title: CD38⁺ endothelial remodeling marks spatially patterned vasculopathy in rapidly advancing periodontitis and peri-implantitis

city: Richmond

first: Kevin

last: Byrd

state: Virginia

address: 521 N 11th St

department: Oral and Craniofacial Molecular Biology

institute: Virginia Commonwealth University

summary: Oral inflammatory diseases affect nearly half of all humans, yet mechanisms underlying rapidly-destructive inflammation remain poorly understood. We compared peri-implantitis with moderate- and high-grade periodontitis using integrated microbial and single-cell sequencing (>967,169-cells; single-cell RNA-seq, spatial proteotranscriptomics). Laser capture microdissection with compartmental microbiome analysis revealed reduced bacterial load and diversity in peri-implantitis. Expansion of the Human Periodontal Atlas with peri-implantitis single-cell RNA-seq data (36-samples; 121,395 cells) identified CD34+ vascular endothelial cell (VEC) rarefaction and oxidative stress, hypoxia, and NAD⁺ metabolism-associated transcriptional programs enriched in a TNFRSF6B⁺/ICAM1⁺ post-capillary venule (PC-VEC) subpopulation. NAD⁺-consuming ectoenzyme CD38 was selectively enriched and orthogonally confirmed by spatial transcriptomics (6-samples; 283,377-cells) and proteomics (23-samples; 562,397-cells). Spatial neighborhood analyses demonstrated CD38⁺-high PC-VEC expansion, closer proximity, and higher IL16–CD4 T cell signaling in peri-implantitis. Matched high-grade periodontitis biopsies confirmed spatially restricted CD38⁺-VECs despite similar microbial burden, identifying endothelial vasculopathy underlying rapidly advancing oral inflammation and a potential therapeutic axis.

overall_design: RNA-seq profiling of three peri-implantitis biopsies collected upon diagnosis

first: Quinn

last: Easter

first: Khoa

middle: L

last: Huynh

first: Camila

last: Stolf

first: Jialiu

last: Xie

first: Bruno

middle: F

last: Matuck

first: Akira

last: Hasuike

first: Zabdiel

last: Alvarado-Martinez

first: William

last: Kim

first: Zhaoxu

last: Chen

first: Apoena

last: Aguiar Ribeiro

first: Nivedita

last: Pareek

last: Azcarate-Peril

first: Di

last: Wu

first: Renato

last: Casarin

first: Kang

middle: I

last: Ko

first: Jinze

last: Liu


title: Homoharringtonine, a novel senotherapeutic, mitigates diet- and age-associated obesity and insulin resistance and extends the lifespan of mice

status: Public on May 08 2026

city: Toronto

first: Qiwei

last: Zhang

state: Ontario

address: 27 King's College Circle

country: Canada

institute: University of Toronto

type: Expression profiling by high throughput sequencing

summary: The accumulation of senescent cells in white adipose tissue (WAT) is closely associated with the functional decline of WAT and plays a causal role in the pathogenesis of metabolic diseases. Therefore, the elimination of senescent cells in WAT holds promise for the treatment and prevention of age-related metabolic diseases. Using a drug-repositioning strategy for 2,150 clinically applied compounds, we discover that homoharringtonine (HHT), an FDA-approved anti-leukemic drug, manifests senotherapeutic activity in vitro in multiple cell types including human preadipocytes, while inflicting minimal cytotoxicity to non-senescent cells. HHT treatment prevents diet- or age-induced metabolic abnormalities in mice targeting senescent adipocytes and preadipocytes to improve WAT function and reduce WAT inflammation. Moreover, HHT treatment attenuates age-associated phenotypes of human adipose tissue. Mechanistically, the senotherapeutic effects of HHT are mediated through the direct interaction of HHT with heat shock protein family A member 5 (HSPA5). Importantly, we found that HHT treatment delays aging and extends the lifespan in progeroid and aged mice. Our study demonstrates the novel senotherapeutic potential of HHT to mitigate age- and obesity-related metabolic dysfunction and extend longevity in mice.

overall_design: snRNA-seq profiling of nuclei isolated from adipose tissue of a mouse treated with HHT, as part of a study comparing transcriptomic changes between HHT-treated and PBS-treated control groups.

first: So-Young

last: Park

first: Jae-Ryong

first: Hoon-Ki

last: Sung


title: Single cell RNA seq of Healthy, covid-19 infected, recovered and long recovered individuals.

city: Delhi

first: Rajesh

last: Pandey

address: Mall road

country: India

institute: CSIR-IGIB

summary: We performed scRNA sequencing to understand the cellular heterogeneity, immune response, intracellular microbes associated with immune cells and  their role in COVID-19 pathophysiology. We combine this with Ab-Seq, oligo-attached antibody-based quantification of cell surface proteins to better understand the cell type and state of the cells. Samples were multiplexed using BD single-cell multiplexing kit (Human) in order to measure these data simultaneously

overall_design: PBMCs were isolated from Healthy (n = 9), COVID-19 (n = 24), recovered (n = 16) and longitudinal recovered (n = 8) individuals. PBMCs were isolated using Histopaque®-1077 (Sigma-Aldrich) density gradient centrifugation. Samples were multiplexed using BD single cell multiplexing kit (Human), followed by tagging with a pool of 50 oligo-attached antibody for surface markers (Ab-Seq). Around 25000 cells were loaded per cartridge, followed by cell lysis, cDNA synthesis and final library preparation using BD WTA amplification kit as per manufacturer's recommendation. A poly-A transcripts library (WTA), Ab-Seq library and library from oligos of Sampe multiplexing kit (SMK) were constructed from each batch, and were sequenced on NovaSeq 6000 platform.

first: Soni

last: Jyoti

first: Ali

last: Raiyan

first: Chattopadhyay

last: Partha

first: Devi

last: Priti

first: Mehta

last: Priyanka

first: Yadav

last: Aanchal

first: Pandey

last: Rajesh


title: IDH1-R132H Enhances Oncolytic HSV-1 Therapy by Facilitating Viral Entry and Immune Activation in Glioma

city: Boston

first: Eleni

last: Eleni

state: MA

department: Surgery

country: Greece

institute: BETH ISRAEL DIACONESS MEDICAL CENTER

summary: Oncolytic virotherapy represents a promising yet under-explored approach for precision cancer treatment, particularly when tailored to tumor-specific molecular profiles. Patients with high-grade isocitrate dehydrogenase (IDH) mutant astrocytomas have limited treatment options and experience poor prognoses. Here, we investigate the therapeutic potential of rQNestin34.5v.2 (CAN-3110), an engineered oncolytic herpes simplex virus 1 (oHSV-1), in the context of IDH1-R132H-mutant high-grade diffuse gliomas. We demonstrate that the IDH1-R132H mutation increases glioma susceptibility to viral infection through upregulation of Nectin 1, the main cellular entry receptor for HSV-1 found in gliomas. Concurrently, IDH1-R132H-driven DNA hypermethylation suppresses interferon (IFN) signaling, an essential antiviral pathway, contributing to a permissive tumor microenvironment that facilitates viral replication and increases tumor cell susceptibility to virus-induced apoptosis. In immunocompetent IDH1-R132H murine glioma models, intratumoral administration of rQNestin34.5v.2 elicits robust immune activation, characterized by increased immune cell infiltration into the tumor and systemic IFN-γ release. However, elevated expression of poliovirus receptor (PVR or CD155) and the immune checkpoint T-cell immunoreceptor with immunoglobulin and ITIM domain (TIGIT) on tumor-infiltrating lymphocytes suggested a potential resistance mechanism to virotherapy. Combining rQNestin34.5v.2 with TIGIT blockade enhanced therapeutic efficacy and improved survival outcomes compared to monotherapy. These data show that IDH1-R132H modulates viral entry and immune evasion, identifying it as a predictive biomarker for oncolytic virotherapy response.

overall_design: RNA-seq profiling of MGG8-IDH1-wildtype and MGG8-IDH1-mutant human glioma cells grown in-vitro and treated with either vehicle (HBSS) or oncolytic HSV-1 rQNestin34.5v.2 at an MOI of 1, 40 hours post-treatment.

last: Panagioti


title: Complement factor B deficiency promotes lung cancer progression via FOS-mediated tryptophan metabolism and immune suppression

city: Kunming

first: Chenglu

last: He

address: Daguang Street

country: China

institute: The First Affiliated Hospital of Kunming Medical University

summary: To investigate the molecular consequences of CFB deficiency in lung adenocarcinoma, we conducted RNA-sequencing on CFB-silenced (sh-CFB) and control (sh-NC) NCI-H1299 cells.

first: chenglu


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [WGBS Tn-Aged]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

type: Methylation profiling by high throughput sequencing

summary: Maintenance of T cell naïve (Tn) state and restricting effector T cell differentiation upon basal level stimulations would be critical for immune homeostasis and prevention of autoimmunity. To understand how Tn state is regulated by nutrient cues in a cell-intrinsic manner, here we perform an in vivo CRISPR screening to identify required solute carrier (SLC) proteins that transport metabolites and ions into T cells. Among SLC proteins revealed by this experiment, vitamin C transporter Slc23a2 appears to play a role. Conditional ablation of Slc23a2 in T cells by genetic approaches reduces intracellular vitamin C levels by approximately 80%, accompanied by spontaneous activation and differentiation of Tn cells, autoantibody production, and autoimmune pathology in select organs. Slc23a2-deficient Tn cells exhibit profound DNA hypermethylation, dysregulation of genes controlling signaling transduction and transcription, and enhanced differentiation of helper T cells upon stimulation. These results define a broad regulatory space of vitamin C as a cofactor of Tet enzymes in controlling active DNA demethylation. In agreement, conditional deletion of Tet genes impairs Tn state and increases helper T cell differentiation. Thus, our study reveals a cell-intrinsic mechanism by which micronutrient vitamin C via Slc23a2 maintains Tn state and self-tolerance by promoting Tet-mediated DNA demethylation.

overall_design: CD4Tnaive cells were sorted from spleen and pLNs from aged (12-month-old) C57BL/6J mice.

first: Xiaolei

last: Hao

first: Lu

last: Bai

first: Yiping

last: Fan

first: Wojciech

last: Rosikiewicz

first: Yongqiang

last: Feng


title: ETS1 Orchestrates a Hybrid EMT Program Driving in vivo Metastasis and Immune Evasion

city: Los Angeles

first: Yuhao

last: Pan

state: CA

address: 2250 Alcazar st

department: CCMB

institute: University of Southern California

summary: Transcriptional Intratumoral heterogeneity (ITH) is a hallmark of aggressive cancers, yet how transcriptional ITH programs drive tumor metastasis and immune evasion in upper aerodigestive squamous cell carcinoma (UASCC) remains unclear. Through single-cell RNA sequencing analysis of UASCC cells and patient tumors, we uncovered a hybrid EMT (hEMT) ITH program linked to metastatic dissemination. The transcription factor ETS1 was identified as a master regulator of hEMT program, directly activating pro-metastatic genes and promoting distant spread in vivo. Unexpectedly, ETS1 also orchestrated an immune-cold tumor microenvironment by transcriptionally activating the STAT1-PDL1 axis, suppressing T lymphocyte infiltration and elevating immune checkpoint molecules. Clinically, ETS1-high tumors strongly correlated with poor survival and resistance to immune checkpoint blockade across multiple cohorts. Leveraging drug screens, we discovered that ETS1-high cancers are vulnerable to HSP90 inhibitors (e.g., Alvespimycin), which suppress ETS1 by disrupting HIF1A-mediated transcriptional activation. Together, our work reveals ETS1 as a dual driver of tumor distal metastasis and immune evasion in UASCC, while nominating HSP90 inhibition as a tailored strategy for ETS1-driven tumors. These findings provide a roadmap for targeting aggressive ITH subsets and overcoming immunotherapy resistance.

