: Xiao

last: Tong

first: Ma

last: Anjun

first: Li

last: Zihai


title: Antigen-specific immunotherapy with a CD4 hybrid insulin peptide neoepitope arrests CD8 T cell differentiation in islet grafts

city: Aurora

first: James

last: DiLisio

address: 1775 Aurora Ct

department: Immunology and Microbiology

institute: University of Colorado

summary: Antigen‐specific immunotherapies aim to induce peripheral tolerance in autoreactive T cells without the collateral risks of broad immunosuppression. In type 1 diabetes, certain class II HLA molecules strongly predict disease risk, indicating the centrality of CD4 T cell epitopes in disease. However, CD8 T cells targeting islet-antigens are predominant in human islet infiltrates and critical for disease progression. Understanding how peripheral tolerance induction to CD4 peptide autoantigens can generate the suppression of antigen-specific CD8 T cells is still not entirely understood.  Here, we show that nanoparticles conjugated to a single CD4 T cell epitope, a hybrid insulin peptide, can reshape the fate of antigen‐specific CD8 T cells in islet grafts. Induction of tolerance arrested the functional differentiation of antigen-specific CD8 T cells and restricted their TCR repertoire towards a lower‐avidity public TCR. Antigen-specific CD8 T cells are arrested in part by the expansion of interleukin-10 (IL-10)-producing antigen-specific CD4 regulatory populations that function through indirect suppression of dendritic cell licensing in grafts. Neutralization of IL-10 during hybrid insulin peptide tolerance induction abrogates graft protection, restores CD8 effector differentiation and TCR affinity, and rescues dendritic cell licensing, establishing an IL-10 dependent suppression axis. These findings help explain how antigen‐specific therapy to a single CD4 hybrid insulin peptide epitope can arrest autoreactive CD8 T cell effector fates in transplanted islets, prolonging graft survival.

overall_design: Following syngeneic islet transplant and 2.5HIP-nanoparticle tolerance induction, IGRP-tetramer+ CD8 T cells were sorted by FACS from the graft (8 days post-transplant) from 2.5HIP-nanoparticle treated or control HEL-nanoparticle treated animals and submitted for scRNAseq. CD4 T cells were also sorted in the sequencing event and must be removed by transcript expression of the Cd4 gene to leave the remaining CD8+ IGRP-specific T cells.

first: Kathryn

last: Haskins


title: ZFP148 is a transcriptional regulator of effector CD8+ T cell differentiation

summary: In the setting of chronic antigen stimulation, such as chronic viral infection and cancer, antigen-specific CD8+ T cells differentiate into a heterogeneous pool of progenitor/stem-like, effector, and exhausted/dysfunctional subsets. Though genetic and epigenetic programs that contribute to the generation of each subset have been reported, how these subsets are dynamically regulated and how their balance can be shifted from exhausted toward cytolytic effector cells remain as outstanding questions. Here, we identified Zinc-Finger Protein 148 (ZFP148) as a novel transcriptional checkpoint for CD8+ T cell effector differentiation. We performed CUT&Tag followed by seuqencing (CUT&Tag-seq) of ZFP148 in activated CD8+ T cells from healthy C57BL/6J mice to identify direct DNA-binding activity of ZFP148.

overall_design: Naïve CD8+ T cells were isolated from the spleens of healthy mice and activated with 5 μg/ml plate-bound anti-CD3 and 2 μg/ml soluble anti-CD28 antibody for 24 hours in 24-well plate. A total of 1 million cells were used for library construction of each target (ZFP148 or IgG control) using the CUT&Tag-seq following the stepwise protocol from Epicypher https://www.epicypher.com/resources/protocols/cutana-cut-and-tag-protocol/. Libraries with equal molar ratio were pooled together. Paired-end sequencing was performed on an Illumina Novaseq X plus platform by Azenta Life Sciences, and 50 million reads were generated for each sample.

