title: Effects of GOLPH3 knock-out on the mouse liver transcriptomic profile

city: Lausanne

first: Giovanni

last: D'Angelo

address: Station 19

department: SV-IBI

institute: EPFL

summary: The Golgi complex serves as the central hub of the biosynthetic pathway, where anterograde and retrograde trafficking converge. How cargo and Golgi-resident proteins traverse this organelle has long been debated. Recent studies have identified a molecular machinery that sorts resident proteins into retrograde-directed COPI vesicles during cisternal maturation. Golgi phosphoprotein 3 (GOLPH3) is a key component of this system; however, its physiological relevance and regulatory mechanisms remain poorly defined. Here, we show that GOLPH3 depletion in mice alters both protein and lipid glycosylation, causes partially penetrant embryonic lethality and severely impairs growth and bone mineralization. At the molecular level, we find that GOLPH3 is regulated by functionally antagonistic S-acylation events that control the topology of its membrane association. To mediate retrograde trafficking of Golgi-resident glycosyltransferases, GOLPH3 must bind their cytosolic tails. This occurs via a negatively charged surface region, which is correctly oriented only in one of the S-acylated GOLPH3 conformations. Together, these findings reveal a lipid-mediated regulatory mechanism for intra-Golgi trafficking and establish the critical role of GOLPH3 in vertebrate development.

overall_design: Bulk RNA-seq profiling of  WT or GOLPH3-knockout mice liver samples obtained from both female and male cohorts.

first: Anastasia

last: Theodoropoulou

first: Anita

last: Nasrallah

first: Luciano A.

last: Abriata

first: Laurence

last: Abrami

first: Juliane

last: Da Graca

first: Irmak

last: Kaysudu

first: Francesco

last: Talotta

first: Maria J.

last: Marcaida

first: Muhammad U.

last: Anwar

first: Ondrej

last: Kovac

first: Sergey Y.

last: Vakhrushev

first: Alejandro

last: Calleja

first: Sylvia

last: Ho

first: Antonino

last: Asaro

first: Francisco S.

last: Mesquita

first: Leila

last: Alieh

first: Charlotte

last: Gehin

first: Lucie

last: Bracq

first: Nika

last: Gorsek

first: Sarah

last: Vacle

first: Arthur

last: Samurkas

first: Alessio

last: Prunotto

first: Miroslav

last: Machala

first: Olaia

last: Naveiras

first: Katrine T.

last: Schjoldager

first: F. Gisou

last: Van der Goot

first: Matteo

last: Dal Peraro


title: RNA-seq analysis of lenvatinib-sensitive and lenvatinib-resistant tumor tissues from a subcutaneous HCC mouse model

status: Public on Apr 23 2026

city: Shanghai

first: Yunkai

last: Lin

address: Qianju Road 366

department: National Center for Liver Cancer

country: China

institute: Second Military Medical University

type: Expression profiling by high throughput sequencing

summary: To investigate the molecular mechanisms underlying acquired resistance to lenvatinib in hepatocellular carcinoma (HCC), we established a lenvatinib-resistant mouse model using H22 cell-based subcutaneous xenografts. Tumor tissues were collected from lenvatinib-sensitive (H22-NR) and lenvatinib-resistant (H22-LR) mice. We performed RNA-sequencing to identify differentially expressed genes and signaling pathways that mediate lenvatinib resistance. Comparative gene expression profiling analysis between the NR and LR groups was conducted to screen for key drivers of drug resistance.

overall_design: We established a syngeneic subcutaneous HCC mouse model with acquired lenvatinib resistance by intermittent high-dose lenvatinib administration. Tumor tissues were harvested from lenvatinib-sensitive (H22-NR) and lenvatinib-resistant (H22-LR) mice, with three biological replicates per group (NR1, NR2, NR3; LR1, LR2, LR3). Total RNA was extracted from the six tumor samples and subjected to RNA-seq for gene expression profiling. Comparative gene expression profiling analysis of RNA-seq data between H22-NR and H22-LR groups to identify key genes and pathways involved in lenvatinib resistance.

first: Xiaomeng

last: Wang


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [snRNA-seq]

city: New Haven

first: Kevin

middle: C

last: Johnson

state: CT

address: 333 Cedar Street

department: Neurosurgery

country: USA

institute: Yale University

summary: Isocitrate dehydrogenase (IDH)-mutant gliomas are malignant brain tumors that typically arise in early- to mid-adulthood and nearly always recur following treatment. However, the genetic and cellular state changes that drive IDH-mutant glioma progression under treatment remain incompletely understood. Here, we integrated single-nucleus transcriptomic profiles, chromatin accessibility profiles and bulk DNA/RNA sequencing from 75 temporally separated gliomas across 35 patients comprising both the oligodendroglioma and astrocytoma IDH-mutant glioma tumor types. We show that malignant cell states transcriptionally resemble stages of normal glial-neuronal lineage development or a reactive mesenchymal-like state, mirroring states previously described in IDH-wildtype glioblastoma. Malignant cell states displayed distinct chromatin accessibility profiles that were comparable between both IDH-mutant glioma types. The abundance of less differentiated malignant cells increased with grade and with genetic alterations such as PDGFRA amplification. Longitudinal analysis highlighted two major malignant cell state transition patterns. First, reduced lineage differentiation and increased proliferative malignant cells at recurrence were pronounced in gliomas that acquired recurrence-associated genetic events, including treatment-associated hypermutation, increased copy number changes, and cell cycle alterations. Second, increased mesenchymal-like state abundance occurred independently of acquired genetic alterations and instead coincided with heightened macrophage expression. Overall, our findings provide an integrative model that traces the cell-intrinsic and extrinsic factors that shape cellular states during IDH-mutant glioma disease progression.

overall_design:
Nuclei from frozen IDH-mutant glioma tissues were isolated and submitted to a 10x Genomics workflow for profiling by single-nucleus RNA-sequencing.

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

first: Avishay

last: Spitzer

first: Frederick

middle: S

last: Varn

first: Masashi

last: Nomura

first: Luciano

last: Garofano

first: Anna

last: Lasorella

first: Mario

middle: L

last: Suvà

first: Antonio

last: Iavarone

first: Itay

last: Tirosh

first: Roel

middle: G

last: Verhaak


title: Complement-regulated Homeostatic Proliferation Controls Memory B Cell Longevity and Repertoire Composition

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Memory B cell (Bmem) survival is essential for guarding against reinfection, yet processes ensuring their longevity remain unclear. As decay-accelerating factor (DAF, CD55), a negative regulator of complement activation, is requisitely downregulated on germinal center B cells and is re-expressed on Bmem, we investigated the effects of deleting DAF on murine (B1-8hi) Bmem in competitive settings. Kinetic analysis showed a progressive reduction in DAF-/- Bmem numbers over six weeks, without affecting Bmem production, pool size, or their ability to respond to rechallenge. Following transfer into unimmunized hosts, wild-type Bmem proliferated to maintain stable Bmem pool sizes, outcompeting DAF-/- Bmem, reflecting homeostatic proliferation. Reduced proliferation and increased cell death in DAF-/- Bmem associated with transcriptional differences in metabolism and migration pathways. Wild type Bmem proliferation increased in C3-/- hosts, and vaccination with a heterologous antigen, which induces local complement activation, locally inhibited bystander B1-8hi Bmem proliferation. Thus, complement-dependent regulation of Bmem homeostatic proliferation influences Bmem longevity and repertoire composition in mice.

overall_design: RNA-Seq profiling of flow-sorted wildtype and DAF/CD55-null memory B cells (B220+ IgD- CD38+ GL7- Igλ+ NP+), sorted using congenic markers (CD45.2 for wildtype, CD45.2 for DAF KO). Each replicate is a pool of 2-3 mice. Cells isolated 4 weeks after immunization.

first: Evan

last: Cody

first: Peter

last: Heeger


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [snATAC]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
Nuclei from frozen IDH-mutant glioma tissues were isolated and profiled by 10x Genomics Multiome ATAC and Gene Expression. ATAC fragments are provided here.