overall_design: Human esophageal squamous cell carcinoma cell line TE5 was transfected with either a control plasmid vector (empty backbone) or a vector encoding human ETS1 for stable overexpression. Following selection, bulk RNA sequencing was performed in duplicate for each condition to assess transcriptomic changes associated with ETS1 overexpression.

first: Benjamin

last: Ziman

first: Talia

last: Wenger

first: Chehyun

last: Nam

first: Daniel

last: Arnaudov

first: Qian

last: Yang

first: Megha

last: Sheth

first: Zhixuan

last: Jing

first: Matthew

middle: G

last: Rees

first: Melissa

middle: M

last: Ronan

first: Jennifer

middle: A

last: Roth

first: Yong

last: Teng

first: Uttam

last: Sinha

first: Young

last: Park

first: De-Chen

last: Lin


title: SLX4IP limits replication stress globally and at ALT telomeres

city: Cologne

first: Robert

last: Hänsel-Hertsch

department: CMMC

country: Germany

institute: University of Cologne

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Faithful DNA replication is essential for genome stability, yet replication forks face constant stress. The Bloom syndrome helicase (BLM) safeguards fork integrity, but excessive BLM activity can itself induce replication stress. We identify SLX4IP as a genome-wide regulator that restrains BLM to maintain replication fork stability. SLX4IP localizes broadly across chromatin with recruitment enhanced under replication stress. Loss of SLX4IP slows replication forks, remodels the replisome, and generates post-replicative single-stranded DNA gaps that are accompanied by elevated nuclear ADP ribose, reflecting compromised replication integrity. These defects are driven by dysregulated BLM activity, establishing SLX4IP as a negative regulator of BLM-dependent replication stress. At ALT telomeres, SLX4IP deficiency triggers ATR signaling, telomere fragility, and accumulation of ALTassociated PML bodies. Here, SLX4IP functions in parallel with FANCM to restrain BLM at ALT telomeres, with co-depletion of SLX4IP and FANCM causing synthetic lethality in ALT-positive cells, a phenotype fully rescued by BLM loss. Together, our results define SLX4IP as a critical genome-wide regulator of replication fork integrity and reveal SLX4IP as a potential vulnerability in ALTpositive cancers.

overall_design: CUT&Tag of SLX4IP in HEK cells and U2OS cells with and without HU treatment.


title: Gene expression profile of immune cells at single cell level from the thalamus of mice after traumatic brain injury and after anti-CD9 Ab treatment

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South, SC729

department: Psychiatry

institute: University of Alabama at Birmingham

summary: Loss of synapses and cognitive impairment were mitigated by anti-CD9 Ab after cortical injury. We used single-cell RNA-seq (scRNA-seq) to analyze how microglial gene expression was altered by anti-CD9 Ab treatment after cortical injury.

overall_design: Microglia in the thalamus of C57B6/J mice after cortical injury and after anti-CD9 Ab treatment or Control Ab treatment were obtained.

first: Shin-ichi

first: David

middle: K

last: Crossmann

first: Ken

last: Matoba

first: Takahiro

last: Kochi


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [CutRun-TCF7TET2]

first: Beisi

last: Xu

overall_design: CD4Tnaive cells were sorted from spleen and pLNs from Slc23a2fl/fl mice and Slc23a2fl/flCD4Cre mice.

first: Xiaolei

last: Hao

first: Lu

last: Bai

first: Yiping

last: Fan

first: Wojciech

last: Rosikiewicz

first: Yongqiang

last: Feng


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [RNA Slc23a2KO]

overall_design: CD4T naive cells were sorted from spleen and pLNs of Slc23a2fl/fl mice and Slc23a2fl/flCD4Cre mice


title: Gene expression profile of immune cells at single cell level from the hippocampus and thalamus of mice after traumatic brain injury

summary: Substantial microglial activation in the thalamus is observed after cortical injury. We used single-cell RNA-seq (scRNA-seq) to analyze the diversity of microglia in the hippocampus and thalamus after cortical injury.

overall_design: Microglia in the hippocampus and thalamus of C57B6/J mice after cortical injury were obtained


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [CutTag]

overall_design: Bone marrow from Slc23a2fl/fl mice and Slc23a2fl/flCD4Cre mice were co-transferred with CD45.1+CD45.2- wild-type B6 mice into CD45.2+CD45.1+ recepient mice at 1:1 ratio. 12 weeks after bone marrow transfer, CD4Tnaive cells were sorted from spleen and pLNs from recipient mice and in vitro stimulated for 3hours with anti-CD3/CD28 antibodies


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [ATAC-Seq]


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [WGBS TET]

overall_design: CreER-expressing Tet1fl/flTet2fl/flTet3fl/fl retrogenic mice were generated. Briefly, LSK cells were isolated from Tet1fl/flTet2fl/flTet3fl/fl RosatdTomato mice, activated in vitro, transduced with CreER retrovirus, and then injected intravenously into lethally irradiated (10.5 Gy) CD45.1+CD45.2+ wild-type B6 mice. These recipient mice were treated with 2 mg/ml neomycin in drinking water for 3 weeks. Two months later, they were injected with 3 doses of tamoxifen or oil (control) once every other day. Mice were euthanized for analysis 2 weeks after the first dose of tamoxifen injection.


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [WGBS Slc23a2]

overall_design: Bone marrow from Slc23a2fl/fl mice and Slc23a2fl/flCD4Cre mice were co-transferred with CD45.1+CD45.2- wild-type B6 mice into CD45.2+CD45.1+ recipient mice at 1:1 ratio. 12 weeks after bone marrow transfer, CD4Tnaive cells were sorted from spleen and pLNs from recipient mice.


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [WGBS Gulo]

overall_design: CD4Tn (CD4+CD25-CD62L+CD44-) cells were sorted from spleens and pLNs of Gulo-/- C57BL/6J mice with or w/o ASC-water.


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [RNAseq Gulo]

overall_design: CD4Tn (CD4+CD25-CD62L+CD44-) cells were sorted from spleens and pLNs of Gulo-/- C57BL/6J mice.


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [RNAseq T cell subtypes]

overall_design: CD4Tn (CD4+Foxp3-CD62L+CD44-), CD4Te(CD4+Foxp3-CD62L-CD44+), Atreg(CD4+Foxp3+CD44hi) and Rtreg(CD4+Foxp3+CD44lo) cells were sorted from spleens and pLNs of Foxp3-GFP C57BL/6J mice.


title: Single nucleus gene expression profiles of mouse thalamus after cortical brain damage

summary: Thalamus is a brain area where most intense inflammation is observed after cortical brain injuries. Using mice as model, we have examined the gene expression changes of cells in the thalamus after cortical brain damage at the single-nucleus level.

overall_design: Young adult C57BL/6 mice were given cortical ablation damage or sham injury (n = 4 per group). On day 21, nuclei were extracted from the ipsilateral thalamus and single nuclei were sorted with FACS. Then, nuclei were pooled per group and processed with 10x genomics protocol (CG000124 Rev F.).

last: Crossman


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [RNAseq Tet]


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity [scRNA]

overall_design: Bone marrow from Slc23a2fl/fl mice and Slc23a2fl/flCD4Cre mice were co-transferred with CD45.1+CD45.2- wild-type B6 mice into CD45.2+CD45.1+ recepient mice at 1:1 ratio. 12 weeks after bone marrow transfer, TCRbeta+ T cells were sorted from spleen and pLNs from recipient mice

first: Jeremy

middle: C

last: Crawford


title: Impact of Sex Chromosomes and Gonad Type in Stress Susceptibility in Corticostriatal Brain Regions

status: Public on May 07 2026

city: Pittsburgh

first: Marianne

last: Seney

state: PA

address: 450 Technology Drive

department: Department of Psychiatry

institute: University of Pittsburgh School of Medicine

summary: Major depressive disorder (MDD) is characterized by symptom heterogeneity and sex differences in prevalence. To gain insight into these sex differences, we utilized the subchronic variable stress paradigm (SCVS) in which female mice are susceptible, while males are behaviorally resilient. We used the Four Core Genotypes mice to differentiate between sex chromosome complement (XX vs. XY) and gonad type (ovaries vs. testes) in stress susceptibility, uncoupling these factors by removing the testes-determining SRY gene from the Y chromosome. Mice were subjected to SCVS followed by assays to assess anxiety-/depressive-like behaviors. Regardless of gonads, XX mice were stress susceptible, while XY mice were stress resilient, underscoring the importance of sex chromosome effects to sex differences in susceptibility to SCVS, independent of gonad type. We then performed RNA-sequencing of the prefrontal cortex (PFC) and nucleus accumbens (NAc). Consistent with human MDD and previous rodent SCVS findings, there was little overlap in genes altered by SCVS across sex. In stress susceptible XX mice, stress exposure altered pathways related to immune function, while in resilient XY mice, stress exposure altered pathways involved in neuronal function. There was brain region specificity to how sex chromosome complement and gonad type contributed to sex-specific stress effects. In the NAc, sex chromosome complement was the primary contributor to stress-induced gene expression, while in the PFC, both sex chromosome complement and gonad type contributed. These findings underscore a complex relationship between sex chromosome complement and gonadal factors in shaping stress vulnerability, partly through immune-related pathways.

overall_design: Bulk RNA-seq profiling of prefrontal cortex (PFC) and nucleus accumbens (NAc) from Four Core Genotypes (FCG) mice subjected to subchronic variable stress (SCVS) or left as unstressed controls. The FCG model decouples chromosomal sex (XX vs XY) from gonadal sex (ovaries vs testes), enabling independent assessment of sex chromosome complement and gonadal hormone effects on stress-related gene expression. Four genotypes were studied: XX (gonadal female), XXSry (gonadal male), XY- (gonadal female), and XY-Sry (gonadal male). 48 animals per brain region (96 total libraries) across 3 cohorts.