first: Zihai

last: Li


title: Functional characterization of podocyte-expressed THSD7A in experimental membranous nephropathy

city: Hamburg

first: Ming

last: Huang

address: Martinistrasse 52

department: III. Department of Medicine

institute: University Medical Center Hamburg-Eppendorf

summary: Although the pathogenic role of autoantibodies targeting the podocyte protein THSD7A in membranous nephropathy (MN) is well described, the consequences of autoantibody binding for podocyte homeostasis and the function of THSD7A remain unclear. Here, we induced an MN model in control and podocyte-specific Thsd7a-KO (Thsd7a-/-) mice using rabbit anti-THSD7A antibodies, followed by transcriptome and proteome analyses. Anti-THSD7A antibodies in WT mice caused significant loss of key slit diaphragm (SD) proteins, such as nephrin and NEPH1, without transcriptional downregulation. Glomeruli showed substantial transcriptomic and proteomic reconfiguration indicative of extensive podocyte injury, including disruptions in podocyte adhesion, cytoskeletal dynamics, and marked upregulation of ubiquitin-proteasome system components, cathepsins, and ADAM proteases. Notably, experiments in C3-deficient mice revealed that proteolytic activation and SD protein loss are driven by complement-independent pathways. Thsd7a-/- mice only displayed a mild phenotype under basal conditions, and they were completely protected from MN development upon anti-THSD7A antibody transfer. Finally, interactome analysis identified a protein complex, including THSD7A and integrin α3, linking THSD7A complexes to pathogenic regulation of cytoskeleton, adhesion, and membrane signaling in MN. Thus, anti-THSD7A antibodies induce profound molecular reconfiguration, including dysregulated proteolytic systems via a complement-independent pathway, revealing potential therapeutic targets in MN.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data in mouse kidney glomerulus (THSD7A-associated MN vs. control mice).

first: Nicola

last: Tomas


title: Genome-wide profiling of histone modification H3K27ac and CTCF transcription factor binding following VPA treatment in HEK293 cells

first: Yutaka

last: Saito

summary: Valproic acid (VPA), a histone deacetylase (HDAC) inhibitor induces epigenetic changes through histone hyperacetylation which lead to alteration to H3K27ac and CTCF binding in the genome. To determine the effects of VPA on 3D chromatin organization, we performed ChIP-seq  on untreated and VPA-treated HEK293T cells. VPA treatment results in elevated H3K27ac marks and slightly reduced CTCF binding, which supports the evidence of active transcription triggered upon histone hyperacetylation induced by VPA.

overall_design: We performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac and transcription factor CCCTC-binding factor (CTCF) in both untreated and VPA-treated HEK293T cells. The experiments were performed in triplicates. Peak calling and differential ChIP-seq peak analysis was performed to elucidate the genomic changes triggered by VPA.

first: Wang

last: Yicheng

first: Ab

last: Nur Syatila

first: Dutta

last: Munmee

first: Adachi

last: Shungo

first: Katoh

last: Kaoru

first: Namihira

last: Masakazu

first: Mitsuyama

last: Toutai

first: Saito

last: Yutaka


title: Ontogeny and transcriptional regulation of Thetis cells

city: New York

first: Chrysothemis

last: Brown

state: NY

address: 417 East 68th Street

department: Immunology Program, Sloan Kettering Institute

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Genome-wide gene expression profiling with RNA-seq following VPA treatment in HEK293 cells

summary: Valproic acid (VPA), a histone deacetylase (HDAC) inhibitor induces epigenetic changes through histone hyperacetylation which could affect gene expression. To determine the effects of VPA on gene expression changes, we performed RNA-seq on untreated and VPA-treated HEK293T cells. Differentially-expressed genes (DEGs) induced by VPA exposure were enriched in signaling processes, regulation of ion transport and extracellular matrix organization, known to be associated with HDAC activities.

overall_design: We performed RNA-seq in HEK293T cells. The experiments were performed in triplicates. Gene count and differential RNA-seq peak analysis was performed to identify differentially expressed genes (DEGs). DEGs were further used for Gene Ontology and KEGG pathway analysis.


title: Genome-wide chromatin interaction profiling with Hi-C following VPA treatment in HEK293 cells

summary: Valproic acid (VPA), a histone deacetylase (HDAC) inhibitor induces epigenetic changes through histone hyperacetylation which lead to chromatin remodeling, including the alteration of compartments, TAD boundaries and chromatin loops. To determine the effects of VPA on 3D chromatin organization, we performed Hi-C sequencing on untreated and VPA-treated HEK293T cells. VPA treatment results in increased A compartments which represents regions associated with active transcription, with more switching from B-to-A compartments. In VPA-treated HEK293T cells, reduced TAD boundaries and increased chromatin loops were also observed, which supports the evidence of active transcription triggered upon histone hyperacetylation induced by VPA.