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


title: Distinct activity in prefrontal projections promotes temporal control of action

city: Iowa

first: Nandakumar

last: Narayanan

state: IA

address: 169 Newton Road

department: Neurology

institute: University of Iowa

summary: Prefrontal neurons can have diverse activity during cognitive functions such as working memory, attention, and timing; however, the importance of this heterogeneity is unclear. Our goal was to better understand the diversity of prefrontal activity through anatomical connectivity. We harnessed circuit-specific tools in mice to capture activity within prefrontal projections during interval timing, a highly translational cognitive process that requires working memory for temporal rules and attention to the passage of time to estimate a temporal interval of several seconds. We used neuronal recordings to capture prefrontal activity during interval timing, with major patterns characterized by monotonic time-dependent ramping over a temporal interval. We then leveraged retrograde viruses to interrogate prefrontal cortex (PFC) projections to the mediodorsal thalamus (PFC-MD) and to the dorsomedial striatum (PFC-DMS). We report three novel results. First, circuit-specific calcium fiber photometry revealed that PFC-MD and PFC-DMS activity encoded distinct temporal signals, with PFC-MD projections ramping down and PFC-DMS ramping up to interval timing response times. Second, circuit-specific inactivation revealed that PFC-DMS inactivation disrupted animals’ internal estimates of time. Third, circuit-specific single-nucleus RNA sequencing of prefrontal projections revealed distinct transcriptomic profiles between PFC-MD and PFC-DMS projections, with enriched genes for cortical layers as well as genes such as Cux2, Camk2n1, Htr4, and Foxp2. These data suggest differences in gene expression and connectivity distinguish prefrontal activity during interval timing. These findings advance our fundamental understanding of prefrontal function and dysfunction in human disease.

overall_design: To label PFC projection neurons, male and female H2B-TRAP mice received bilateral stereotaxic injections of retrograde AAV-Cre into either the mediodorsal thalamus (MD) or dorsomedial striatum (DMS). After a 2-week recovery period, mice were sacrificed, and dorsal and ventral PFC tissues were microdissected based on mCherry fluorescence. mCherry-positive nuclei were isolated and collected by fluorescence-activated nuclei sorting for downstream single-nucleus analyses.

first: Xin

last: Ding

first: Trevor

last: Butler

first: Jon

middle: M

last: Resch

first: Matthew

middle: A

last: Weber

first: Alexandra

last: Bova

first: Stephanie

last: Guerrero

first: Rachel

last: Cole

first: Christopher

last: Hunter

first: Hannah

middle: R

last: Stutt

first: Madison

last: McMurrin

first: Mackenzie

last: Spicer

last: Conlon

first: Shane

last: Heiney

first: Youngcho

last: Kim


title: Gene expression profiling of H1299 cells with or without SAMD4A expression

city: Kobe

first: Junji

last: Otani

state: Hyogo

address: Kusunoki-cho 7-5-1, Chuo-ku

department: Department of Medicine

country: Japan

institute: Kobe university

summary: The transcriptional cofactors YAP1 and TAZ regulate target gene expression by binding to the transcription factor TEAD. Due to their roles in cancer initiation, progression, and drug resistance, YAP1 and TAZ are promising targets for cancer therapy. SAMD4A/B are RNA-binding proteins that are broadly expressed across human tissues, but few of their molecular targets and biological functions have been identified. In Drosophila, the SAMD4A/B homolog Smaug participates in early embryonic development by disrupting the stability and translation of maternal mRNA. To discover targets inhibiting the YAP1/TAZ-TEAD oncogenic transcription program, we screened a whole-genome siRNA library and identified siSAMD4B as potently suppressing TEAD activity in human cancer cells. We showed that SAMD4A/B increased TEAD activity by destabilizing and repressing the translation of VGLL4 mRNA, promoting cancer progression in vitro. Conversely, inhibiting either SAMD4A or SAMD4B elevated VGLL4 mRNA, which suppressed TEAD activity and inhibited cancer progression. Notably, transgenic mice expressing liver-specific SAMD4B exhibited accelerated development of intrahepatic cholangiocarcinomas in an Nf2-deficient background. These tumors appeared in the mutants at one week of age and caused death due to hepatic failure by 100 days. Thus, SAMD4A/B may be a promising target for anticancer drugs designed to inhibit TEAD activation.

overall_design: H1299 cells lacking SAMD4A/B and carrying a Dox-off SAMD4A expression module were cultured in the presence or absence of Dox for 48 h

first: Miki

last: Nishio

first: Makoto

last: Nishimori

first: Tomohiko

last: Maehama

first: Akira

last: Suzuki


title: Gene expression profiling of HepG2 cells with or without SAMD4B overexpression

overall_design: HepG2 cells carrying a Dox-on SAMD4B expression module were cultured in the presence or absence of Dox for 48 h


title: HNF4a controls growth, identity and response to KRAS inhibition in IMA [ATAC-seq]

city: Salt lake City

first: Headtlove

last: Essel Dadzie

state: UT

address: 2000 circle of Hope

institute: University of Utah

summary: Cellular plasticity is a key feature of cancer that enables tumor cells to switch lineage identities, driving disease progression and resistance to therapy. In invasive mucinous adenocarcinoma (IMA), a pronounced pulmonary-to-gastric lineage switch occurs as NKX2.1 is lost and HNF4α, a master regulator of gastric differentiation, is upregulated. Although absent in normal alveolar type 2 cells, HNF4α is aberrantly expressed in most IMA tumors. In this study, we investigate the role of HNF4α within established IMAs and find that it directly activates a gastric differentiation program, particularly in pit cells. Loss of HNF4α disrupts this program and permits FOXA1 and FOXA2 to bind new regulatory sites, leading to the upregulation of neuronal and liver-like gene modules. In light of the poor response of mucinous tumors to KRAS inhibitors, we investigated whether HNF4α modulates sensitivity to KRASG12D targeted therapy. Treatment with MRTX1133 revealed that loss of HNF4α significantly increases IMA sensitivity by reducing the IC50 in vitro and enhancing tumor regression in vivo. Mechanistically, HNF4α deletion impairs cell-cycle progression in drug-tolerant persister cells, while tumors retaining HNF4α maintain these cell-cycle regulators despite KRAS inhibition, promoting persister cell survival. Our findings establish HNF4α as a critical driver of IMA biology governing both gastric differentiation and resistance to KRAS inhibitors and support the development of combination strategies to overcome therapeutic resistance in IMA.

overall_design: ATACseq was performed on 1311G#5  treated with with or without HNF4α after single cell breakdown.

first: Eric

last: Snyder


title: Transcriptomic adaptations of human muscle after short- and long-term exercise

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

summary: The molecular mechanisms that govern muscle hypertrophy (as induced by increased physical activity) remain incompletely defined. Through RNA-seq of human muscle, we confirm observations from mice that extensive remodeling of the neuromuscular junction (NMJ) occurs in human muscle after exercise.

overall_design: RNA-seq of of human muscle biopsies from different exercise interventions (either 24 hours or 6 weeks). For the 24 h samples, percutaneous muscle biopsies from the vastus lateralis were obtained from young healthy volunteers after an eccentric exercise protocol. Muscle biopsies were obtained from resting individuals and at 24 h after completion of an eccentric exercise session consisting in downhill running on a treadmill (-15%) for 40 min at 60% VO2max. Individuals were not subjected to previous exercise programs. For the 6 week samples, human muscle biopsies were taken from quadriceps femoris muscle of healthy volunteers pre- and post-exercise training (six-week resistance training program).

first: Silvia

last: Campanario

first: Mercedes

last: Grima-Terrén

first: Megan

last: Rommelfanger

first: Stefania

last: Dell’ Orso

first: Xuesong

last: Feng

first: Ignacio

last: Ramírez-Pardo

first: Aina

last: Calls

first: Andrés

last: Cisneros

first: Kyung

last: Dae Ko

first: Esther

last: García-Domínguez

first: Laura

last: Pena-Couso

first: Grace

last: Chou

first: Yuewen

last: Zheng

first: Nasun

last: Hah

first: Davide

last: Randazzo

first: Alberto

last: Pérez-Garcia

first: Mari Carmen

last: Gómez-Cabrera

first: Tovah

middle: E

last: Markowitz

first: Iago

last: Pinal-Fernandez

first: Andrew

last: Mammen

first: Jose

last: Milisenda

first: Benjamin

last: Yang

first: Antonio

last: Serrano

first: Eusebio

last: Perdiguero

first: Vittorio

last: Sartorelli

first: Joan

last: Isern


title: Transcriptomic adaptations of human muscle in patients with polyarteritis nodosa and muscle denervation

first: Pura

last: Muñoz-Cánoves

summary: The molecular mechanisms that govern muscle atrophy (as seen in disuse or aging) remain incompletely defined. Through RNA-seq of human muscle, we confirm observations from mice that extensive remodeling of the neuromuscular junction (NMJ) occurs in human denervated muscle.

overall_design: RNA-seq of human muscle biopsies collected from five patients with polyarteritis nodosa and muscle denervation and from healthy comparators at the Muscle Research Unit, Internal Medicine Service, Hospital Clinic (Barcelona, Spain).