first: Kelly N

last: Barko

first: Micah A

last: Shelton

first: Dawson R

last: Kropp

first: Thien Quy

last: Pham

first: Jennifer R

last: Rainville

first: Xiangning

last: Xue

first: George C

last: Tseng

first: Georgia E

last: Hodes

first: Marianne L


title: Microglia coordinate activity-dependent protein synthesis in neurons through metabolic coupling

city: New York City

first: Mauricio

last: Oliveira

address: 1 Washington Square Village

institute: New York University

summary: De novo protein synthesis is required for long-lasting synaptic plasticity and memory, but it comes with a great metabolic cost. In the mammalian brain, it remains unclear which cell types and biological mechanisms are critical for sensing and responding to increased metabolic demand. Here we demonstrate that microglia, resident macrophages of the brain, coordinate metabolic coupling between endothelial cells, astrocytes, and neurons to fuel protein synthesis in active neurons. Increasing metabolic demand via a motor task stimulates microglia to secrete the hypoxia-responsive protein CYR61, increasing glucose transporter expression in brain vasculature. Depleting microglia reduces training-induced metabolic fluxes and neuronal protein synthesis, which can be reproduced by blocking CYR61 signaling. Thus, we define a neuroimmune metabolic circuit required for on-demand protein synthesis in mouse motor cortex.

overall_design: TRAP-sequencing and total lysate of the motor cortex isolated from either home cage or mice that underwent 1h exercise on the rotarod

first: Eric

last: Klann

first: Drew

last: Adler


title: A novel selective strategy for bioactive limbal stem cells primary culture using deep-cryopreservation and IL-1β precondition

city: Guangzhou

first: Yinglin

last: Liu

address: Huangpu Ave.

institute: Jinan University

summary: By combining cryogenic preservation with IL-1β induction, we established an optimized approach that yields LSCs with a higher stem cell proportion and enhanced proliferative potential.

overall_design: cornea tissues were treated with cryogenic preservation and IL-1β induction for one week then using the limbus to harvest limbal stem cells

first: Liling

last: Xu

first: Yanmei

last: Li

first: Cheng

last: Lu

first: Zepei

last: Fan

first: Jun

last: Ling

first: Yingwei

last: Wang

first: Zheng

last: Wu


title: Control of naive T cell reactivity and peripheral tolerance by ascorbate and TET activity

first: Beisi

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

overall_design: Refer to individual Series


title: Transcriptomic responses and survival of kidney xenograft with triple carbohydrate antigen knockout (3KO) with or without multiple human transgenes (HTGs)

first: Tatsuo

last: Kawai

address: 2 Avery Street, Apt:17E

institute: Massachusetts General Hospital

summary: The addition of human transgenes (HTGs) to 3KO kidney xenografts significantly suppressed rejection-related transcriptomic pathways and prolonged xenograft survival. Notably, the inclusion of anti-inflammatory HTGs (A20 and HO-1) was particularly important, leading to greater suppression of rejection-associated pathways and improved graft survival compared with HTG combinations lacking these genes.

overall_design: Bulk mRNA analysis was performed from formalin-fixed paraffin embedded xenograft biopsies and a sample from the non-transplanted contralateral donor kidney, using the nCounter instrument (Bruker Spatial Biology, Seattle WA) following the methods and data analysis previously published for human allograft biopsies.  The B-HOT panel contains 770 probes for human transcripts. Pathways were manually curated from KEGG, Gene Ontogeny and Reactome datasets (genome.jp/kegg/pathway.html, GeneOntology.org and reactome.org) and from prior publications.  The probe sequences were screened for homology with pig and NHP transcripts. The probe sequences that had >85% homology with pig sequences for parenchymal cells or endothelium and probes that had >85% homology for NHP leukocytes were used, supplemented with 35 pig specific probes.  The final panel, termed “B-HOTx” had 549 probes, as listed in the probe annotations file.  Results were compared with well-phenotyped human allograft samples analyzed with the B-HOT panel and previously published, and normalized with seven housekeeping probes (NRDE2, POLR2A, ABCF1, OAZI, PPIA, G6PD, TBP) with >90% homology with the corresponding porcine transcripts. Pathway analysis was performed in nSolver software (Bruker Spatial Biology, Seattle WA).

first: Ahmad

last: Karadagi


title: Reversible suppression of autophagy in a mouse model reveals neuronal resilience

city: Bunkyo-ku

first: Noboru

last: Mizushima

state: Tokyo

address: Hongo 7-3-1

department: Graduate School and Faculty of Medicine

country: Japan

institute: The University of Tokyo

summary: Impairments in intracellular quality control mechanisms, including autophagy, affect neuronal integrity and function. Despite numerous studies aiming to slow neuronal deterioration, it remains unclear whether neuronal functions and intracellular quality can be restored once impaired. Here, we developed a mouse model in which autophagy could be rapidly and reversibly regulated to investigate the reversibility of such defects.. Suppressing autophagy led to proteome and transcriptome changes, inclusion body accumulation, and axonal swelling, all of which were largely ameliorated after autophagy restoration. Consistent with these cellular abnormalities, autophagy suppression induced motor and cognitive dysfunction, which was also significantly reversed upon autophagy restoration. Our findings elucidate the potential resilience of neuronal function and quality enabled by intracellular clearance.

overall_design: We developed a mouse model that enables reversible autophagy suppression using a doxycycline-dependent transcriptional silencer and insertion of a tetracycline operator element into the endogenous Atg101 locus. Using this model, mice were divided into three groups: before autophagy suppression, after 4 weeks of autophagy suppression, and after 4 weeks of autophagy rescue following 4 weeks of suppression (n = 4, 4, 4 male mice). Cerebrum tissues were dissected, and poly(A)-selected RNA was subjected to RNA sequencing.

first: Tomoya

last: Eguchi


title: Longitudinal analysis of viral and host RNA in blood and saliva during controlled human dengue virus 3 infections

city: Boulder

first: Sara

last: Sawyer

state: CO

address: 3415 Colorado Ave

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado Boulder

summary: Dengue viruses are mosquito-borne human pathogens whose global incidence in human infections is rising. Surveillance is hampered by the requirement for blood-based diagnostics. Interestingly, in several prior research studies dengue virus nucleic acids and proteins could be detected in saliva, making saliva-based diagnostics a plausible alterative. However, the temporal relationships between exposure, viremia, salivary accumulation, and symptom onset remain poorly defined. To address this knowledge gap, nine participants were enrolled in clinical trial NCT04298138 to receive an inoculation with an attenuated dengue virus (DENV-3 strain CH53489). Matched blood and saliva specimens were collected over 10 days. Dengue virus genomes could be detected by RT-qPCR in both blood and saliva before the onset of symptoms in most individuals. The earliest time of detection in blood and saliva was 3.4 and 5.0 days post infection, respectively. Using this sample set, we also measured host transcriptional responses to dengue infection in both biospecimens from two participants using RNA sequencing. Strikingly, far more human genes showed increased transcript abundance exclusively in PBMCs (4%) or saliva (15%) than in both compartments simultaneously (5%), revealing compartment-specific host responses. For 21 of the human transcripts that increased in response to dengue infection, we quantified their daily abundance across the course of DENV-3 infection in all study participants. Together, these findings demonstrate that sensitive dengue virus detection in saliva should be possible and establish that both blood and saliva capture early host responses to infection.

overall_design: RNA-seq of extracted PBMC and saliva samples from two individuals at day 0 and day 8 post-DENV-3 infection (strain CH53489), with duplicate library preparations.

first: Sharon

middle: S

first: Jennifer

middle: N

last: Bjerke

first: Casey

middle: E

last: Middleton

first: Arturo

last: Barbachano-Guerrero

first: Joshua

middle: R

last: Dye

first: Emma

last: Worden-Sapper

first: Amy

middle: B

last: Emerman

first: Timothy

middle: P

last: Endy

first: Stephen

middle: J

last: Thomas

first: Adam

middle: T

last: Waickman

first: Daniel

last: Larremore

first: Nicholas

last: Meyerson


title: Transcriptomic Effects of Human Neural Stem Cell Derived Extracellular Vesicle Supplementation Following Chemoradiotherapy for Brain Cancer

city: Irvine

first: Munjal

last: Acharya

address: 811 Health Sciences Road, MedSci B-149

department: Anatomy and Neurobiology

institute: University of California, Irvine

summary: Expression of 757 genes related to neuroinflammation was analyzed across 7 treatment groups of male mice to investigate the neuroprotective effects of two different human neural stem cell (hNSC)-derrived extracellular vesicles (EVs) against chemoradiotherapy for brain cancer; the two stem cell lines are Shef6 and UCI-191, kindly provided from our collaborators.

overall_design: Samples from 24 male mice, age 27 weeks at the time of perfusion, were analyzed using the commercially available nCounter® Mouse Neuroinflammation Panel from NanoString™, with 3-4 samples for each of the 12 treatment groups. C57BL/6J mice were randomly assigned to treatment groups with the following parameters: with or without brain tumor (CT2A glioma cell line); with or without chemoradiotherapy consisting of fractionated cranial irradiation (9 Gy x 3) with concomitant (25 mg/kg) and adjuvant (66.7 mg/kg) temozolomide (TMZ);  and with or without human neural stem cell (hNSC)-derived extracellular vesicles (EVs) from either Shef6 or UCI-191 cell line.

last: Hudson

first: Robert

last: Krattli


title: Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization [ATAC-seq]

city: Jinan

first: Xianglin

last: Zhang

state: Shandong

address: 247 Beiyuan Street

department: The Second Hospital of Shandong University

institute: Shandong University

summary: Cohesin complex shapes 3D genome organization by extruding DNA loops, yet the mechanisms underlying its chromatin entry remain poorly understood. Here, we reveal that the cohesin loader NIPBL exhibits highly tissue-specific chromatin binding, in stark contrast to the conserved binding profiles of CTCF and RAD21. We identify pioneer transcription factors (TFs), notably FOXA1, as key mediators of NIPBL recruitment to chromatin. FOXA1 directs NIPBL to intra-TAD regions, enabling symmetric loop extrusion, while factors like ETS1 target NIPBL to TAD boundaries, supporting one-sided extrusion. Rapid depletion of FOXA1 disrupts NIPBL binding and intra-TAD loops, whereas loss of NIPBL impairs both intra-TAD and inter-TAD interactions, highlighting their roles in 3D genome folding. Strikingly, a recurrent FOXA1 mutation (R219S) in prostate cancer redirects NIPBL to TAD boundaries by recognizing a non-canonical motif, fostering a more insulated and tumor-aggressive genome. Evolutionary analysis points to a potential conserved role for TF-NIPBL cooperation in cohesin chromatin entry across species with tissue-specific adaptations. Our findings reveal that pioneer factors orchestrate cohesin loading to shape tissue-specific chromatin accessibility and 3D genome dynamics, a mechanism hijacked in diseases like cancer to rewire gene expression.

overall_design: ATAC-seq in prostate cancer cells

first: Haiyang

last: Guo

first: Song

last: Wang

first: Tianwei

last: Jia


title: Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization

overall_design: RNA-Seq in prostate cancer cells


title: Transcriptomic profiling of Pseudomonas aeruginosa wild-type and ΔlasB strains exposed to host-mimicking conditions

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

summary: We performed stranded bulk RNA-seq to compare the transcriptomic response of Pseudomonas aeruginosa wild-type and ΔlasB mutant strains exposed to artificial sputum medium (ASM) or LB broth. Samples were collected after short- (24h) or long-term (15 days) culture to assess the effect of chronic host-like conditions. This study aims to characterize the role of LasB in adaptation to the host environment.