overall_design: We performed Hi-C on untreated and VPA-treated HEK293T cells. Differential analysis was performed to elucidate the genomic changes triggered by VPA.

first: Yicheng

last: Wang

first: Nur

last: Ab Ghani

first: Munmee

last: Dutta

first: Shungo

last: Adachi

first: Kaoru

last: Katoh

first: Masakazu

last: Namihira

first: Toutai

last: Mitsuyama


title: Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets [ChIP-Seq]

city: Baltimore

first: Oscar

last: Camacho

state: Maryland

address: 855 N. Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

summary: Rejuvenation of tissues in physiologically aging mice can be accomplished by long-term partial reprogramming via expression of reprogramming factors (Oct4, Sox2, Klf4 and c-Myc). To investigate the epigenetic determinants of partial reprogramming-mediated rejuvenation, we used whole genome bisulfite sequencing to carry out unbiased comprehensive profiling of DNA methylation changes in skin from mice subjected to partial reprogramming, as well as young and untreated old controls. We found a striking convergence of age- and rejuvenation-related epigenetic alterations on targets of the Polycomb repressive complex 2 (PRC2). These results are also supported by a likewise prominent enrichment of PRC2 targets in gene expression data, suggesting that PRC2 activity can modulate aging and mediate tissue rejuvenation.

overall_design: ChIP-Seq for H3K27me3 and H3K9me2 histone marks in isolated epidermis from tail skin collected from old (22 months) and young (3 months) C57BL/6 mice.

first: Michael A.

last: Koldobskiy

first: Andrew P.

last: Feinberg


title: Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets [WGBS]

overall_design: WGBS on dorsal skin and isolated tail epidermis samples from five mice treated with long-term partial reprogramming from 15 months of age until 22 months, untreated mice (22 months), and young (3 months) mice.

first: Michael

first: Andrew


title: Sex differences in Yap1 oncogene function in immune evasion [EndPoint_Bulk RNA-seq]

city: Houston

first: Nourhan

last: Abdelfattah

state: TX

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

summary: The incidence of many human cancers differs according to sex, but little is known about the interplay between oncogenic events and sex as a variable in tumorigenesis. Here we report that the oncogene Yap1 is sexually dimorphic in medulloblastoma progression and immune suppression. We show that Yap1 promotes stemness and blocks differentiation in sonic hedgehog (SHH)-subtype medulloblastoma by at least two distinct but complementary molecular mechanisms to regulate the RNA expression and protein functions of Sox2, Atoh1, NeuroD1, and Zic1/2. Yap1 also promotes an immune suppressive tumor microenvironment by directly regulating Csf1, Igf1, and Igfbp3 transcription and modulating IL6-JAK-STAT3, TNFR1, TGF-β, and CCL5 immune pathways. Notably, Yap1 function is more critical in males and this is evolutionarily conserved: genes downstream of YAP1 identified in mouse models stratify male but not female medulloblastoma patient survival. In summary, we demonstrate a sex-based function for an oncogene, underscoring the critical need to incorporate sex as a variable in cancer mechanism and clinical response studies, particularly those involving YAP1

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fSMO-M2;hGFAPcre (SG)  and rescued  fYap1;fSMO-M2;hGFAPcre (YSGr) at end point

first: Kyuson

last: Yun


title: Sex differences in Yap1 oncogene function in immune evasion [ChIP-seq]

overall_design: YAP1 ChIPseq data from male and female  fSMO-M2;hGFAPcre (SG) tumors


title: Clonal memory of colitis accumulates and promotes tumor growth [ATAC-Seq]

status: Public on Feb 01 2026

city: Cambridge

first: Surya

last: Nagaraja

address: 7 Divinity Ave, Bauer 2nd Floor 208

department: HSCRB

institute: Harvard University

summary: Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution that persists for over 100 days. We find memory of colitis to be characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity, with more durable changes to chromatin as well. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerates tumor growth and this phenotype is dependent on AP-1 activity. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

overall_design: To idenitfy whether transcription factor motif accessbility varied by region within the colon, bulk ATAC-seq was performed on six sigments between the rectum and cecum.