title: Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: UCSF Gladstone Institutes

summary: Host factors that promote or restrict human immunodeficiency virus (HIV) infection in human CD4+ T cells have not been comprehensively identified. We performed orthogonal genome-wide CRISPR activation (CRISPRa) and CRISPR knockout (CRISPRn) screens in primary human CD4+ T cells to systematically discover pro- and anti-HIV host factors. Candidate hits were validated using secondary pooled screens and arrayed perturbations and were further characterized using assays for HIV infection, T cell activation, and HIV receptor/co-receptor expression. CRISPRa identified multiple potent antiviral factors including PI16, PPID, SHISA3, and ITM2A. PI16 interacts with host pathways involved in HIV fusion and inhibits viral entry, while PPID (Cyp40) binds HIV capsid and restricts infection by reducing nuclear import of the HIV core. Structural modeling, evolutionary analyses, and targeted mutagenesis identified domains and residues required for PPID-mediated restriction, including non-human primate ortholog substitutions that enhance antiviral activity. Together, these data define the functional HIV–host interaction landscape in primary human CD4+ T cells and reveal new mechanisms modulating HIV infection.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Primary human CD4+ T cells were genetically perturbed at genome scale using pooled lentiviral CRISPR knockout (CRISPRn) or CRISPR activation (CRISPRa) libraries and challenged with replication-competent GFP-tagged HIV. After infection, cells were sorted by flow cytometry into GFP-positive (infected) and GFP-negative (uninfected) bins and sgRNA representation was quantified by deep sequencing. Top hits were validated in secondary pooled screens and arrayed perturbations and were profiled across additional conditions including different HIV inoculum concentrations, VSV-G pseudotyped HIV-GFP, and FACS-based assays for CD4, CXCR4, CD25, and CD69

first: Ujjwal

last: Rathore

first: Eli

last: Dugan

first: Hunter

last: Thornton

first: Vigneshwari

last: Kumar

first: Rama

last: Dajani

first: Ryan

last: Burdick

first: Janet

last: Young

first: Zachary

last: Steinhart

first: Reanna

last: Lao

first: Krista

last: Delviks-Frankenberry

first: Wooyoung

last: Choi

first: William

last: Henriques

first: Ignacia

last: Echeverria

first: Emma

last: Dann

first: Ishaan

last: Dureja

first: Nandini

last: Pathak

first: Maya

last: Arce

first: Justin

last: McKetney

first: Jennifer

last: Umhoefer

first: Simrun

last: Parulekar

first: Ralf

last: Schmidt

last: Polacco

first: Jason

last: Neidleman

first: Mauricio

last: Montano

first: Vinh

middle: Q

last: Nguyen

first: Andrej

last: Sali

first: Jay

last: Levy

first: Jeannette

last: Tenthorey

first: Yifan

last: Cheng

first: Nadia

last: Roan

first: Danielle

last: Swaney

first: Robyn

last: Kaake

first: Stacie

last: Dodgson

first: Joseph

last: Hiatt

first: Vinay

middle: K

first: Harmit

last: Malik

first: Nevan

middle: J


title: Single-cell multi-omic and spatial landscape of primate pineal gland reveals circadian and melatonin regulatory architecture

first: jihong

last: zheng

state: Shanghai

address: XinSongjiang Road, Songjiang District

institute: Shanghai General Hospital

summary: The mammalian pineal gland maintains circadian rhythms and homeostasis by secreting melatonin. However, the lack of a cell-resolved regulatory map limits our understanding of how these neuroendocrine functions are orchestrated in primates. Here, we constructed a multi-omics atlas of the Macaca fascicularis pineal gland by integrating snRNA-seq, snATAC-seq, and spatial transcriptomics. We identified pinealocytes as the predominant cell type, alongside six glial and vascular lineages. Chromatin accessibility analysis delineated cell-type-specific regions enriched for melatonin synthesis and phototransduction genes. Notably, we resolved a dual-layer regulatory architecture: while melatonin synthesis programs are robustly organized, circadian clock regulators exhibit a distinct, sparse spatial pattern. Co-expression networks further identified core modules and regulatory hubs—including CRX/OTX2, LHX4, and RORA—that integrate these circadian and light-responsive signals. Cell-cell communication analysis identified signaling axes, such as PTN-ALK/SDC2, RA-RORB, and NRG1-ERBB4, that potentially coordinate this spatial functional organization. Integrating genetic traits showed that sleep and neuropsychiatric risk variants preferentially map to these pineal regulatory modules. Specifically, sleep-associated loci converged on MEIS1-linked elements, while bipolar disorder-associated loci highlighted candidate genes RDH12 and SDK2. Overall, this study reveals the cellular diversity and spatial regulatory logic of the primate pineal gland, providing a foundation for investigating circadian and neuroendocrine regulation in health and disease.

overall_design: We constructed a multi-omics atlas of the Macaca fascicularis pineal gland by integrating single-nucleus RNA sequencing (snRNA-seq), single-nucleus ATAC sequencing (snATAC-seq), and spatial transcriptomics. This approach identified pinealocytes as the predominant cell type, alongside glial and vascular lineages. Chromatin accessibility analysis pinpointed regions associated with melatonin synthesis and circadian clock regulation. Co-expression network analysis identified key regulatory hubs, including CRX/OTX2, LHX4, and RORA, that integrate circadian and light-responsive signals. Additionally, cell-cell communication analysis revealed signaling axes, such as PTN-ALK/SDC2 and RA-RORB, coordinating spatial functions in the pineal gland. Integrating genetic risk variants for sleep and neuropsychiatric disorders linked these modules to human traits. This multi-omics data provides a comprehensive map of cellular diversity and regulatory mechanisms in the primate pineal gland, serving as a resource for studying circadian and neuroendocrine regulation.

first: Jihong

last: Zheng

first: Yuchen

last: Xiao

first: Jianjun

last: Lyu

first: Hongtao

last: Xu

first: Yaqun

last: Zhang

first: Yanchuan

last: Li

first: Yihao

first: Tianjun

last: Wang

first: Liu

last: Liu

first: Lingjing

last: Jin

first: Xuhui

last: Zhou

first: Chao


title: H3 dopaminylation and CaMKII modulate diffuse midline glioma response to CDK9 inhibition

city: Houston

first: Rebecca

middle: Lauren

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Aberrant neurotransmitter signaling and transcriptional dysregulation are hallmarks of gliomagenesis and represent potential therapeutic targets. Monoamine neurotransmitters such as dopamine and serotonin primarily activate GPCRs but can also function epigenetically as histone H3 modifications. Here, we uncover mechanisms of crosstalk between monoamine neurotransmitter signaling, H3 dopaminylation, and RNA polymerase II (Pol2) transcription in diffuse midline glioma (DMG). We find that co-treatment with Pol2 targeting CDK9 inhibitors (CDK9i) and FDA approved neuropsychiatric drugs, including selective serotonin reuptake inhibitors (SSRIs), synergistically reduces DMG growth. Mechanistically, CDK9i+SSRI treatment alters H3 dopaminylation patterns and represses synaptic and neurodevelopmental gene transcription associated with CDK9i resistance. Further phospho-proteomic analyses show that CDK9i monotherapy activates pro survival CaMKII signaling, which can be suppressed by co-treatment with neuromodulatory drugs. These studies establish roles for H3 dopaminylation and neurotransmitter signaling in DMG gene regulation and response to CDK9i, suggesting that monoamine neurotransmitter pathways may be exploited as a therapeutic strategy for DMG.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [organoids]

first: Kevin

last: Johnson

overall_design:
Freshly resected glioma samples were used to produce IDH-mutant glioma organoids as described by Jacob et al Cell 2020 (PMID: 31883794). Tumor tissue diagnosis was performed by pathological assessment and confirmed with molecular information provided by clinical whole exome sequencing. All three organoid models were confirmed to be IDH1-mutant astrocytomas with immunohistochemistry confirming that the organoids maintained the IDH1 R132H mutation. For each patient-derived glioma organoid model (GBO), samples were either treated with a single 10Gy dose of irradiation or were not exposed to irradiation (control) followed by recovery for 7 days before single-cell RNA sequencing.

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

first: Tanyeri

last: Barak

first: A. Gulhan

last: Ercan-Sencicek

first: Ayse Buket

last: Peksen

first: Linbin

first: Jennifer

last: Moliterno

first: Roel

last: Verhaak


title: Transcriptomic profiling of E0771 breast tumors grown in wild-type versus uPAR-deficient hosts

city: Montreal

first: Shafaat

last: Ahmed Rabbani

state: Quebec

address: 1001 Decarie Blvd

country: Canada

institute: McGill University Health Center - Glen Site

summary: The goal of this study is to define the contribution of host-derived urokinase plasminogen activator receptor (uPAR) to the tumor microenvironment in breast cancer. While uPAR is well recognized for its tumor-intrinsic roles, its functions within the host compartment, particularly in shaping immune and stromal responses, remain poorly understood. Using the syngeneic E0771 murine breast cancer model, we compared transcriptomic profiles of primary tumors grown in wild-type versus uPAR-deficient hosts to identify gene expression programs associated with loss of host uPAR. Bulk RNA sequencing was employed to capture global changes in tumor-associated transcriptional networks, with particular emphasis on immune-related pathways, antigen presentation, extracellular matrix remodeling, and tumor–host crosstalk. The objective of this work is to establish host-derived uPAR as a regulator of the tumor microenvironment and to provide a transcriptomic framework linking uPAR deficiency to altered immune contexture and microenvironmental signaling. This dataset is intended to support mechanistic interpretation of tumor–host interactions and to serve as a resource for future studies investigating uPAR-targeted strategies in breast cancer.

overall_design:
Primary E0771 tumors were harvested from wild-type and uPAR knockout mice (n=4 per group). RNA was extracted from tumors and subjected to bulk RNA sequencing. Differential gene expression analysis was performed to compare tumors from wild-type versus uPAR-deficient hosts.