overall_design: Six experimental conditions were defined based on strain genotype (wild-type PAO1 or ΔlasB mutant), culture medium (LB or artificial sputum medium, ASM), and duration of exposure (24 hours or 15 days). For each condition, five independent biological replicates were processed.

first: Youssouf

last: Sereme

first: Delphine

last: Beury

last: Maurier

first: Ségolène

last: Caboche

first: David

last: Hot

first: Jean-Michel

last: Sallenave


title: Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization [Hi-C]

overall_design: Hi-C experiements were performed for FOXA1-dTAG 0h, 1h, 24h; siNIPBL; R219S mutant of FOXA1 in 22Rv1 cell line. Two biological replicates for each condition.


title: Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization [4C-Seq]

overall_design: 4C in prostate cancer cells


title: Growth factors-infused cellulose scaffolds support cost-efficient proliferation and differentiation of bovine stem cells for cultivated meat

city: Rehovot

first: Sharon

last: Schlesinger

address: Herzl 229

department: Animal Science

country: Israel

institute: Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem

summary: Cultivated meat, which aims to replicate traditional meat using tissue engineering and stem cell biology, is a promising approach to sustainably supplementing traditional meat production to meet increasing global demand. The production of structured cultivated whole-cut-like meat constructs is not trivial; it requires a complex structure that supports cell growth, enables nutrient and waste exchange, and mimics natural texture. Here, we develop a biocompatible, porose, and anisotropic scaffold, based on directional freezing of nano and microcrystalline cellulose, which supports the growth and differentiation of bovine mesenchymal stem cells toward fat and muscle lineages. Furthermore, we show that preloading the scaffolds with growth factors directing the cells for proliferation or differentiation is a promising alternative to conventional media delivery since these pretreated scaffolds yield similar proliferation and differentiation efficiencies using at least 10 times lower masses of prohibitively expensive factors, and thus may significantly lower one of the primary boundaries to price parity with traditional meat. Together, these findings propose a strategy that supports the development of structured, muscle-like cultivated constructs and represents a step toward whole-cut meat as a sustainable and ethically preferable alternative to meet the growing demand for a widely studied target product.

overall_design: One day after seeding mesenchymal stem cells (MSCs) on plastic plates (d0_P), myogenic differentiation media was placed, and the cells were cultured for 21 days. RNA sequencing was performed on day 0, day 3 of differentiation (d3_P), and day 21 of differentiation (d21_P). For cells plated on scaffolds, two types were used: one scaffold where cells were seeded and cultured with the same differentiation media as the plastic plates, and a 'smart scaffold,' where the growth factors normally present in the differentiation media were instead attached to the scaffold itself. For the smart scaffold, these growth factors were excluded from the media. RNA sequencing was performed for day 0 (d0_S) and day 21 of differentiation (d21_mS for media scaffold, d21_sS for smart scaffold) on both types of scaffolds. The biological replicates for each condition were as follows: d0_P - 3, d3_P - 3, d21_P - 2, d0_S - 2, d21_mS - 4, and d21_sS - 3.

first: Alon

last: Gershkoviz

first: Joseph

last: Kippen

first: Yael

last: Gilad

first: Ivana

last: Ribarski-Chorev

first: Eran

last: Lavi

first: Itai

last: Rotem

first: Einat

last: Zelinger

first: Ido

last: Braslavsky

first: Oded

last: Shoseyov


title: Gene expression profile at single cell level of colorectal tumors from Col1a2-Cre/ERT2 and Col1a2-Cre/ERT2;TXNDC5fl/fl mice

city: Taipei

first: Kai-Lin

last: Cheng

address: No.1 Jen Ai road section 1

department: Pharmacology

country: Taiwan

institute: National Taiwan University

summary: Cancer-associated fibroblasts (CAFs) are reported to remodel the extracellular matrix to modulate immune escape and tumor progression. We performed single-cell RNA sequencing (scRNA-seq) to evaluate whether aberrant expression of TXNDC5 in CAFs modulates the tumor immune system.

overall_design: AOM/DSS-derived colorectal tumors from control (Col1a2-Cre/ERT2) and CAF-specific TXNDC5 knockout (Col1a2-Cre/ERT2;TXNDC5fl/fl) mice were digested with an immune-preserved protocol and analyzed using scRNA-seq.

first: Chih-I

last: Chen

first: Shu-Han

last: Yu

first: Huai-Wen

last: Liang

first: Yi-Wei

last: Tsai

first: Chen-Ting

last: Hung

first: Yu-Shan

last: Lin

first: Gang-Hui

last: Lee

first: Po-Yu

first: Ming-Jer

last: Tang

first: Yueh-Feng

last: Wu

first: Sung-Jan

first: Jen-Kuang

first: Linda Chia-Hui

first: Shuei-Liong

first: Shih-Yu

first: Wen-Chih

first: Yung-Ming

last: Jeng

first: Ruby Yun-Ju

last: Huang

first: Ruey-Hwa

first: Ching-Chow

first: Kai-Chien

last: Yang


title: Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization [ChIP-seq]

first: Xianglin

last: Zhang

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq in prostate cancer cells

first: Haiyang

last: Guo

first: Song

last: Wang

first: Tianwei

last: Jia


title: Reprogramming the Immune Suppressive Tumor Microenvironment in Glioma Enhances the Efficacy of Immune-Mediated Gene Therapy

status: Public on May 06 2026

city: Ann Arbor

first: Maria

last: Castro

state: MI

address: 1150 East Medical Center Drive

department: Neurosurgery

institute: University of Michigan Medical School

summary: Gliomas account for ~80% of primary malignant brain tumors. Many CNS WHO grade 2–3 and some grade 4 gliomas harbor mutant isocitrate dehydrogenase 1 (mIDH1), which causes a gain of function mutation (IDH1 R132H) leading to the production of 2-hydroxyglutarate (2HG). Mutant IDH1-induced 2HG, through epigenetic reprogramming elicits an immune-permissive tumor microenvironment (TME). An immunosuppressive mechanism in the glioma TME involves adenosine production via the ectoenzyme CD73. This study investigates mIDH1’s influence on CD73 expression and adenosine levels. We demonstrate that mIDH1 glioma cells exhibit reduced CD73 expression, driven by DNA hypermethylation, leading to reduced adenosine levels.

overall_design: Examining DNA methylation in wtIDH1 and mIDH1 glioma cells.

first: Ziwen

last: Zhu

first: Pedro

last: Lowenstein


title: Dissecting Semaglutide-dependent transcriptome response in obesity and osteoarthritis across tissues at single-cell resolution

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: The clinical observations of semaglutide cannot be fully explained by the classical GLP-1R signaling, indicating that semaglutide may exert its effects through a more complex multi tissue regulatory network. Based on this background, this study utilized high-fat diet (HFD) - induced obesity and surgery induced osteoarthritis (OA) models to simulate metabolic joint complications. By systematically collecting peripheral blood (PB), bone marrow (BM), liver, brain tissue, and skeletal muscle from C57BL/6 mice, and integrating 10x Genomics single-cell transcriptome sequencing, we constructed a cross tissue cell atlas that covers the immune, nervous, and motor metabolic systems under treatment with semaglutide. In addition, we compared the gene expression disturbances in mouse tissues after administration of semaglutide. Through these comparisons, we can more accurately decipher the specific effects of semaglutide treatment on gene expression in mice, thereby gaining a deeper understanding of their mechanisms of action in vivo.

overall_design: We constructed healthy mice (CSV), high-fat diet induced obese mice (HSV), surgically constructed osteoarthritis mice (CAV), and a combined model of the two diseases (HAV). And treatment with semaglutide (CSS, HSS, CAS, HAS) was performed in both healthy and diseased mice. Single cell sequencing was used to compare gene expression profiles in peripheral blood, bone marrow, brain, liver, and skeletal muscle of 8 mouse models.

first: Yuchen

last: Tian


title: Interplay between cohesin and TORC1 links chromosome segregation and gene expression to environmental changes

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Cohesin is a DNA tethering complex essential for chromosome structure and function. In fission yeast, defects in the cohesin loader Mis4 result in chromosome segregation defects and dysregulated expression of genes near chromosome ends. A genetic screen for suppressors of the thermosensitive growth defect of mis4‐G1487D identified several hypomorphic mutants of the Target of Rapamycin Complex 1 (TORC1), a conserved kinase that integrates cellular signals to regulate growth and metabolism through substrate‐specific phosphorylation. Here, we demonstrate that the TORC1 pathway modulates cohesin functions in chromosome segregation and gene expression. In the context of compromised cohesin loading, the incidence of chromosome segregation defects was modulated by the growth medium in a TORC1‐dependent manner. Pharmacological or genetic down‐regulation of TORC1 activity restored cohesin binding to its chromosomal sites and improved mitotic chromosome segregation. Notably, reduced TORC1 activity also increased cohesin binding and chromosome transmission fidelity in wild‐type cells. These results suggest that environmental cues influence chromosome stability via TORC1. Biochemically, TORC1 co‐purified with cohesin and reduced TORC1 activity correlated with decreased phosphorylation of specific residues on Mis4 and cohesin. Mutations in cohesin that mimic the non‐phosphorylated state mirrored the effects of TORC1 downregulation, showing that TORC1 is part of the  network that controls cohesin phosphorylation to modulate its functions. Finally, we show that the functional interaction between TORC1 and Mis4 extends to the regulation of stress‐responsive genes. Our findings reveal a TORC1‐cohesin link that may facilitate cellular adaptation to environmental changes. Given that TORC1 inhibitors and calorie restriction extend lifespan in diverse species, this connection raises the intriguing possibility that cohesin‐mediated changes in chromosome structure contribute to these effects.

overall_design: RNA‐sequencing of wild‐type, mis4‐G1487D, mip1‐R401G and the double mutant in various experimental conditions. These included cycling cells in the rich complete medium YES at 25°C (V25) and upon a temperature shift to 36.5°C for one doubling (V36.5) or arrested in G1 (cdc10-129) at this temperature (G1_36.5). We also looked upon nitrogen starvation by shifting actively cycling cells from the synthetic medium EMM2 to EMM2 deprived of a nitrogen source (EMM2-N). Total RNA from biological triplicate samples was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing, rRNA was depleted using the Ribominus kit (Thermo Fisher) starting with 2000 ng total RNA and then followed by the Illumina stranded ligation sample preparation protocol starting with 100 ng rRNA depleted RNA. The protocol includes fragmentation, denaturation of RNA, cDNA synthesis, ligation of adapters, and amplification of indexed libraries. The yield and quality of the amplified libraries were analyzed using Qubit (Thermo Fisher) and the quality of the libraries was checked by using the Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Nextseq 2000 machine using a P3 100 cycle sequencing run, producing a sequencing length of 58 base paired end reads with dual index.