first: Lety

last: Ojeda-Miron

first: Ruochi

last: Zhang

first: Ena

last: Oreskovic

first: Conrad

last: Hock

first: Yan

last: Hu

first: Daniel

last: Zeve

first: Karina

last: Sharma

first: Roni

last: Hyman

first: Qiming

last: Castillo

first: David

middle: T

last: Breault

first: Öme

middle: H

last: Yilmaz

first: Jason

last: Buenrostro


title: Dopamine neuron specific RNA-sequencing reveals Neprilysin 1 acts downstream of the cohesin complex to suppress learning

city: Edmonton

first: Anna

last: Phan

state: AB

address: Z-1111 BioSci

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

summary: We previously identified Stromalin, a cohesin complex subunit, as a learning suppressor in Drosophila melanogaster that acts by limiting synaptic vesicle numbers in dopamine neurons. However, the mechanism by which Stromalin modulates synaptic vesicles remains unclear. We hypothesized that this occurred through the cohesin complex’s function in developmental gene regulation. Through dopamine neuron-specific RNA-sequencing followed by RNAi screening, we identified Neprilysin 1 (Nep1), a zinc-dependent metallopeptidase, to be positively regulated by the cohesin complex and a key downstream effector of Stromalin. Nep1 knockdown phenocopies Stromalin knockdown effects, enhancing learning and memory and increasing synaptic vesicle markers in dopamine neurons. Like Stromalin, Nep1 suppresses synaptic strength between dopamine and mushroom body neurons. Finally, we show Nep1 overexpression rescues both memory and synaptic vesicle phenotypes caused by Stromalin reduction. Interestingly, while cohesin complex appears to set the expression levels for Nep1 during development, Nep1 function in adult flies supports its learning effects.

overall_design: Dopamine neuron specific RNA-sequencing of WT and Stromalin knockdown neurons

first: Ronald

last: Davis

first: Courtney

last: MacMullen


title: Sex differences in Yap1 oncogene function in immune evasion [scRNA-seq]

first: Nourhan

last: Abdelfattah

overall_design: Comparative scRNA-seq data for fSMO-M2;hGFAPcre (SG)  and rescued  fYap1;fSMO-M2;hGFAPcre (YSGr) males and females at end point

first: Kyuson

last: Yun


title: Sex differences in Yap1 oncogene function in immune evasion


title: Clonal memory of colitis accumulates and promotes tumor growth [Visium]

first: Surya

last: Nagaraja

overall_design: Visium spatial transcriptomics was performed to compare gene expression of adenomas formed following resolution of colitis and under normal conditions.

first: Lety

last: Ojeda-Miron

first: Andrew


title: Clonal memory of colitis accumulates and promotes tumor growth [tissue EM-seq]

overall_design: Enzymatic methyl seq (EM-seq) was performed to examine methylation changes following recovery from colitis and the impact of AP-1 inhibiton with T-5224 on these marks.

first: Ruochi

last: Zhang

first: Ena

last: Oreskovic

first: Conrad


title: Clonal memory of colitis accumulates and promotes tumor growth [IVFP]

overall_design: To examine binding relationships between AP-1 factors and FOX transcrption factors, in vitro binding assays were performed. Purified transcription factor proteins were incubated with cloned naked DNA sequences and binding was assessed using Tn5 transposition.

last: Hock

first: Yan

last: Hu

first: Daniel

first: Karina


title: Clonal memory of colitis accumulates and promotes tumor growth [CUT&Tag]

overall_design: CUT&Tag was performed for the Fos protein to map binding sites in healthy and colitis recovered tissue and banchmark computational predictions.

last: Zeve

last: Sharma

first: Roni

first: Qiming

first: David


title: Clonal memory of colitis accumulates and promotes tumor growth [organoid EM-seq]

overall_design: Enzymatic methyl seq (EM-seq) was performed to examine cell-intrinsic methylation changes following recovery from colitis in organoids.