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Submitter states that missing raw files are due to file loss.
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first: Mehran

last: Alizadeh Harzevili

first: Niaz

last: Mahmood

first: Ani

last: Arakelian


title: ATF7ip inhibits the tumor immune response by promoting terminal CD8+ T cell Exhaustion II

first: Jun Hyung

last: Sin

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

summary: CD8+ T cell exhaustion limits the immune response to tumors because of ineffective T cell effector functions. Thus, therapies that inhibit T-cell exhaustion are critical for optimizing cancer treatment. Recent studies have implicated epigenetic proteins in T-cell exhaustion. Here, we identified activating transcription factor 7 interacting protein (ATF7ip) as an epigenetic protein critical for inducing T cell exhaustion. Loss of Atf7ip in CD8+ T cells results in decreased terminal exhaustion and increased numbers of progenitor-exhausted cells in both chronic viral infections and cancer. Owing to decreased exhaustion, Atf7ip-deficiency in CD8+ T cells leads to an enhanced immune response to tumors. Mechanistically, ATF7ip functions to stimulate the deposition of repressive H3K9me3 at critical immune-effector gene loci, such as Il7r and Il2 leading to enhanced exhaustion. Our data suggest that ATF7ip may be a rational target for deletion in adoptive T-cell therapies to reduce CD8+ T-cell exhaustion.

overall_design: p14+Cd8+ T cells from tumors of 3-4 Atf7ip-sufficient and Atf7ip-deficient mice were pooled and FACS sorted into 1.5 ml tubes containing DMEM with 2 FBS. About 20,000 cells per 100 ul were sent out for 10X sequencing. Single cells were captured using the 10X chromium microfluidics system and barcoded and sequenced on the Illumina NovaSeq.

first: Sujit

last: Kashyap

first: Michael

last: Waterfield


title: MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment [RNA-Seq]

first: Anthony

last: Flamier

state: QC

address: 3175 chemin de la Côte-Sainte-Catherine

department: Neurosciences

institute: Université de Montreal

summary: Rett syndrome arises from loss-of-function mutations in the X-linked chromatin regulator MECP2, yet the earliest molecular derailments in human development remain poorly defined. Using isogenic hESC models carrying three patient-derived MECP2 mutations, we followed the transcriptome from pluripotency through neuro-ectoderm, neural stem, and neural progenitor stages and into four-month cerebral organoids. Stage dominated transcriptional variance, but mutants shared a secondary program enriched for synaptic-membrane and extracellular-matrix genes. Single-cell profiling revealed a naïve-like, hyper-proliferative state marked by up-regulation of ZFP42 at ESC stage. Strikingly, EMX1, a cortical radial-glia determinant, was consistently suppressed from the earliest stage onward, and cerebral organoids subsequently generated fewer excitatory neurons in favour of inhibitory and glial lineages. These data chart a continuous developmental trajectory for MECP2-mutant human cells and nominate ZFP42 and EMX1 dysregulation as tractable entry points for dissecting Rett pathogenesis.

overall_design: Bulk RNA sequencing on MECP2-WT, MECP2-R133C, MECP2-R168X and MECP2-R270X hESC lines differentiated for 0 (hESC), 3 (Neuroectoderm), 7 (Neural progenitor) and 21 (Neural stem) days.

first: Marion

last: Guillon

first: Margaux

last: Brin


title: MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment

overall_design: Single-cell RNA sequencing on MECP2-WT, MECP2-R133C, MECP2-R168X and MECP2-R270X hESC lines.


title: RNA-seq analysis for the Fluo-4 abnormal myofibers in aged mice

city: Obu

first: Naoki

last: Ito

state: Aichi

address: 7-430, Morioka-cho

department: Geroscience Research Center

institute: National Center for Geriatrics and Gerontology

summary: In a rapidly aging society, the age-related decline in muscle mass and force, sarcopenia, is an urgent medical and economic issue. However, the molecular mechanisms of sarcopenia are still largely unknown. Using Ca2+ indicator Fluo-4, we identified the presence of the Fluo-4 abnormal muscle fibers only in aged mice. The Fluo-4 abnormal muscle fibers had a tubular aggregate-like structure and morphologically abnormal mitochondria. Furthermore, a cluster of mitochondria-related genes, including mitochondrially-encoded genes, were downregulated in Ca2+-abnormal muscle fibers. These results indicate that the Fluo-4 abnormal muscle fibers are accumulated in aged mice, and that age-related mitochondrial abnormalities are more prominent in these fibers.

overall_design: RNA-seq profiling of young myofibers, Fluo-4 normal fibers and Fluo-4 abnormal fibers in aged mice.

first: Takahiro

last: Eguchi


title: Transcriptional and immune repertoire profiling of mismatch repair-deficient colorectal cancer

city: Southampton

first: Stephen

middle: Mark

last: Thirdborough

state: Hants

address: Tremona Road

department: School of Cancer Sciences

country: United Kingdom

institute: University of Southampton

summary: Colorectal cancers (CRC) with deficient mismatch repair (dMMR) exhibit variable responses to immune checkpoint inhibitors, despite their immunogenic nature. To investigate the molecular basis of this heterogeneity, we performed integrated bulk RNA sequencing and immune repertoire profiling on tumor and adjacent normal mucosa from treatment-naïve dMMR CRC patients. Using weighted gene co-expression network analysis, we identified transcriptional modules associated with T and B cell clonality, immune-metabolic interactions, and therapeutic responsiveness. Our dataset provides a valuable resource for understanding the tumor microenvironment in dMMR CRC and supports the development of biomarkers for patient stratification beyond mismatch repair status.

overall_design: Bulk RNA-sequencing of dMMR CRC tumors (n=30) and immune repertoire sequencing (TRB and IGH) of matched tumor and normal adjacent mucosa.

first: Sheah Lin

last: Lee


title: Micropeptide UEIS attenuates cGAS-STING-type I IFN signalling to repress anti-tumour immunity

city: Harbin

first: Xingwen

last: Wang

state: Heilongjiang

address: Xidazhi

institute: HIT

summary: Immune checkpoint blockade (ICB) has achieved remarkable success in cancer treatment; however, enhancing its efficacy remains a significant challenge. Selectively restoring tumour-induced immune deficiency within the tumour   microenvironment is considered an ideal strategy for unleashing antitumour   immunity without causing severe toxicity. Here, we describe an immunoregulatory micropeptide encoded by a long non-coding RNA (lncRNA) gene identified through comprehensive bioinformatic screening, which we designate as UEIS. UEIS was found to be upregulated in tumour-associated macrophages (TAMs) and to drive macrophages toward a pro-tumorigenic phenotype, thereby inhibiting antitumour T-cell immunity. Mechanistically, the expression of UEIS is induced by cGAS-STING-type I interferon (IFN) signalling at a relatively late stage following tumoral DNA stimulation. Thus, we identify the endogenous existence of a lncRNA-encoded micropeptide and reveal its inhibitory effect on cGAS-STING-type I IFN signalling via a feedback loop in TAMs. These findings highlight UEIS as a promising therapeutic target for cancer treatment.

overall_design: The MC38 tumour tissue grown in UEIS LSL and UEIS KI mice were dissected and digested into single-cell suspension. Tumour-infiltrating immune cells (CD45+ cells) were sorted for scRNA-seq

first: Yi

last: Zhang

first: Ying

last: Hu


title: PROX1 loss in adult mouse Schlemm’s canal causes permanent ocular hypertension

city: Chicago

first: Benjamin

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

summary: Glaucoma is associated with ocular hypertension and lowering intraocular pressure is a key objective of glaucoma therapies. Recent studies have established a role for the Schlemm’s canal endothelium in this pressure increase and have shown it to have a unique, lymphatic-like, hybrid phenotype. However, the role of these lymphatic phenotypes in the adult canal remains uncertain. Long-term functional studies have been limited by systemic importance of lymphatic genes and lack of Schlemm’s canal–specific animal models. Here, we designed and validated a strategy using 4OH-tamoxifen-loaded nanocarriers to generate targeted, Schlemm’s canal specific knockout mice lacking lymphatic phenotypes. Using this system, we selectively deleted Prox1, the master transcription factor governing lymphatic fate. Within four weeks, intraocular pressure significantly increased, and ocular hypertension was maintained for at least 24 weeks. Unlike lymphatic vessels, which degenerate following Prox1 deletion, Schlemm’s canal reverted to a less functional vein-like phenotype with no change in size or morphology.  These results highlight the utility of nanocarriers for tissue-specific genetic recombination and demonstrate that changes in lymphatic phenotypes alter intraocular pressure, providing new targets for glaucoma therapy. Moreover, as we found that PROX1 was downregulated with age in human Schlemm’s canal, these canal-specific conditional Prox1 knockout mice are a valuable new adult-onset model of ocular hypertension that captures key features of age-related human disease.