first: Dorian

last: Besson

first: Sabine

last: Vaur

first: Stéphanie

last: Vazquez

first: Sylvie

last: Tournier

first: Yannick

last: Gachet

first: Adrien

last: Birot

first: Stéphane

last: Claverol

first: Adèle

last: Marston

first: Karl

last: Ekwall

first: Jean‐Paul

last: Javerzat


title: Brain FGF2 and NCAM1 contribute to FGFR1-dependent progression of ER+ breast cancer brain metastases in young and aged hosts

city: Aurora

first: Diana

last: Cittelly

address: 12801 East 17th Avenue, Research Complex 1 South, L18-5402G

institute: University of Colorado

summary: Estrogen receptor positive (ER+) breast cancer (BC) represents a significant proportion of BC brain metastasis (BCBM) but remains understudied. Here, we report that FGFR1-amplification, a well-established driver of ER+ BC endocrine resistance, promotes ER+ BCBM colonization in young and aged mice, through brain-dependent mechanisms. FGFR1-dependent brain colonization in young and aged mice occurs via canonical FGF2/FGFR1 signaling and non-canonical NCAM1/FGFR1  interactions. Astrocytic FGF2-mediated paracrine activation of FGFR1 promoted BCBMs in estrogen36 treated young mice, but FGF2 signaling decreased in the brain with aging and estrogen-depletion. Neuronal and glial NCAM1, which remain unchanged in young and aged brains, promoted adhesion to neurons and migration of ER+ BC cells, suggesting that interactions with astrocytes and neurons facilitate early ER+ BCBM colonization through FGFR1. Importantly, FDA-approved FGFR inhibitors effectively blocked early but not late metastatic progression only in young mice, suggesting limited efficacy of FGFR inhibitors to block non-kinase-dependent FGFR1 functions in vivo.

overall_design: RNA-sequencing of UCD12 and UCD65 cell treated with FGF2, NCAM1, or vehicle for 24hrs.

first: Morgan

last: Fox

first: Jenny

last: Jaramillo-Gómez

first: R. Alejandro

last: Marquez-Ortiz

first: Karen

last: Alvarez-Eraso

last: Contreras-Zárate

first: Stella

last: Koliavas

first: Peter

last: Kabos

first: Natalie

last: Serkova

first: Carol

last: Sartorius

first: Elizabeth

last: Wellberg


title: Single-nucleus profiling reveals a core disease signature and cell-type-specific vulnerabilities in early Rett syndrome

city: Houston

first: Yan

last: Li

state: TX

address: 1250 Moursund Rd

department: Department of Molecular Human Genetics

institute: Baylor College of Medicine

summary: Rett syndrome (RTT) is an X-linked neurological disorder caused by MECP2 mutations. Like other X-linked disorders, RTT patients have sex-specific differences in clinical presentation due to distinct cellular environments, where females have ~50% of cells expressing either a mutant or wild-type copy of MECP2 (mosaic) and males have 100% of cells expressing a mutant MECP2 (non-mosaic). Typical RTT females have a short window of normal early development until ~6-18 months, followed by regression and progressive decline, whereas neonatal encephalopathy is more likely in RTT males. How these sex-specific differences in cellular context contribute molecularly to RTT pathogenesis, particularly in the presymptomatic stages of RTT females, remains poorly understood. Here, we profiled the hippocampal transcriptomes of female (Mecp2+/-) and male (Mecp2-/y) RTT mice at early timepoints using both bulk and single-nucleus RNA-seq, including sorted MeCP2 positive (MeCP2+) and MeCP2 negative (MeCP2-) neurons in female mice. We identified a core disease signature consisting of 12 genes consistently dysregulated only in MeCP2- cells across RTT models. Moreover, we uncovered non-cell-autonomous effects exclusively in female MeCP2+ excitatory neurons, but not inhibitory neurons, suggesting excitatory circuits are more vulnerable early in the mosaic RTT environment. The single-nuclei data also revealed that a previously underappreciated MeCP2- interneuron subtype had the most transcriptional dysregulation in both male and female RTT hippocampi. Together, these data highlight the different effects of MeCP2 loss on excitatory and inhibitory circuits between the mosaic and non-mosaic environment that appear early in RTT pathogenesis.

overall_design:
Early transcriptional signatures of MeCP2 positive and negative cells in Rett syndrome
BulkRNAseq: P28 and P45 male and female mouse model of Mecp2(tm1.1Bird), 4 replicates for each genotype(WT_M, Null_M, WT_F, Het_F)
snRNAseq: P45 3 replicates for each genotype (WT_M, Null_M, WT_F, Het_F)
female sorted MeCP2 pos and neg snRNAseq: P45 2 replicates for each group (WT, HET_POS, HET_NEG). WT: sorted MeCP2 positive population using antibody in WT, HET-POS: sorted MeCP2 positive population using antibody in HET, and HET-NEG: sorted MeCP2 negative population using antibody in HET.


title: CK2α deletion in the hematopoietic compartment leads to mild alterations in terminally differentiated cells and expansion of stem cells

city: Hershey

first: Chandrika

last: Behura

address: 50 University Drive

institute: Penn State College of Medicine

summary: Casein Kinase II(CK2) is a ubiquitously present serine/threonine kinase essential for mammalian development. CK2 holoenzyme is a tetramer with two highly related catalytic subunits (α or α’) and two regulatory ß subunits. Global deletion of the α or β subunit in mice is embryonically lethal. We and others have shown that CK2 is overexpressed in leukemia cells and plays an important role in cell cycle, survival, and resistance to apoptosis of leukemia stem cells (LSC). To study the role of CK2α in normal hematopoiesis, we generated hematopoietic-specific CK2α-deficient mice (Vav-iCreCK2 f/f). Here we report the generation and validation of a novel mouse model that lacks CK2α in the hematopoietic compartment.  Vav-iCreCK2α f/f were viable without dysmorphic features and showed a mild phenotype under baseline conditions. Vav-iCreCK2α f/f   blood count showed a significant decrease in total red blood cells and platelets. Spleen was enlarged in Vav-iCreCK2α f/f mice with evidence of extramedullary hematopoiesis. HSC and early progenitor cell compartments showed expansion in CK2α null bone marrow, suggesting that the absence of CK2α impaired their proliferation and differentiation. Given the established roles of CK2 in cell cycle regulation and findings reported here, further functional studies to investigate the role of CK2α in HSC self-renewal and differentiation are warranted. This mouse model serves as a valuable tool for understanding the role of CK2α in normal and malignant hematopoiesis.

overall_design: Bulk RNA-Seq profiling of genetically engineered mouse model (GEMM) harboring single knock-out (SKO), double knock-out (DKO), and wild-type control (CTR) of CK2a sampled from bone marrow (BM) and spleen (SPL). The wild type Vav-iCreCK2α+/+ (WT,CTL), Vav-iCreCK2αf/f (KO,DKO) and Vav-iCreCK2αf/+ (Het,SKO) mice .

first: Rajesh

last: Rajaiah

first: Muhammad

last: Daniyal

first: Marudhu

last: Pandiyan Shanmugam

first: Hannah

last: Valensi

first: Koby

last: Duke

first: Katie

last: Mercer

first: Morgann

last: Klink

first: Lanza

last: Matthew

first: Yasin

last: Uzun

first: Suming

last: Huang

first: Sinisa

last: Dovat

last: Gowda Behura


title: Newly-diagnosed IDHwt MGMT unmethylated glioblastoma patients treated with standard radiation, nivolumab, and BMS-986205

city: Chicago

first: Derek

last: Wainwright

state: IL

address: 2160 South First Avenue

department: Cancer Biology

institute: Loyola University Chicago Stritch School of Medicine

type: Methylation profiling by genome tiling array

summary: Improving immunotherapeutic efficacy for patients with glioblastoma (GBM) has been suggested to be limited by a number of factors including indoleamine 2,3 dioxygenease 1 (IDO; IDO1); an enzyme that converts L-tryptophan (Trp) into L-kynurenine (Kyn). Here, we report the results of a first-in-human phase 1 trial for 12 patients with newly-diagnosed IDHwt MGMT unmethylated GBM treated with standard radiation, nivolumab, and BMS-986205 – the latter being a potent IDO1 enzyme inhibitor. The treatment regimen was found to be safe and tolerable when administered at 50mg. Treated patients experienced decreased L-kynurenine levels without changes in L-tryptophan. No other kynurenine-pathway metabolites were altered while on treatment. The median overall survival (OS) was 11.5 months for all patients, with 4 individuals alive at ≥28 months, and 2 patients alive at 5 years post-diagnosis. Analysis of resected tumor at the time of first recurrence revealed intratumoral IDO1 expression to be primarily enriched in myeloid lineage cells. Higher systemic levels of naïve and early effector CD8+ T cells, higher systemic levels of microbial-derived aryl-lactates, lower systemic levels of microbial-derived aryl acetates, higher levels of fecal-derived Massilioclostridium coli, GGB3819-SGB5184, Dysosmobacter welbionis, Phocaeicola plebeius, an age of <65 years old, and patients who underwent subtotal but not gross total tumor resection, were significantly more likely to live past 28 months while on treatment. This study provides a biological rationale for use of RT, PD-1 mAb, and IDO1 enzyme inhibitor treatment in temodar naïve GBM patients who survive well after 2 years while on treatment (ClinicalTrials.gov: NCT04047706).

overall_design: To determine the epigenetic status of peripheral blood leukocytes (PBLs) from newly diagnoased GBM patients enrolled in current clinical trial , blood samples were collected  at baseline and different treatment stages during the trial. PBLs were isolated and subject to bisulfite array for epigenomic analysis.

first: Lijie

last: Zhai

first: Bobby

last: Brooke

first: Steve

last: Horvath

first: Juozas

last: Gordevicius

first: Milda

last: Milčiūtė


title: The functional antagonism between SIRT2 and MOF regulates cell cycle progression and genome stability [ChIP-seq]

city: Badalona

first: Gerard

last: Martinez-Cebrian

state: Barcelona

address: Edifici Josep carreras, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Institut Josep carreras

summary: The control of G2/M transition is a key event for genome stability as it ensures proper completion of DNA replication and repair before progressing into mitosis. One of the key regulators of G2/M checkpoint is the H4K16Ac-acetyltransferase MOF, which plays a major role in chromatin structure, gene expression, DNA damage and genome stability. Here we show that SIRT2, a member of the sirtuin family of NAD+-dependent deacetylases, antagonizes the role of MOF in G2/M. SIRT2 promotes specific inactivation of MOF through deacetylation and degradation of MOF, which results in re-expression of G2/M cell-cycle genes regulated by MOF. Underscoring the functional relevance of this antagonism, both factors play opposed roles in the deposition of the key mark H4K20me1 during G2/M. Consistently, loss of MOF in wt but not in SIRT2-/- cells induces a genome-wide deregulation of H4K20me1 distribution, which results in a premature loading of condensins. Our studies suggest that the G2/M checkpoint is shaped by the balance between both factors and involves condensing regulation and underscores the role of sirtuins in cell cycle control and genome stability under stress.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H4K20me1 in Wt, Sirt2-/-, Mof-/- and Sirt2-/-/Mof-/- MEFs and Wt and kmut  HeLa cells.