last: Hyman

last: Castillo

first: Öme

first: Jason


title: Soybean Pol IV and V Mutants

city: Riverside

first: Brandon

last: Le

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

type: Non-coding RNA profiling by high throughput sequencing


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration [multiomics]

first: Can

last: Aztekin

summary: Why mammals cannot regenerate limbs, unlike amphibians, presents a longstanding puzzle in biology. We show that exposing ex vivo amputated embryonic mouse limbs to subatmospheric oxygen environment, or stabilizing oxygen-sensitive HIF1A enables not only rapid wound healing, but alters cellular mechanics, and reshapes the histone landscape to prime regenerative fates. Conversely, regenerative Xenopus tadpole limbs display low oxygen-sensing capacity, robust wound healing, a regenerative histone landscape, and glycolytic programs even under high oxygen. This reduced oxygen-sensing capacity, in stark contrast to mammals, associates with decreased HIF1A-regulating gene expressions. Our findings thus uncover species-specific oxygen sensing as a unifying mechanism for limb regeneration initiation across vertebrates, reveal how aquatic subatmospheric habitats may enhance regenerative capabilities, and identify targetable barriers to unlock latent limb regenerative programs in adult mammals.

overall_design: Multiome-seq: Single nuclei were extracted from mouse limbs at intact (no amputation), 6 hpa (hours post-amputation), 1 dpa (days post-amputation), and 3 dpa. Joint snRNA-seq and snATAC-seq libraries were prepared using the 10x Genomics platform.

first: Georgios

last: Tsissios

first: Marion

last: Leleu


title: Clonal memory of colitis accumulates and promotes tumor growth [ATAC-seq]

first: Surya

overall_design: To deternine the efffects of AP-1 inhibition on transcription factor binding, colonic organoids were derived from mice with chronic colitis or healthy controls and subsequently treated with AP-1 inhbitor T-5224.

first: Lety

last: Breault

last: Yilmaz

last: Buenrostro


title: Transcription elongation can be sufficient, but is not necessary, to advance replication timing [b-del_RNA-seq]

city: San Diego

middle: M

last: Gilbert

address: 3525 John Hopkins Ct., Ste. 200

institute: San Diego BioMEd

summary: DNA replication timing (RT) often correlates with transcription during cell fate transitions, yet notable exceptions indicate a complex relationship. Using a reductionist system in mouse embryonic stem cells, we manipulate transcriptional length and strength at a single locus upstream of the silent, late-replicating Pleiotrophin (Ptn) gene. Small reporter genes driven by two of four promoters advance RT, whereas all promoters advance RT when driving the 96-kb endogenous Ptn gene. Inducible transcription of Ptn, but not the reporter, triggers a rapid and reversible RT advance, providing a system to manipulate RT independent of differentiation. Strikingly, deletion of the Ptn promoter and enhancers abolishes transcription yet does not prevent the developmental RT switch to early replication during neural differentiation. These findings, supported by parallel genome-wide analyses during differentiation, demonstrate that transcriptional elongation can causally advance RT in a rate-dependent and context-specific manner, but that transcription is neither necessary nor sufficient for RT advancement. Our results provide a solid empirical base with which to re-evaluate decades of seemingly contradictory literature.

overall_design: To investigate the relationship between RT regulation and transcription, we focused on mouse Pleiotrophin (Ptn) gene locus the replication timing and transcription of which are developmentally regulatged; switching from late RT and transcription "OFF" in embryonic stem cell to early RT and transcription "ON" in NPC. We inserted various promoters in one allele on the same locus in F121-9 hybrid embryonic stem cell expressing the tetracycline transactivator from the Rosa26 locus to see how transcription induction and replication timing differ between the WT allele and manipulated allele. In addition, to investigate position effect, we inserted hPGK promoter-eGFP casette to multiple loci using PiggyBac as described in PMC7073462. We also deleted Ptn gene transcription start site in another mESC line 46C and induced the differentiation to NPC to observed how the depletion of Ptn gene transcription affects RT in NPC.