overall_design: Bulk RNA sequencing of total RNA isolated from primary human Schlemm's canal endothelial cells treated with either scrambled control siRNA or PROX1-specific siRNA

first: Sofia

last: Ochoa

first: Hoi Lam

last: Li

first: Hyeohn

last: Kim

first: Zihang

last: Yan

first: Natalia

last: Mendonca

first: Pan

last: Liu

first: Hyunjoo

middle: P

last: Vincent

first: Hao

middle: F

first: Haiyan

last: Gong

first: Evan

last: Scott

first: Mark

last: Johnson


title: RXR Agonist V-125 Induces Distinct Transcriptional and Im-munomodulatory Programs in Mammary Tumors of MMTV-Neu Mice Compared to Bexarotene

city: Indianapolis

first: Afrin

last: Chowdhury

address: Walter hall

institute: Indiana University School of Medicine

summary: Background: The retinoid X receptor (RXR) is a ligand-activated nuclear receptor that heterodimerizes with numerous partners to regulate diverse transcriptional programs. RXR agonists, in-cluding the FDA-approved drug bexarotene, show anti-tumor activity but are limited by adverse side effects. V-125 is a next-generation RXR agonist engineered for improved se-lectivity, pharmacokinetics, and reduced lipogenic effects. This study compares the mo-lecular and functional effects of V-125 and bexarotene in HER2⁺ breast cancer models. Methods: Female MMTV-Neu mice bearing mammary tumors were treated with control, V-125 (100 mg/kg diet), or bexarotene (100 mg/kg diet) for 10 days. RNA sequencing was used to identify differentially expressed genes and pathways. Candidate targets were validated by qPCR and immunohistochemistry (IHC). Immune modulation was evaluated by IHC staining for CD8 cells and CD206⁺ macrophages in tumors to capture the tumor microen-vironment. Functional assays in JIMT-1 human HER2⁺ cells assessed RXR target activation and clonogenic potential in tumor cells. Results: V-125 induced broader transcriptional changes than bexarotene, including selective up-regulation of Nrg1, Nfasc, Lrrc26, and Chi3l1 genes associated with improved patient sur-vival. Pathway analysis revealed regulation of immune activation, cancer signaling, and lipid metabolism. Both V-125 and bexarotene suppressed colony formation in JIMT-1 cells, confirming previous observations about RXR-dependent inhibition of tumor cell growth. Moreover, V-125 in vivo had distinct capabilities to increase CD8 cell infiltration and reduced CD206⁺ macrophages, whereas bexarotene did not. Conclusion: V-125 but not bexarotene reprograms tumor transcriptional programs and the immune landscape in an anti-tumor manner in MMTV-neu mouse model and in in vitro models of HER2⁺ breast cancer. This highlights its promise as a selective RXR agonist with anti-tu-mor and immunomodulatory activity in HER2⁺ breast cancer.

first: Lyndsey

last: Reich

first: Karen

last: Liby

first: Elizabeth

last: Yeh

first: Ana

last: Leal


title: Numb-Ifi204 inhibits microglial activation and the hippocampal inflammation induced by LPS

city: Xi'an

first: Zhang

last: Siyu

state: ShanXi

address: GaoQiao

institute: Xi'an Jiaotong University

summary: This study aimed to identify the mechanisms regulating microglial activation and to explore potential therapeutic targets for neuroinflammation-related cognitive dysfunction disorders. We uncover a novel role for Numb in regulating microglial activation and highlight its interaction with Ifi204 in the LPS-induced TLR4 signaling pathway. We demonstrate that Numb promotes the autophagic degradation of Ifi204, thereby inhibiting the TLR4 signaling pathway and reducing excessive inflammatory responses in microglia. Furthermore, our findings show that Numb-mediated inhibition of microglial inflammation protects hippocampal neurons from synaptic damage, morphological abnormalities, and apoptosis.

overall_design: 6-8 weeks mice were randomly assigned to treatment groups and were injected intraperitoneally with bacterial lipopolysaccharides (LPS from Salmonella enterica serotype typhimurium, Sigma, L2630) at a dose of 1mg/kg bodyweight. The control mice were injected with sterile saline. The brain tissue samples were collected 24 hours after the injection for subsequent experiments.


title: ATF7ip inhibits the tumor immune response by promoting terminal CD8+ T cell Exhaustion III

first: Jun Hyung

last: Sin

overall_design: Approximately 500 intratumoral P14+/Atf7ip-sufficient or 500 intratumoral P14+/Atf7ip-deficient CD8+ T cells per sample were sorted directly into lysis buffer from the SMART-seq v4 [Takara Bio] kit. Lysed cells were given to the UCSF Genomics COLAB for Library Preparation. Libraries prepared by the core were submitted to the UCSF Center for Advanced Technology for single-end sequencing.

first: Sujit

last: Kashyap

first: Michael

last: Waterfield


title: MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment II

first: Anthony

last: Flamier

overall_design: Single-nucleus RNA sequencing on MECP2-WT, MECP2-R133C, MECP2-R168X and MECP2-R270X cerebral organoids (3 months old).

first: Marion

last: Guillon

first: Margaux

last: Brin


title: Patient-Derived Lymphoma Spheroids Reveal Predictive Markers of Glofitamab Resistance in Relapsed/Refractory B-NHL

city: Toulouse

first: Marie

last: Tosolini

address: 2 avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

summary: Bispecific antibodies (bsAbs) such as glofitamab represent a promising therapeutic approach for relapsed/refractory B-cell non-Hodgkin's lymphoma (R/R B-NHL), but resistance mechanisms remain poorly understood. This study aimed to identify predictive markers of bsAbs resistance based on the response of 3D patient-derived lymphoma spheroids (PDLS) established from R/R B-NHL samples. PDLS were treated with 0.1 nM glofitamab for 3 days and B-cell depletion was quantified as measure of ex vivo treatment response. Comprehensive immune profiling were performed on patient samples using multiparametric flow cytometry, single-cell RNA sequencing, CODEX spatial proteomics and functional assays. This study revealed that high responders to glofitamab possessed more activated CD8+ T-cells with higher cytotoxic signatures, while low responders showed enriched exhausted CD8+ T-cell populations with enhanced expression of exhaustion markers (TIGIT, LAG3, PD1). Moreover, low responders demonstrated elevated functional CD4+ T-follicular helper (Tfh) cells in close proximity to malignant B-cell thus promoting their survival through IL21 and CXCL13 signaling pathways. Functional experiments have shown that adding anti-TIGIT co-treatment enhanced glofitamab efficacy in low responder samples, and Tfh depletion improved cytotoxic T-cell function. Our findings identify CD8+ T-cell exhaustion and functionally activated Tfh cells as key resistance mechanisms to glofitamab in R/R B-NHL. Targeting these pathways represents a promising strategy to overcome bsAb resistance and improving therapeutic outcomes.

overall_design: relapse and/or refractory (R/R) B-NHL patient samples were collected from either PBMC or LN biopsies according to the Declaration of Helsinki. Dissociated cryopreserved cells were prepared according to 10X Genomics protocol.

first: Paul

last: Marcoux

first: Fabien

last: Gava

first: Pauline

last: Gravelle

first: Christine

last: Bezombes

first: Camille

last: Laurent


title: In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [sgRNA]

city: Hong Kong

first: Yang

last: Fu

address: Prince of Wales Hospital, N.T, H.K, 32 Ngan Shing St, Sha Tin

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: CRISPR/Cas9 has revolutionized genome editing with broad therapeutic applications, yet its repair patterns in vivo remain poorly understood. Here, we systematically profile CRISPR/Cas9 editing outcomes at 95 loci using our established CRISPR/Cas9/AAV9-sgRNA system in skeletal muscle stem cells (MuSCs). Through comprehensive characterization of the repair outcomes, our findings demonstrate that the general rules governing CRISPR/Cas9-mediated editing in vivo largely align with those observed in vitro. Additional to the anticipated small editing indels such as MMEJ mediated deletions and NHEJ mediated templated insertions, we uncover a prevalent occurrence of large on-target modifications, including large deletions (LDs) characterized by microhomology (MH) and large insertions (LIs). Notably, the LIs comprise not only exogenous AAV vector integrations but also endogenous genomic DNA fragments (Endo-LIs). Endo-LIs preferentially originate from active genomic regions, with their integration shaped by three-dimensional chromatin architecture. By disrupting key components of the NHEJ and MMEJ repair pathways in vivo, we identify their distinct roles in regulating the large on-target modifications. Together, our work systematically profiles the CRISPR/Cas9 repair outcomes in vivo and offers valuable guidance for improving the safety of CRISPR/Cas9-based gene therapies.