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Marazuela-Duque

first: Alejandro

last: Vaquero


title: Astrocyte circadian regulation in neurodegeneration: in vivo BMAL1 occupancy mapping using MACS-Calling Cards

status: Public on May 05 2026

city: St. Louis

first: India

last: Reiss

state: Missouri

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University in St. Louis

summary: Astrocytes maintain neuronal homeostasis through cellular programs that are frequently disrupted early in neurodegenerative disease, many of which are regulated by the circadian clock. The core clock transcription factor BMAL1 is required for normal astrocyte function, yet whether its regulatory activity is altered during neurodegeneration remains unclear. BMAL1 expression changes in disease are often inconsistent, suggesting that transcription factor binding, rather than expression levels, may be a more informative readout of BMAL1 function. We used a CLN3Δex7/8 model of neurodegeneration, which exhibits early astrocyte dysfunction prior to widespread neuronal loss, to test whether degenerative pathology reprograms BMAL1 binding in astrocytes. We developed an in vivo strategy to record transcription factor genomic occupancy specifically in astrocytes (MACS-Calling Cards, MACS-CC) and used it to map BMAL1 binding in wild-type and CLN3Δex7/8 mice. BMAL1 binding was extensively redistributed, with comparable numbers of wild-type–specific and disease-specific sites. Wild-type-specific BMAL1 binding was enriched near genes involved in circadian regulation and astrocyte differentiation, whereas disease-specific sites lacked coherent functional enrichment. Consistent with these changes, RNA-seq of sorted astrocytes revealed reduced expression of mature astrocyte markers in CLN3Δex7/8 mice. To define the mechanisms underlying BMAL1 retargeting in CLN3Δex7/8 astrocytes, we tested whether changes in chromatin accessibility could explain disease-associated gains and losses of BMAL1 binding. Although chromatin accessibility was broadly remodeled, differential accessibility did not predict BMAL1 binding gains or losses. Instead, motif analyses supported a model in which loss of normal cooperative transcription factor partnerships contributes to BMAL1 retargeting. Together, these findings demonstrate that MACS-CC enables in vivo TF occupancy mapping in astrocytes and reveals the mechanisms behind early rewiring of circadian regulatory programs within a model of neurodegeneration.

overall_design: BMAL1 Calling Card, Mnase-seq, and RNA-seq datasets from astrocytes (enriched from MACS), as well as BMAL1 Calling Card datasets from HepG2 cells.


title: TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration

city: San Francisco

first: Eric

address: 513 Parnassus Ave

department: Pathology

institute: UC San Francisco

summary: Single cell RNA sequencing (scRNA-seq) dataset characterizing cells isolated from GRN(+/+), GRN(-/-), and GRN(R493X/R493X) iPSC-derived cortical organoids at three time-points of differentiation (5 weeks, 16 weeks, and 25 weeks).

overall_design: Cells were isolated from organoids using a papain dissociation system and prepared for scRNA-seq using Single Cell 3’ Gene Expression kit v3.1 (10x Chromium). Generated scRNA-seq libraries were sequenced using an Illumina NovaSeq 6000.

first: Arren

last: Ramsey

first: Xiaoyan

last: Tang


title: The functional antagonism between SIRT2 and MOF regulates cell cycle progression and genome stability [RNA-seq]

overall_design: To investigate the relevance of SIRT2 and MOF antagnism in the regulation of cell cycle we performed gene expression profiling analysis using data obtained from RNA-seq of Wt, Sirt2-/-, Mof-/- and Sirt2-/-/Mof-/- MEFs and Wt and Kmut Hela cells


title: A NOTCH2 Pathogenic Variant Alters the Osteoblast and Vascular Cell Transcriptome of Mouse Femurs

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

summary: Pathogenic variants of NOTCH2 that lead to a gain or loss of function are associated with serious clinical consequences. A recently reported novel NOTCH2 4006G>C variant was associated with decreased Notch signaling and skeletal fragility in humans and mouse (Notch2em1Ecan) lines. In the present study, we analyze the transcriptome of femoral bones from mature control and Notch2em1Ecan mice following the exclusion of hematological cells. Single cells were analyzed following microfluidic partitioning on a Chromium X instrument using a 3' gene expression library. Uniform manifold approximation and projection (UMAP) for non-linear dimensional reduction defined 15 different cell clusters comprised of macrophages, red blood cells, endothelial, vascular and smooth and striated muscle cells and cells of the osteoblast lineage. Notch2 and Hes1 were the prevalent Notch receptor and target gene in most clusters. Independent clustering analysis of transcriptomes from control and Notch2em1Ecan femurs revealed a 35 – 45% decrease in cells forming the osteogenic and a 50 – 55% decrease in cells comprising the vascular cluster in Notch2em1Ecan femurs. Expression of Hes1 was decreased in Notch2em1Ecan cells. Analysis of nascent transcripts (intron/exon sequences) using the scVelo pipeline revealed suppressed velocity in vascular and osteogenic clusters from Notch2em1Ecan cells implying decreased transcription of genes constituting these clusters. In conclusion, a novel NOTCH2 deleterious variant associated with skeletal fragility alters the osteogenic and vascular transcriptome in femurs from adult mice.

overall_design: Control and Notch2em1Ecan female whole femurs at 6-9 months were flushed for marrow, subjected to ACK lysis buffer, and sorted by FACs for CD45 and TER119 negative cells.

first: Lauren

last: Schilling

first: Emily

last: Denker


title: A conserved Notch-Meis1-Pbx cascade specifies secretory progenitors into spatially diverse intestinal best4+ cells

city: Bethesda

first: Jeffrey

middle: Allen

last: Farrell

state: MD

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

summary: best4+ cells are a recently described vertebrate intestinal epithelial cell type. best4+ cells are reduced in inflammatory bowel disease and transcriptionally altered in colorectal cancer, suggesting that stimulation of their homeostatic replenishment may have therapeutic potential. However, it is unclear what function best4+ cells perform or how they develop, which is crucial to understand to therapeutically manipulate them. Since best4+ cells are evolutionarily lost in mice, here we established zebrafish as a tractable in vivo model to observe, manipulate, and remove best4+ cells in an organismal context. We dissected best4+ cell developmental regulation in vivo from birth to differentiation and specialization, focusing on factors that we show are evolutionarily conserved in best4+ cells across vertebrates. We demonstrate with lineage tracing that best4+ cells arise from secretory progenitors, where Notch/Dll4 signaling mediates a decision between best4+ and enterochromaffin cells by triggering expression of meis1b. Following specification by meis1b, we identify a role for pbx3a in the spatial diversification of best4+ cells, which develop regional heterogeneity in gene expression and intracellular pH that implies potential functional specialization. Together, in vivo live imaging, in vivo removal of best4+ cells, and non-autonomous effects on goblet cells suggest these cells have a sensory or communicative function. Altogether, this study experimentally delineates a comprehensive best4+ cell developmental program and develops a genetic toolkit to dissect their function in vivo, both of which will be instrumental to understand how best4+ cells are altered in disease and to stimulate the birth of new best4+ cells in patients.

overall_design: To investigate the role of candidate transcription factors meis1b and pbx3a in best4+ cell development, we performed scRNAseq on dissected intestines from 6 dpf meis1b and pbx3a mutant zebrafish larvae and their wild-type (WT) siblings. Droplet emulsions of single cell capture were generated using the 10X Genomics Chromium controller with Single Cell 3’ v3.1 consumable reagents for pbx3ay731 mutant samples, and the 10X Genomics Chromium GEM–X platform with Single Cell 3’ v4 reagents for the meis1by730 mutant samples.

first: Abhinav

last: Sur


title: Host-Botrytis co-transcriptomics reveals finely tuned interactions with closely related legumes

city: Davis

first: Daniel

last: Kliebenstein

address: One Shields Ave

institute: University of California Davis

summary: Generalist pathogens infect diverse plants, yet how these interactions differ across hosts is poorly understood. Here, we conduct a molecular analysis of a generalist pathogen interacting with closely related hosts. A co-transcriptomic framework is used to dissect host–pathogen interactions between the generalist necrotroph Botrytis cinerea and two closely related legume hosts, common bean (Phaseolus vulgaris) and cowpea (Vigna unguiculata). Using 72 diverse Botrytis isolates, we quantified lesion development alongside host and pathogen gene expression. Although lesion formation was driven primarily by pathogen genetic variation, transcriptomic responses in both host and pathogen exhibited significant host x isolate interactions. This indicated that extensive, fine-scale transcriptional plasticity created similar disease outcomes. Botrytis genes showing host-specific expression were enriched for cell wall–modifying enzymes and some specialized metabolic genes, indicating greater host responsiveness of these core virulence mechanisms than previously appreciated. Co-expression network analysis in both host and pathogen further showed that in both organisms, gene membership for individual networks are restructured in response to genetic diversity. Both legume species exhibited extensive isolate-dependent transcriptional reprogramming, with approximately two-thirds of expressed host genes responding to pathogen diversity. While conserved defense pathways such as jasmonate/ethylene signaling and phenylpropanoid metabolism were upregulated in both hosts, the specific genes in the networks differed markedly, highlighting lineage-specific rewiring of defense strategies. These results suggest that generalist pathogen success is underpinned by pervasive gene expression plasticity in both host and pathogen, allowing similar phenotypic outcomes to emerge from highly divergent molecular states.

sample_organism:
Phaseolus vulgaris
Vigna unguiculata

platform_organism:
Phaseolus vulgaris
Vigna unguiculata

overall_design: Co-transcriptomic profiling of 72 Botrytis isolates on 1 genotype of common bean and 1 genotype of cowpea at 48 hours after inoculation.

last: Muhich

first: Ritu

last: Singh

first: Cloe

last: Tom

first: Celine

last: Caseys


title: Intermolecular 3′UTR-3′UTR interactions drive Wnt gene activation through heteromeric protein assembly

city: New York

first: Christine

last: Mayr

state: New York

address: 417 E 68th street

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Stem cell differentiation depends on transcription factors that are often encoded by mRNAs with highly conserved 3′UTRs. To determine their functional roles, we performed 3′UTR loss-of-function studies. Partial deletion of endogenous 3′UTRs altered stem cell differentiation efficiency in 7/10 cases. As 6/7 3′UTR deletions did not affect expression level of the encoded proteins, we reveal widespread abundance-independent regulatory roles of 3′UTRs. For example, 3′UTR deletion of CTNNB1, an mRNA that encodes the essential Wnt co-activator β-catenin, keeps β-catenin levels unaffected but impairs zebrafish embryogenesis and induction of the Wnt transcriptional program during human stem cell differentiation. We show that long intermolecular 3′UTR-3′UTR interactions between Wnt transcription factor mRNAs and CTNNB1 enable co-translational protein complex assembly of these transcription factors with β-catenin. As antisense oligonucleotide-mediated blocking of 3′UTR interactions impairs Wnt program induction, our findings indicate that transcriptional regulators can form functional units during protein biogenesis to be fully active.

overall_design: RNA-seq profiling of control (Ctrl), CTNNB1 3′UTR deletion (Udel), and CTNNB1 knockout (KO) clonal lines at the stem cell stage and at 24 hours of definitive endoderm (DE) differentiation.

first: Cai

last: Ting

first: Mayr

last: Christine


title: Systematic Profiling of Essential Fungal Transcription Factors Uncovers Ezt1 as a Central Pathobiological and Morphogenic Regulator in Cryptococcus neoformans [ChIP-Seq]