first: Athanasios

last: Vouzas

first: Takayo

last: Sasaki

first: Juan Carlos

last: Rivera-Mulia

first: Jesse

last: Turner

first: Amber

middle: N

last: Brown

first: Karen

last: Alexander

first: Laura

last: Brueckner

first: Bas

last: van Steensel


title: Transcription elongation can be sufficient, but is not necessary, to advance replication timing [Repli-seq]

first: David

overall_design:
To investigate the relationship between RT regulation and transcription, we focused on mouse Pleiotrophin (Ptn) gene locus the replication timing and transcription of which are developmentally regulatged; switching from late RT and transcription "OFF" in embryonic stem cell to early RT and transcription "ON" in NPC. We inserted various promoters in one allele on the same locus in F121-9 hybrid embryonic stem cell expressing the tetracycline transactivator from the Rosa26 locus to see how transcription induction and replication timing differ between the WT allele and manipulated allele. In addition, to investigate position effect, we inserted hPGK promoter-eGFP casette to multiple loci using PiggyBac as described in PMC7073462. We also deleted Ptn gene transcription start site in another mESC line 46C and induced the differentiation to NPC to observed how the depletion of Ptn gene transcription affects RT in NPC. The processed data files for samples F121_WT_4DN_E_Rep1, F121_WT_4DN_E_Rep2, F121_WT_4DN_L_Rep1, F121_WT_4DN_L_Rep2 were genrated from 4DN public data. Their raw data files are available at 4DN data portal, specifically, https://data.4dnucleome.org/experiment-set-replicates/4DNESWPIPVZT/#raw-files and https://data.4dnucleome.org/experiment-set-replicates/4DNES1PHNYOP/#raw-files

NIH Common Fund "4D Nucleome" Program grant U54DK107965 (BvS and DMG).


title: ΔNp73 isoform defines a TP53mutant-like poor risk subgroup of acute myeloid leukemia

city: Groningen

first: Diego A

last: Pereira-Martins

state: Groningen

address: Hanzeplein 1

department: Hematology

institute: University Medical Center Groningen

summary: Among acute myeloid leukemia (AML) patients, a subgroup remains notoriously refractory to current treatment options, with underlying mechanisms poorly understood. Here, using a multi-omics approach, we reveal that this resistant patient subgroup is characterized by high expression of the oncogenic TP73 isoform ΔNp73, exhibiting similarly poor outcomes as TP53-mutant AML. ΔNp73, which lacks a transcriptional activation domain but retains chromatin binding properties, competes with TP53 for specific gene targets, thereby downregulating TP53 signaling. We demonstrate that the transcription factor CEBPA controls ΔNp73 expression in AML cells by binding to an intragenic enhancer region. Genetic or pharmacological inhibition of the transcriptional activity of CEBPA with guanfacine reduces ΔNp73 levels and restores drug sensitivity involving ferroptosis-mediated cell death, acting synergistically with venetoclax. Our study sheds light on a previously undercharacterized poor risk subgroup of AML, which may support patient stratification and inform treatment considerations.

overall_design: RNA-seq profiling of MOLM13 cell models containing 1) cDNA-DNp73 to overexpress the DNp73 isoform, 2) CRISPR-Cas9 knockout of the intragenic region +24Kb TSS of the TP73 gene and 3) the empty vector/scrambled control.

first: Diego

first: Jan Jacob

last: Schuringa


title: Convergence of aging- and rejuvenation-related epigenetic alterations on PRC2 targets

first: Oscar

last: Camacho

overall_design: Refer to individual Series


title: The type I and III interferon responses restrict infection with tick-borne orthoflaviviruses through IFI6

city: Paris

first: Felix

last: Streicher

address: Rue du Dr. Roux 25-28

country: France

institute: Institut Pasteur

summary: Tick-borne orthoflaviviruses (TBOVs) are a growing global health concern. Several representatives of this viral family cause fatal disease in humans with increasing case numbers throughout the last decades. The innate immune response, especially interferon (IFN)-dependent signaling, is an essential part of the human defense system that counteracts infection with TBOVs and other viruses. Even though they activate the same signaling cascade, IFNs belonging to the type I and III families trigger differing gene expression patterns. Which genes the two IFN families induce to restrict infection with TBOVs remains poorly characterized. Here we show that type I and III IFNs are both capable of restricting TBOV infection of human cell lines in a cell type-specific manner. Infection of C57BL/6J mice with knockouts for either IFN type I or III receptors further underscored the critical role of IFN signaling in controlling TBOV replication in vivo. To assess the contribution of single genes to controlling TBOV infection in human cells, we used a CRISPR/Cas9-KO-based screening approach. This strategy identified IFI6 as a central player for IFN type I- and III-driven responses against TBOVs. We further defined IFI6 as an ER-resident protein that restricts TBOV replication at a post-entry step. Our work thus opens new perspectives for targeting weak points in the life cycle of TBOVs and other orthoflaviviruses, potentially paving the way for the development of new antiviral therapeutics.