overall_design: Targeted deep sequencing was performed across three experimental cohorts: (i) 44 single-sgRNA and 51 dual-sgRNA target sites, along with their respective controls (notably, several single- and dual-sgRNA samples shared control data); (ii) one single-sgRNA and one dual-sgRNA target site evaluated across a multiple-dose treatment gradient; and (iii) enzyme knockout models versus control groups. Additionally, ATAC-seq and ChIP-seq assays were conducted to explore the chromatin features influencing indel formation.


title: Mutant TP53 hijacks RNA-splicing factor RBM28 to suppress double-strand RNA triggered antitumor immunity

city: Beijing

first: Tao

last: Xiang

state: Beijing

address: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: TP53 mutation may not only compromise its multifaceted tumor-suppressive functions but confer oncogenic properties. Here, we demonstrate that DNA-binding domain mutations of TP53 unexpectedly confer a transcriptional regulatory function, directly driving RNA-splicing factor RBM28 overexpression. Overexpressed RBM28 excessively splices transposon elements, inhibiting dsRNA formation, thereby suppressing dsRNA-triggered type I IFN signaling and subsequent anti-tumor immunity. We demonstrate in mouse tumorigenesis models and human multi-stage esophageal cancer development that mutp53-driven aberrant RBM28/dsRNA/IFN axis plays a crucial role in cancer initiation, progression and resistance to immune checkpoint blockade (ICB) therapy through innate immune suppression. Pan-cancer analysis indicates that this mechanism underlies ICB resistance in most cancers. Pharmacological restoration of normal p53 conformation or targeted RNA-splicing inhibition enhances anti-tumor immunity and ICB efficacy. Collectively, our study has unveiled a novel function of mutp53 in establishing immunosuppressive tumor microenvironment, which provides an actionable framework for new avenue for intervention and therapy in TP53-mutated cancers.

overall_design: To investigate the effects of RBM28, we performed RNA sequencing on KYSE30 cells with and without RBM28 knockout.

first: Ziyi

last: He

first: Xiaoyuan

last: Wang

first: Shaosen

last: Zhang

first: Shihao

last: Zhu

first: Jie

last: Yang

first: Xiao

last: Hu


title: A time-resolved atlas of histone modifications during mitotic entry

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: Mitotic chromosome formation is essential for faithful chromosome segregation in metazoans. While condensin complexes are critical for the formation of rod-shaped mitotic chromosomes, additional mechanisms—particularly those involving phosphorylation and deacetylation of specific histone residues—have been proposed to contribute a further 2- to 4-fold reduction in mitotic chromatin volume. In this study, we employ high-resolution mass spectrometry to determine the kinetics of histone modifications in cell cultures undergoing a highly synchronous mitotic entry at 2.5-minute resolution. Our analysis reveals three different programmes of histone H3 phosphorylation on T3, S10 and S28. These modifications are consistent with methyl-phos switches regulating the association of readers with chromatin other than at promoters. Mass spectrometry and quantitative ChIP-Seq reveal that H3 T3 phosphorylation is a general marker of heterochromatin and not specifically centromeres as previously suggested. Finally, we show that histone acetylation undergoes only modest changes as rod-shaped chromosomes form during unperturbed mitotic entry. Thus, previously reported reductions in acetylation associated with chromosome formation were apparently attributable to delays in mitotic exit used as part of mitotic synchronisation protocols. The mechanism of condensin-independent chromatin compaction in mitosis remains unexplained.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me1, H3K4me2, H3K4me3, H3K9me3 and Caliburated ChIP-seq for H3T3ph and CENP-H in G2, prophase, and prometaphase.

first: Moonmoon

last: Deb

first: Natalia

middle: Y

last: Kochanova

first: Axel

last: Imhof

first: William

last: Earnshaw


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [Spatial Transcriptomics]

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Vascular endothelial growth factor receptor-targeting tyrosine kinase inhibitors (VEGFR-TKIs) and aPD1 combinations are effective in multiple solid tumors, particularly in clear cell renal cell carcinoma (ccRCC), due it’s characteristic pseudo-hypoxic, hyper-angiogenic state driven by biallelic VHL-loss. However, long-term durability is inferior to dual aPD1/aCTLA4 regimens, yet the mechanisms underlying these differences remain unclear. Since tumor-associated macrophages (TAMs) are implicated in therapeutic resistance, we used scRNAseq to investigate TAM evolution following VEGFR-TKI, aPD1 and combined VEGFR-TKI/aPD1 treatment in a transgenic ccRCC mouse model. We identify hypoxia-responsive SPP1+ TAMs that are absent in baseline pseudo-hypoxic tumors. This proxy of true hypoxia tracks with successful response to VEGFR-TKI/aPD1 in mouse and human on-treatment samples, reflecting treatment-induced hypoxic necrosis. Paradoxically, pretreatment hypoxia predicted worse outcomes across multiple VEGFR-TKI/aPD1 trial and real-world cohorts and extended exposure to hypoxia-inducing VEGFR-TKIs and aPD1 exacerbated metastasis in mice, highlighting the dual implications of hypoxia in ccRCC disease trajectory.

overall_design: FFPE sections from advanced ccRCC tumors surgically resected following various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations, were analysed by Visium (v1) spatial transcriptomics.

first: Lynda

last: Vuong

first: Abraham

last: Hakimi


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma

overall_design: Individual tumors from KVpR mice treated with Lenvatinib, aPD-1, CSF1Ri or combinations were dissected, digested, flow sorted for live cells, and analysed by scRNAseq.


title: A Genome-Wide CRISPR Screen Identifies DTX4 Modulating Alveolar Macrophage Cholesterol Efflux in Pulmonary Alveolar Proteinosis [CRISPR]

city: Nanjing

first: Xinmei

last: Huang

address: No.321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

summary: Pulmonary alveolar proteinosis (PAP) is a rare pulmonary syndrome characterized by impaired surfactant clearance, driven by dysfunctional cholesterol efflux in alveolar macrophages (AMs). However, the molecular determinants governing AM cholesterol homeostasis remain largely elusive. Here, through a genome-wide CRISPR activation screen in foamy macrophages and bulk RNA sequencing of AMs from PAP patients, we identify Deltex E3 Ubiquitin Ligase 4 (DTX4) as a pivotal regulator of cholesterol efflux in AMs. Adeno-associated virus (AAV) -mediated silencing of DTX4 led to excessive lipid accumulation in AMs, exacerbated alveolar proteinosis, increased lung opacities on imaging, and significantly deteriorated pulmonary function in mice. Similarly, DTX4 depletion in primary AMs impaired cholesterol efflux and promoted intracellular lipid deposition. In contrast, AM-specific overexpression of DTX4 markedly alleviated lipid accumulation, mitigated alveolar proteinosis, restored lung densities on computed tomography, and rescued pulmonary function in Csf2ra-/-mice, a model of PAP. Mechanistically, DTX4 deficiency downregulated PPAR-γ expression, driving foamy AM formation. Notably, the regulatory function of DTX4 in lipid homeostasis was partially mediated by PPAR-γ but independent of its canonical E3 ubiquitin ligase activity. Collectively, our findings establish DTX4 as a central orchestrator of AM cholesterol efflux and surfactant homeostasis, positioning it as a promising therapeutic target for PAP and a potential paradigm for cholesterol dysregulation in related disorders.

overall_design: Genome-wide CRISPR activation (CRISPRa) screening was performed in oxLDL-loaded THP-1 macrophages using the SAM pooled library to identify regulators of cholesterol efflux; cells were sorted into BODIPY^high and BODIPY^low populations based on intracellular lipid content, and gRNA abundance was quantified by next-generation sequencing.

first: Zimu

first: Jingwei

last: Shi

first: Yonglong

last: Xiao

first: Mengshu

last: Cao

first: Yingwei

first: Xinye

last: Xia


title: Runx3 instructs Aire+ mTEC development, TSA gene expression, and central tolerance

first: Jun Hyung

last: Sin

summary: The transcription factor Runx3 modulates key gene expression programs important for the development of multiple tissues. Here, we uncover new functions for Runx3 in thymic epithelial lineage development and show Runx3 expression in medullary thymic epithelial cells (mTECs) is required for both Autoimmune Regulator + (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Consequently, TEC-specific deletion of Runx3 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, loss of Runx3 in TECs results in an expansion of immature CCL21+ mTECs and a loss of Aire-dependent mimetic cells. Single-cell analysis reveals Runx3 modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Runx3 in mTEC development and thymic central tolerance.