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

summary: Cryptococcus neoformans is a global fungal pathogen that causes fatal cryptococcosis, underscoring the urgent need for novel therapeutics given the limitations of current antifungals. Here, we systematically investigate essential transcription factors (TFs) in C. neoformans, focusing on their roles in growth and their potential as drug targets. We developed experimental pipelines to assess growth requirement, essentiality, and function using conditional gene expression, constitutive overexpression, and random spore analysis. Through these systematic analyses, we identify one quasi-essential (growth-required but non-essential) TF, Fhl1, and 13 essential TFs, including three (Ezt1, Ezt2 and Cbf1) that are highly divergent from counterparts in other eukaryotes. Notably, Ezt1 emerged as a central TF regulating over 1,200 genes, controlling growth, antifungal drug and stress responses, sexual development, and virulence. Collectively, our findings define the essential TF landscape of C. neoformans and provide a framework for leveraging these regulators, particularly Ezt1, to develop targeted therapies for cryptococcosis.

overall_design:
The C. neoformans Ezt1-4×FLAG strain was cultured in liquid YPD at 30℃ overnight. The culture was transferred to fresh YPD liquid medium and incubated until the OD600 reached 0.8. In vivo crosslinking was achieved by adding 37% formaldehyde to a final concentration of 1%, and the mixture was incubated at 30℃ for 5 min under agitation. To quench the crosslinking, samples were treated with 2.5 M glycine (300 mM final concentration) and the mixture was further incubated at 30℃ for 5 min with agitation. Cells were collected, washed twice with ice-cold PBS, washed once with ice-cold FA lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, and protease inhibitor), and resuspended in 0.8 ml of ice-cold FA lysis buffer. Cells were homogenised with a bead beater (FastPrep-24 5G, MP biomedicals) for 5 intervals of 2 min of bead beating, with 1 min of cooling on ice between intervals. The complete cell lysate was spun down for 2 min at 4000 rpm, and the supernatant was subjected to sonication until the DNA fragment size reached 150 bp to 500 bp. Finally, 20 μl of the chromatin samples were obtained as input control, and DNA was purified using a DNA purification kit (Cosmogenetech, South Korea).
Protein A Dynabeads® (60 μl per sample) were washed twice with ice-cold PBS containing 5 mg/ml of bovine serum albumin (BSA). The beads were resuspended in 60 μl of PBS with 5 mg/ml of BSA and anti-FLAG antibody (Sigma Aldrich, USA) was added. Each sample was incubated at 4℃ overnight with gentle rotation. The conjugated beads were washed twice with ice-cold PBS containing 5 mg/ml BSA and then aliquoted into four tubes. The extracted chromatin was added to the washed beads, and each sample was incubated at 4℃ for three hours with gentle rotation. After incubation, the beads were washed three times with FA lysis buffer, three times with FA lysis buffer containing 0.5 M NaCl, and once with TE buffer (10 mM Tris-HCl and 10 mM EDTA; pH 8.0), using a magnetic separator (General Electric, USA). Finally, DNA was eluted from the beads with 35 μl of elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, and 1% SDS) at 65℃ for 1 minute. The eluted samples were treated with 15 μl of 10% SDS, 1 μl of RNase H, and 3 μl of RNase cocktail (A&T, Ambion, USA) at 65℃ overnight. The samples were then treated with 7 μl of proteinase K at 42℃ for 90 min to reverse the crosslinking. Reverse-crosslinked DNA samples were purified using a PCR purification kit (Cosmogenetech, South Korea).
Following the evaluation of DNA quality via absorbance measurements using the Nanodrop system (Thermo Scientific, USA), sequencing libraries were constructed using the TruSeq ChIP-seq library preparation kit (Illumina, USA). These libraries were then sequenced on an Illumina sequencing platform.

first: Seung-Heon

last: Lee

first: Sheng

last: Sun

first: Yu-Byeong

last: Jang

first: Seong-Ryong

last: Yu

first: Yeseul

last: Choi

first: Jin-Tae

first: Eui-Seong

last: Kim

first: Jong-Seung

first: Joseph

last: Heitman

first: Kyung-Tae


title: Dietary supplementation with ursolic acid preserves skeletal muscle mass and strength in mouse models of cancer cachexia [RNA-seq]

city: Gainesville

first: Andrew

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

summary: Skeletal muscle atrophy is a devastating and defining feature of cancer cachexia that reduces quality of life, treatment tolerance, and survival, but cannot be prevented or reversed by current management strategies. Ursolic acid is a natural dietary compound that has been shown to inhibit atrophy-associated changes in skeletal muscle mRNA expression in rodents and dogs, leading to beneficial changes in skeletal muscle structure and function.  We hypothesized that dietary supplementation with ursolic acid might help support skeletal muscle mass and function during cancer.  To test this hypothesis, we investigated ursolic acid's effects in five in vivo mouse models of cancer cachexia that are driven by pancreatic, colon, and lung cancer cells of mouse and human origin.  We found that dietary supplementation with ursolic acid has broad-spectrum effects towards cancer-induced skeletal muscle atrophy, significantly preserving muscle mass in all five cancer cachexia models.  Ursolic acid's positive effects on muscle mass and muscle fiber size led to significant improvements in grip strength and muscle tetanic force, persisted in the presence of chemotherapy, and were not associated with discernable changes in food intake or tumor growth.  Ursolic acid appeared to generate its beneficial effects in skeletal muscle by acting directly on muscle cells, inhibiting catabolic effects of tumor-derived secreted factors, and inhibiting > 90% of cancer-induced changes in skeletal muscle mRNA expression.  These results strongly nominate ursolic acid as a promising potential nutritional approach for supporting muscle mass and function in individuals with cancer.

overall_design: To test the hypothesis that ursolic acid might have similar effects in skeletal muscle of mice with pancreatic cancer, we isolated tibialis anterior muscles from KPC tumor-bearing animals who had received either standard chow or standard chow supplemented with ursolic acid.  As a negative control, we isolated tibialis anterior muscles from tumor-free animals who had received standard chow lacking ursolic acid.  We then performed comprehensive transcriptomic analyses (RNA-Seq) on the muscles from the three groups of mice (cancer-free control animals, cachectic KPC tumor-bearing animals with cancer-induced muscle atrophy, and KPC tumor-bearing animals who received dietary supplementation with ursolic acid).

first: Jeremy

last: Ducharme

first: Scott

last: Ebert

first: Miles

last: Cameron

first: Martin

last: Schonk

first: Chandler

last: Callaway

last: D'Lugos

first: John

last: Talley

first: Sarah

first: Christopher

last: Adams


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [ATAC-seq]

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: RFX5 is a DNA binding protein known to regulate MHC genes expressions with little studies on its role in maintaining 3D genome architecture. Recent studies have shown its potential in mediating long-range interactions in specific regions, though the underlying mechanism remains poorly understood. Here, using genes related to cancer progression as a paradigm, we studied the role of RFX5 and found that it specifically regulates these genes. It mediates interactions between gene promoters and their distal enhancers, which can be several hundreds of kilobases apart. We also found that RFX5 regulates higher-order structures of TADs and compartments, which become unstable upon loss of RFX5. Our findings elucidate the fundamental role of RFX5 in maintaining proper chromosome architecture and shed light on the relationship between chromatin loops and gene expression.

overall_design: ATAC-seq experiments measuring chromatin accessibility in RFX5 deleted cells and their wildtype control

first: Ge

last: Xiao

first: Zhang

last: Yijun

first: Wang

last: Yongming


title: Transcriptional profile of primary human lung organoid-derived air-liquid interface (ALI) cultures

city: Vienna

first: Joris

last: van der Veeken

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Innate defences of the respiratory epithelium are the first barrier against incoming respiratory viruses. To understand the contribution of both basal (tonic) and induced interferon (IFN) to antiviral defences in a physiologically relevant system, we established air-liquid interface (ALI) cultures of primary human bronchial epithelium (HBE) and small airway epithelium (HSE). Via an organoid intermediate stage, the limited healthy donor material was expanded while preserving stemness and subsequently differentiated. We here perform bulk RNA-seq to characterize the transcriptomes and cellular diversity of our ALI cultures.

overall_design: Bulk RNA-seq profiling of human bronchial epithelium (HBE) and human small airway epithelium (HSE) models in three biological replicates

first: Rinu

last: Sivarajan

first: Paul

last: Kirchgatterer

first: Moritz

last: Gaidt

first: Konstantin

last: Sparrer


title: Spatial Analysis of T Cell Clonality in Autoimmune Kidney Disease Using TRV Probes

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Hypothesizing that the localization of T cell clones correlates with immune function, our goal was to develop an unbiased method to study the spatial distribution of T cells in tissues. We created an in situ hybridization panel with 248 probes that identify immune and tissue cell types, and 132 probes for all variable TRAV, TRBV, TRGV, and TRDV gene segments. Applying this approach to analyze renal biopsies from patients with autoimmune kidney disease, combinations of TRV segments reliably provided spatial information about T cell clonality. Confined clusters of clonally related αβ T cells were found in proximity to increased numbers of antigen-presenting cells, B cells, and other T cells, reflecting local immune cell interactions. γδ T cells were more frequently located outside or at their periphery of T cell infiltration areas. In conclusion, integrating spatial information with TCR clonotype analysis provided new insights into the organization of immune responses at the tissue level.

overall_design: 2 slides containing 13 samples (3 control and 10 ANCA patients) were analyzed with Xenium

first: Cedric

last: Ly

first: Darius

last: Schaub

first: Zeba

last: Sultana

first: Annika

last: Boxnick

first: Zheng

last: Song

first: Tobias

last: Huber

first: Thorsten

last: Wiech

first: Eva

last: Tolosa

first: Ulf

last: Panze

first: Stefan

last: Bonn

first: Christian

last: Krebs

first: Immo

last: Prinz


title: RFX5 as a regulator of spatial chromatin contacts and gene expression

city: Shanghai

first: Xiao

last: Ge

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

overall_design: Refer to individual Series


title: Lipodystrophy and recovery are mediated by the Wnt/lipogenesis axis during skin fibrosis.