overall_design: Two parallel CRISPR screens targeting Interferon-Stimulated Genes in which enrichment of sgRNA sequences in infected cells was monitored in two independent cell lines (Caco2-TC7 and DAOY). Cells were infected with TBEV-Hypr for 24h following 16h treatment with IFN (IFNλ1 for Caco2-TC7 and IFNα2 for DAOY).

first: Devin

last: Kenney

first: Vincent

last: Caval

first: Maxime

last: Chazal

first: Sophie-Marie

last: Aicher

first: Ségolène

last: Gracias

first: Scott

last: Adams

first: Mao

last: Matsuo

first: Ferdinand

last: Roesch

first: Florian

last: Douam

first: Nolwenn

last: Jouvenet


title: Interrupting T cell memory ameliorates exaggerated metabolic response to weight cycling

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: People frequently go through cycles of weight gain and loss. This weight cycling has been demonstrated, in humans and animal models, to increase cardiometabolic disease and disrupt glucose homeostasis. Obesity itself — and to an even greater extent weight regain — causes adipose tissue inflammation, resulting in metabolic dysfunction. Studies show that even after weight loss, increased numbers of lipid associated macrophages and memory T cells persist in adipose tissue and become more inflammatory upon weight regain. These findings suggest that the immune system retains a "memory" of obesity, which may contribute to the elevated inflammation and metabolic dysfunction associated with weight cycling. Here, we show that blocking the CD70-CD27 axis, responsible for immunological memory, decreases the number of memory T cells and reduces T cell clonality within adipose tissue after weight loss and weight cycling. Furthermore, while mice with impaired ability to create obesogenic immune memory have similar metabolic responses as wildtype mice to stable obesity, they are protected from the worsened glucose tolerance associated with weight cycling. Our data are the first to target metabolic consequences of weight cycling through an immunomodulatory mechanism. Thus, we propose a new avenue of therapeutic intervention by which targeting memory T cells can be leveraged to minimize the adverse consequences of weight cycling. These findings are particularly timely given the increasing use of efficacious weight loss drugs, which will likely lead to more instances of human weight cycling.

overall_design: Immune cells from mouse epididymal adipose tissue were isolated by FACS according to the presence or absence of CD45+ and CD4/8+ and analyzed by scRNAseq.

first: Jamie

last: Garcia

first: Nathan

middle: C

last: Winn

first: Alec

last: Rodriguez

first: Anwar

last: Hussein Agha

first: Alyssa

last: Hasty


title: Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

summary: The progression of IDH-mutant gliomas (IDH-G) from slow-growing tumors to fatal disease is associated with transcriptional and DNA methylation changes that remain poorly understood. Here, we profiled a longitudinal cohort of 36 IDH-G samples from 19 patients by joint-capture multi-omic single-nucleus (sn) DNA methylation and snRNA-seq. We show that IDH-G progression is associated with increase in malignant stem-like states, decreased differentiation and with methylation loss, which marks tumors with worse clinical outcome. Methylation loss was uniformly observed across malignant cells within individual tumors, suggesting that it may underlie rather than result from the increase in stem-like states. Analysis of cell state heritability and plasticity based on high-resolution phylogenetic trees connects DNA methylation loss to alterations in glioma cell states encoding and heritability. Our study offers insights on how DNA methylation loss reshapes cellular transitions and how it may mark clinically more aggressive tumors across IDH-G subsets.

overall_design:
Nuclei from frozen tumor tissue were isolated. Nucleus suspensions were inspected by microscope, counted using a hemocytometer, and sorted into 96 well plates by FACS. The single nucleus plates were processed by dual XRBS and Smart-seq2 protocol.

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

last: Ravirum

first: Joshua S.

last: Schiffman

first: Dan A.

last: Landau

first: Mario L.

last: Suvà