overall_design: scRNA-sequencing EpCAM+ mTECs from Runx3 cKO mice and Runx3 WT mice

first: Sloan

middle: H

last: Phillips

first: Michael

last: Waterfield


title: HNF4a controls growth, identity and response to KRAS inhibition in IMA [scRNA-seq]

city: Salt lake City

first: Headtlove

last: Essel Dadzie

address: 2000 circle of Hope

institute: University of Utah

summary: Cellular plasticity is a key feature of cancer that enables tumor cells to switch lineage identities, driving disease progression and resistance to therapy. In invasive mucinous adenocarcinoma (IMA), a pronounced pulmonary-to-gastric lineage switch occurs as NKX2.1 is lost and HNF4α, a master regulator of gastric differentiation, is upregulated. Although absent in normal alveolar type 2 cells, HNF4α is aberrantly expressed in most IMA tumors. In this study, we investigate the role of HNF4α within established IMAs and find that it directly activates a gastric differentiation program, particularly in pit cells. Loss of HNF4α disrupts this program and permits FOXA1 and FOXA2 to bind new regulatory sites, leading to the upregulation of neuronal and liver-like gene modules. In light of the poor response of mucinous tumors to KRAS inhibitors, we investigated whether HNF4α modulates sensitivity to KRASG12D targeted therapy. Treatment with MRTX1133 revealed that loss of HNF4α significantly increases IMA sensitivity by reducing the IC50 in vitro and enhancing tumor regression in vivo. Mechanistically, HNF4α deletion impairs cell-cycle progression in drug-tolerant persister cells, while tumors retaining HNF4α maintain these cell-cycle regulators despite KRAS inhibition, promoting persister cell survival. Our findings establish HNF4α as a critical driver of IMA biology governing both gastric differentiation and resistance to KRAS inhibitors and support the development of combination strategies to overcome therapeutic resistance in IMA.

overall_design: scRNA-seq was performed on tumor cells derived from KN and KNH.

first: Eric

last: Snyder


title: A Genome-Wide CRISPR Screen Identifies DTX4 Modulating Alveolar Macrophage Cholesterol Efflux in Pulmonary Alveolar Proteinosis [RNA-seq II]

overall_design: RNA-seq profiling of flow-sorted alveolar macrophages from BALF of PAP patients, separated into BODIPY^high (foamy) and BODIPY^low (non-foamy) populations based on intracellular lipid content.

last: Wang

last: Zhang


title: Thymic alveolar type II epithelial mimetic cells revealed by Runx1-deficiency [CUT&Run]

summary: The mechanisms used to prevent autoimmune lung disease are incompletely understood. Recent studies in the thymus have identified unique populations of medullary thymic epithelial cells (mTECs) called mimetic cells that transcriptionally mimic peripheral epithelial populations. These mimetic cells have been found to have important functions in the thymus in immune tolerance and the diversity and cell types represented in this pool of cells represents an active area of investigation. Here, we utilized a mouse line with thymic specific deletion of the Runt related transcription factor 1 (Runx1) to identify a novel mimetic cell type that transcriptionally mimic alveolar type II (AT2) lung epithelial cells. Runx1 binds to genomic regions associated with epidermal growth factor receptor (EGFR) signaling suggesting a function for EGFR in regulating AT2 mTEC development.

overall_design:
CUT & RUN of Runx1, IgG, and H3K27ac in EpCAM+ mTECs from B6 control mice:
WT1 = CUT&Run of IgG
WT3 = CUT&Run of Runx1
WT5 = CUT&Run of H3K27ac


title: Thymic alveolar type II epithelial mimetic cells revealed by Runx1-deficiency [scRNA-seq]

overall_design: scRNA-sequencing EpCAM+ mTECs from Runx1 cKO mice and Runx1 WT mice


title: A Genome-Wide CRISPR Screen Identifies DTX4 Modulating Alveolar Macrophage Cholesterol Efflux in Pulmonary Alveolar Proteinosis [RNA-seq 1]

overall_design: RNA-seq profiling of alveolar macrophages isolated from bronchoalveolar lavage fluid (BALF) of patients with pulmonary alveolar proteinosis (PAP) and control donors.


title: SETD2 Deficiency Drives Mitochondrial DNA Leakage and Creates a Druggable Dependency on BCL-XL in Clear Cell Renal Cell Carcinoma

city: Charleston

first: Aguirre

last: de Cubas

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: Medical University of South Carolina

summary: SETD2 is frequently mutated or deleted in clear cell renal cell carcinoma (ccRCC). Loss of SETD2 could create synthetic lethal dependencies that confer therapeutic vulnerabilities. Here, we demonstrated that SETD2 deficiency promotes cytoplasmic mitochondrial DNA (mtDNA) leakage, leading to basal activation of cGAS-STING inflammatory signaling and increased apoptotic priming. This inflammatory state upregulated the BH3-only protein NOXA, constrained MCL-1 function, and enforced a synthetic lethal dependency on the anti-apoptotic protein BCL-xL. Pharmacological inhibition of BCL-xL further amplified cGAS-STING signaling in SETD2-deficient cells through sublethal mitochondrial outer membrane permeabilization, resulting in increased mtDNA release and robust NOXA induction. Elevated NOXA neutralized the compensatory MCL-1-mediated survival signaling, triggering apoptosis. In contrast, SETD2 proficient ccRCC cells exhibited minimal cGAS-STING activation and failed to induce NOXA following BCL-xL inhibition, rendering them resistant. Genetic ablation of cGAS, STING, IRF3, or NOXA rescued sensitivity to BCL-xL inhibition, confirming that mtDNA-driven innate immune signaling is required for this dependency. In vivo, BCL-xL inhibition suppressed tumor growth and prolonged survival in SETD2-deficient xenograft models. Collectively, these findings establish a mechanistic link between SETD2 loss, mtDNA-driven innate immune activation, and enforced BCL-xL dependence in ccRCC, revealing a therapeutically targetable vulnerability in SETD2-deficient tumors.

overall_design: SETD2 WT and deficient Kidney cancer cells


title: Transcriptome of Ag-specific B cells upon stimulation with soluble or particulate Ag

city: San Francisco

first: Julie

last: Zikherman

address: 513 Parnassus Ave

department: Medicine, Rheumatology

summary: Primary B cells from MD4 mice have transgenic B cell receptors that recognize hen egg lysozyme (HEL).  Previous studies have shown that antigens presented in different formats induce qualitatively different signaling responses in B cells.  Here, we compare the transcriptomes induced by the following stimuli: LPS (10 mg/mL), particulate HEL (1pM liposomes with reduced affinity HEL-3X protein conjugated to surface at epitope density 243), soluble HEL (1mg/mL), and co-stimulation with soluble HEL and anti-CD40 (100 ng/mL).

overall_design: Lymph nodes were harvested from MD4 mice and B cells were purified by benchtop negative selection. 10^6 B cell / well were plated into 96 well plates with aforementioned stimuli in abstract in total of 200uL media. Following overnight in vitro stimulation in culture at 37C, B cell pellets were snap frozen for RNA-sequencing. Three biological replicates were prepared for each condition. Unstimulated samples were harvested after 2 hr 27C culture.

first: Julianne

last: Riggs

first: Alexander

last: Ritter


title: Flavonoid and isoflavonoid biosynthetic gene expression is affected by MYB36 transcription factor deficiency in Lotus japonicus

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

country: Spain

institute: Universidad de Sevilla

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

overall_design: Refer to individual Series

first: María

middle: D

last: Monje-Rueda

first: Margarita

last: García-Calderón


title: Tissue-specific VEGF-D overexpression induces lymphangiogenesis and heterotopic bone resorption

city: Dallas

first: Sneha

last: Korlakunta

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

summary: Heterotopic ossification (HO) is a pathological process that commonly occurs after musculoskeletal injury and is characterized by the formation of bone in non-skeletal tissues. Despite advances in research, no effective treatments are available to promote the resorption of heterotopic bone in patients suffering from HO. Lymphatic vessels are associated with the destruction of bone in rare diseases such as Gorham-Stout disease. However, the effect of lymphatic vessels on HO was previously unknown. Here, we use transgenic mice to determine whether targeted expression of the lymphatic growth factor VEGF-D can promote the therapeutic resorption of bone in a mouse model of HO. We show that control mice lack lymphatic vessels in heterotopic bone. In contrast, Vegfd-overexpressing (Vegfd-OE) mice develop lymphatic vessels in heterotopic bone and form significantly less heterotopic bone than control mice. Additionally, we demonstrate that VEGF-D promotes the resorption of established heterotopic bone. Mechanistically, we show that the transition of myeloid cells to osteoclasts and osteoclast-mediated bone resorption are enhanced in Vegfd-OE mice. Our findings suggest that site-directed lymphangiogenesis could be an effective strategy to break down heterotopic bone in HO.