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHC

summary:
Acquired lipodystrophy in the dermal white adipose tissue (DWAT) is an early phenotype of skin fibrosis, followed by accumulation of extracellular matrix (ECM). Lipodystrophy syndromes are estimated to affect 1 in 20,000 people and are associated with metabolic
comorbidities. Recently, we showed that fibrosis-associated lipodystrophy is dependent on sustained Wnt signaling, but the mechanisms remain unclear. Transcriptomic profiling of mature dermal adipocytes in vivo reveal that Wnt activation downregulates the de novolipogenesis (DNL) axis enzymes within 48 hours. We found that protein expression of Fatty Acid Synthase (FASN), a key DNL enzyme, is dependent on sustained Wnt activation in vitro and in vivo. In bleomycin model, human SSc (< 1year of disease) and  keloids, FASN is significantly downregulated. Remarkably, FASN inhibition in mouse during reversal from Wnt induced fibrosis impeded recovery of DWAT lipid content and ECM topography. All together, we demonstrate that acquired lipodystrophy in the context of skin fibrosis is mediated by a new role of the Wnt-DNL axis. These findings underscore the importance of this pathway in lipodystrophy and fibrosis, opening new avenues for therapeutic targets in skin fibrosis.

overall_design: Bulk RNA-Seq profiling of intradermal adipocytes isolated from the floating fraction of mouse dorsal skin collagenase digest at 0-days (control), 2-days and 5-days of beta-catenin/WNT activation in mice

first: Suneeti

last: Madhavan

first: Radhika

last: Atit


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [ChIP-Seq]

overall_design: ChIP-seq experiments to test binding patterns of transcription factor CTCF, RAD21, RFX5 and active enhancer mark of H3K27ac

first: Ge

last: Xiao

first: Zhang

last: Yijun

first: Wang

last: Yongming


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [RNA-Seq]

overall_design: RNA-seq experiments measuring gene expression levels in RFX5 deleted cells and their wildtype control


title: Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code

city: Barcelona

first: Gonzalo

last: Sabarís

address: Passeig del Migdia s/n

institute: IBB-CSIC

summary: Chromatin looping between cis-regulatory elements is essential for precise developmental gene expression, and its disruption is frequently linked to disease. Polycomb Response Elements (PREs) are specialized tethering elements that mediate chromatin loops and are bound by transcription factors (TFs) like GAGA-associated factor (GAF), contributing to the recruitment of Polycomb group (PcG) proteins. While both PcG proteins and GAF have been implicated in looping, their specific roles and the mechanisms of loop specificity remain unresolved. Using genome-wide and locus-specific approaches, we show that high GAF occupancy is required for chromatin looping and gene regulation. However, GAF alone cannot establish loops without additional factors. Surprisingly, PRE looping does not require Polycomb repressive complex 1 (PRC1) or the repressive histone mark H3K27me3. Intriguingly, orthologous PRE sequences can rescue looping, while unrelated PREs with similar GAF levels cannot, indicating that looping specificity depends on both GAF levels and compatible factor combinations at loop anchors. Together, our results support a combinatorial model in which GAF collaborates with additional looping factors to drive PRE-specific interactions, suggesting that certain combinations of factors at PREs may determine which elements form loops and contribute to Polycomb-mediated gene silencing.

overall_design: CUT&RUN assays performed in 16–20h Drosophila melanogaster embryos or third instar larva imaginal discs using GAF, PH, H3K27me3, H3K27ac and IgG (control) antibodies.

first: Marco

last: Di Stefano

first: Sandrine

last: Denaud

first: Lauriane

last: Fritsch

first: Ana-Maria

last: Popmihaylova

first: Giorgio

middle: L

last: Papadopoulos

first: Bernd

last: Schuettengruber

first: Giacomo

last: Cavalli


title: RNA-seq data from gingival crevicular fluid of pregnant women for gestational diabetes mellitus (GDM) prediction

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary: Gingival crevicular fluid samples were collected from pregnant women during the first trimester to investigate early transcriptomic changes associated with gestational diabetes mellitus (GDM). RNA-seq was performed to profile the complete gene expression landscape and identify predictive molecular signatures

overall_design: This study involved RNA-sequencing of gingival crevicular fluid (GCF) samples collected during the first trimester from 10 pregnant women, including 5 who later developed gestational diabetes mellitus (GDM) and 5 healthy controls. Samples were analyzed to identify differentially expressed genes associated with early GDM risk. Total RNA was extracted, and libraries were prepared using the Collibri Stranded RNA Library Prep Kit. Sequencing was performed on an Illumina HiSeq platform.

first: Alejandra

last: Chaparro

first: Maria

last: Bendek

last: Mizgier

first: Carolina

last: Rojas

first: Valeria

last: Ramirez

first: Fernando

last: Bustos

first: Mattew

middle: W

last: Kemp

first: Mahesh

last: Choolani

first: Sebastian

last: Illanes


title: NeuID is a novel neuron-specific lncRNA that regulates neuronal function in Alzheimer’s disease [ChIP-seq]

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

summary: Non-coding RNAs are transcripts that do not encode proteins and comprise 98.5% of the human transcriptome. Among these, long non-coding RNAs (lncRNAs) have been implicated in various biological functions, including the control of gene expression and translation. The central nervous system (CNS) harbors a diverse array of lncRNA transcripts, yet the functions of many remain largely unexplored. In this study, we employed FANS with total RNA-sequencing and single-nuclei RNA sequencing approaches using human and mouse brain tissue to identify novel lncRNAs specific to neurons, and potentially associated with neurodegenerative diseases. We discovered a novel brain-specific lncRNA, the we named 'NeuID', that is specifically expressed in neuronal cells in the mouse and human brains. NeuID expression was found to be reduced in the brains of Alzheimer’s disease (AD) patients. Knockdown (KD) of NeuID resulted in the downregulation of synaptic plasticity genes. Additionally, NeuID KD led to decreased dendritic spine density and reduced neuronal network activity in MEA recordings. Furthermore, we demonstrate that NeuID interacts with EZH2, a component of the PRC2 complex, and mediates the h3k27me3 levels of Olig2 transcription factor. Notably, CRISPRa mediated overexpression of NeuID resulted in the rescue of functional impairment caused by AD-related pathological Aβ oligomers. Overall, our findings identify a novel brain and neuron-exclusive lncRNA that regulates neuronal function, is dysregulated in AD, and might be a potential therapeutic target against neuronal pathology in AD.

overall_design: h3k27me3 ChIP-seq profiling from primary hippocampal neurons treated with either control gapmers or NeuID gapmers to knockdown NeuID

first: Ranjit

last: Pradhan

first: Sadman

middle: M

last: Sakib

first: Iga

last: Grzadzielewska

first: Eren

last: Diniz

first: Dennis

last: Krueger

first: Sophie

last: Schroeder

first: Susanne

last: Burkhardt

first: Anna-Lena

last: Schuetz

first: Jelena

last: Radulovic

first: Farahnaz

last: Sananbenesi

first: André


title: Gut microbiome signatures associate with DNA methylation–based biological aging

city: Honolulu

first: Alika

last: Maunakea

state: Hawaii

address: 1800 East-West Road

department: Anatomy, Physiology and Biochemistry

institute: John A. Burns School of Medicine

summary: Recent advances in machine learning have applied novel tools to aging research, yet the relationship between the gut microbiome and epigenetic aging remains underexplored. This proof-of-concept study investigates whether gut microbial composition is associated with biological aging pace independent of chronological age. Using paired 16S rRNA gene sequencing and DNA methylation data from 123 monocyte-enriched samples in a cohort enriched for Native Hawaiian and Pacific Islander participants, we developed "EpiBiome" models to predict epigenetic age acceleration residuals and DunedinPACE, a DNA methylation biomarker that estimates the instantaneous pace of biological aging. Models predicting residuals of traditional clocks (Horvath, Levine, GrimAge2) showed no predictive signal at either taxonomic rank. By contrast, the EpiBiome-Accel model for DunedinPACE reached statistical significance at both the species level (R² = 0.152, Spearman ρ = 0.408, p = 0.012; permutation p < 0.001) and the genus level (R² = 0.099, permutation p = 0.036). Adding chronological age as a feature did not improve performance (ΔR² = −0.046 at species level), indicating age-independence. SHAP analysis of the species-level ElasticNet model identified Bifidobacterium adolescentis as the dominant contributor and the strongest predictor of decelerated aging, with Succinivibrio dextrinosolvens showing the strongest association with accelerated aging. These findings nominate specific gut taxa as hypothesis-generating candidates for mechanistic follow-up, rather than as individual-level diagnostic markers.Recent advances in machine learning have applied novel tools to aging research, yet the relationship between the gut microbiome and epigenetic aging remains underexplored. This proof-of-concept study investigates whether gut microbial features are associated with biological aging rates independent of chronological time. Using paired 16S rRNA gene sequencing and DNA methylation data from 123 monocyte-enriched samples, we developed "EpiBiome" models to predict epigenetic age acceleration residuals and DunedinPACE, a DNA methylation biomarker that estimates the instantaneous pace of biological aging. While models predicting residuals of traditional clocks (Horvath, Levine, GrimAge2) showed minimal signal, the EpiBiome-Accel model for DunedinPACE showed a modest association (R2=0.125), identifying a microbial signature correlated with the pace of aging. SHAP analysis indicated that Bifidobacterium adolescentis was the top feature associated with decelerated aging, while Faecalibacterium prausnitzii and Gemmiger formicilis were top predictors of accelerated aging in this context. These findings suggest that specific gut taxa are associated with biological aging independent of chronological time. This study offers preliminary evidence linking the gut microbiome to the pace of aging, presenting a potential non-invasive framework for future investigation into the gut-epigenetic aging axis.

overall_design: Human monocytes were isoalted from peripheral blood mononuclear cells (PBMC) via StemCell 'Monocyte Enrichment Kit without CD16 depletion' Kit.  PBMC obtained via venous blood draw. This submission includes methylation data for n=78 samples (32 male, 46 female) of varying type-2-diabetes melitus  (53 non-diabetic, 17 pre-diabetic, 8 type-2 diabetic) and obesity (31 normal, 30 overweight, 17 obese) status.  Methylation data acquired via utilization of the Infinium MethylationEPIC array.

first: Braden

last: Kunihiro


title: DNA methylation gain at polycomb CpG islands is a hallmark of cellular aging

city: Jerusalem

first: Hagit

last: Masika

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

institute: Hebrew University of Jerusalem

summary: Aging is a complex multifactorial process that affects cellular function and tissue homeostasis over time.  Despite extensive research, the molecular mechanisms driving cellular aging remain poorly understood.  Many studies have focused on changes in DNA methylation as an indicator of aging.  In particular, the degree of methylation at polycomb CpG islands has been shown to be predictive of phenotypic changes associated with aging.  Since many age-related pathological processes, are thought to be of single-cell origin (e.g. cancer), we questioned whether polycomb DNA methylation also occurs preferentially in a subset of cells within the overall population.  Using single-cell whole-genome data from multiple ages and tissues, we identify Average Polycomb CpG Methylation (AvPolyMe) as a hallmark of cellular aging.  This revealed that aging occurs at varying rates within specific cells, with proliferating cells showing accelerated levels. Gene expression analysis in “young” and “old” single cells identified changes in immune response, translation regulation, tumorigenesis and other cellular processes associated with aging.  These results challenge traditional models of homogeneous cellular aging and suggest that aging is a highly individualized process at the single-cell level that may be driven by programmed changes in polycomb CpG island DNA methylation.

overall_design: This study investigates DNA methylation dynamics during aging using whole-genome bisulfite sequencing of single crypts isolated from the small intestines of two wild-type B6 mice (aged 22 and 28 weeks) and single follicle cells from black and white hair follicles of a 53-year-old human. Mouse samples were processed using the NEBNext Enzymatic Methyl-seq Kit (E7120) following the manufacturer's instructions, while human samples were prepared using the xGen Methyl-seq Library Prep Kit (10009824, IDT).

first: Howard

last: Cedar

first: Tommy

last: Kaplan