overall_design: Male and female control and Vegfd-OE mice underwent the B/T procedure when they were between 8-12 weeks old (n=5/group). Mice were euthanized 7 days later for tissue collection. Following euthanasia, tissue from the injury site was collected by resecting the soft tissue located posterior to the tibia between the insertion and origin of the Achilles tendon.

first: Neda

last: Vishlaghi

first: Benjamin

last: Levi

last: Dellinger


title: First-in-Class CAR T Cell Therapy Selectively Eliminates Mutant Calreticulin-Driven Malignancies in a Fibrotic Niche

city: Oxford

first: Bethan

last: Psaila

state: Oxfordshire

address: John Radcliffe Hospital MRC Weatherall Institute – Molecular Medicine

department: MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Pathogenic mutations in calreticulin (mutCALR) are found in one third of patients with myeloproliferative neoplasms. All mutCALR variants yield the same protein neoepitope that forms an aberrant complex with the thrombopoietin receptor, driving oncogenic stem cell expansion, megakaryocyte hyperplasia and fibrosis. We developed a novel, first-in-class chimeric antigen receptor (CAR) T-cell therapy targeting mutCALR and evaluated efficacy in a bespoke human chimeroid model of the bone marrow. We used 10x single-cell RNA sequencing (scRNA-seq) to analyze cell composition, transcriptional differences, and cell-cell interactions.

overall_design: Human iPSC-derived bone marrow organoids were engrafted with either mutCALR+ CD34+ stem/progenitor myelofibrosis cells, mutCALR-targeting CAR T cells, none, or both. These 'chimeroids' were pooled together (n=12 per condition) and dissociated after 72 hours in culture. scRNA-seq libraries were prepared with live, FACS-isolated cells.

first: Zoë

middle: C

last: Wong

first: Charlotte

last: Brierley


title: A skeletal muscle atlas shows neuromuscular junction adaptations to growth and atrophy

city: San Diego

first: Pura

last: Muñoz-Cánoves

address: 5510 Morehouse Dr

institute: Altos Labs

summary: The molecular mechanisms underlying the opposing states of muscle atrophy (such as with disuse or in aging) and hypertrophy (such as with increased physical activity) are still not well-defined. Progress has been slowed by challenges in characterizing the niche heterogeneity of skeletal muscle (whereby myofibers are the most abundant) and in obtaining well-characterized samples. Here we describe: i) changes in muscle cell populations that are undergoing atrophy or hypertrophy, with complex, opposing cell transcriptional responses during each process; and ii) a remarkable remodeling of the neuromuscular junction (NMJ) domain, whereby we identify emerging new subpopulations of synaptic myonuclei (SynM) and terminal Schwann cells (tSCs) that are specifically adapted to each growth/atrophy condition. High-resolution 3D imaging and spatial transcriptomics reveal these structural and molecular adaptations at the tissue level. Critically, these changes also occur in the NMJ of both denervated and exercised human muscle. Our study lays the ground for identifying novel targets for medical, pharmacological and lifestyle interventions in aging and disease.

overall_design:
scRNA-seq: Plantaris muscles were harvested from wt mice in basal/unperturbed conditions, as well as at 3- and 7 days post atrophy (denervation, Den) or hypertrophy (overloading, OVL) induction. A single-cell suspension from an average of 10-16 pooled plantaris muscles per condition and time point was subjected to FACS to enrich in minor cell populations in skeletal muscle (muscle stem cells, endothelial cells, Schwann cells and mural cells). The enriched cell suspension was analyzed using scRNA-seq.
snRNA-seq: Plantaris muscles were harvested from wt mice in basal/unperturbed conditions, as well as at 3- and 7 days post-atrophy (denervation, Den) or hypertrophy (overloading, OVL) induction. A single-nucleus suspension from 2 pooled plantaris muscles per condition and time point was analyzed using snRNA-seq.
Spatial Transcriptomics:  Plantaris muscles were harvested from wt mice in basal/unperturbed conditions, as well as at 7 days post-atrophy (denervation, Den) or hypertrophy (overloading, OVL) induction. Two plantaris muscles per condition and time point were analyzed using spatial transcriptomics.

first: Silvia

last: Campanario

first: Mercedes

last: Grima-Terrén

first: Megan

last: Rommelfanger

first: Stefania

last: Dell’ Orso

first: Xuesong

last: Feng

first: Ignacio

last: Ramírez-Pardo

first: Aina

last: Calls

first: Andrés

last: Cisneros

first: Kyung

last: Dae Ko

first: Esther

last: García-Domínguez

first: Davide

last: Randazzo

first: Alberto

last: Pérez-Garcia

first: Mari Carmen

last: Gómez-Cabrera

first: Tovah

last: Markowitz

last: Yang

first: Antonio

middle: L

last: Serrano

first: Eusebio

last: Perdiguero

first: Vittorio

last: Sartorelli

first: Joan

last: Isern


title: HNF4a controls growth, identity and response to KRAS inhibition in IMA.

first: Headtlove

last: Essel Dadzie

state: UT

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Lactate-Induced H3K18 Lactylation Drives CX3CL1-Mediated Immune Cell Recruitment in Sepsis-Associated ARDS

status: Public on Apr 22 2026

city: jinan

first: yuanyuan

last: Zhang

address: jinan

institute: Shandong Second Medical University

summary: Sepsis is characterized by lactate accumulation and immune dysfunction, but the molecular mechanisms linking lactate to chemokine expression remain unclear. Here, we investigated whether lactate regulates chemokine transcription through histone lactylation. Human peripheral blood mononuclear cells (PBMCs) were treated with lactate (LAC group) or PBS control (CON group), followed by RNA sequencing (RNA-seq) to identify differentially expressed genes. Chromatin immunoprecipitation sequencing (ChIP-seq) using H3K18la-specific antibody was performed to detect lactylation-enriched gene promoters. Integration of RNA-seq and ChIP-seq data identified CX3CL1 as a lactylation-regulated chemokine. Functional assays demonstrated that lactate-induced H3K18la promotes CX3CL1 expression, enhances PBMC migration, and facilitates T cell recruitment in vitro. In a cecal ligation and puncture (CLP)-induced sepsis-associated acute respiratory distress syndrome (ARDS) mouse model, elevated lactate increased pulmonary CX3CL1 expression and immune cell infiltration, whereas inhibition of lactate production reduced these effects. These data reveal a lactate–H3K18la–CX3CL1 axis that mediates immune cell recruitment and exacerbates sepsis-related lung injury.

overall_design: Human PBMCs were isolated from healthy donors and divided into two groups: lactate-treated (LAC) and PBS-treated control (CON). After 24 hours of treatment, total RNA was extracted for transcriptome profiling via RNA sequencing (RNA-seq). Parallel chromatin immunoprecipitation sequencing (ChIP-seq) using H3K18la-specific antibody was performed to identify lactylation-enriched gene promoters. Integration of RNA-seq and ChIP-seq datasets was used to identify lactylation-regulated chemokines. Functional validation included in vitro PBMC migration assays and T cell recruitment assays using Transwell systems. For in vivo validation, C57BL/6 mice were subjected to cecal ligation and puncture (CLP) to induce sepsis-associated ARDS and assigned to four groups: LAC, CLP-control, CLP with lactate dehydrogenase inhibitor (CLP-OXA), and sham operation. Plasma lactate levels, pulmonary CX3CL1 expression, immune cell infiltration in bronchoalveolar lavage fluid (BALF), and lung tissue were assessed to evaluate the role of lactate-induced H3K18la in mediating chemokine expression and immune cell recruitment.

first: Shi

first: Yuanyuan


title: HNF4a controls growth, identity and response to KRAS inhibition in IMA [ChIP- seq]

overall_design: ChIP-seq was performed on murine 429A organoids treated with EtOH or 4OHT to delete Hnf4a, murine 1311G#5  treated with cre virus or control delete Hnf4a and sorted GFP(+) nuclei from both KN and KNH GEMMs.

first: Eric

last: Snyder


title: HNF4a controls growth, identity and response to KRAS inhibition in IMA [bulk RNAseq]

overall_design: Bulk RNA-seq was performed on sorted GFP+, DAPI- tumor cells from each GEMM (KN and KNH). To determine whether HNF4α is required to maintain a gastric differentiation program, bulk RNA-seq was performed on 3D organoid lines, 429A and 1311G#5, in the presence and absence of HNF4α as stated in methods.

last: L Snyder


title: Hepatocyte-specific PPARγ Deletion Uncovers Role of an Antagonistic PPARγ–HNF4α Transcriptional Axis in MASLD Progression

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Systemic PPARγ agonist therapies have been investigated for clinical use in MASLD. Previous studies, however, have shown that PPARγ activation in hepatocytes worsens MASLD. Overall, the precise molecular mechanisms regulated by PPARγ in hepatocyte during MASLD remain incompletely defined. Hepatocyte-specific PPARγ knockout mice were fed a clinically-relevant fast-food diet (FFD) for 2 or 5-months to characterize the role of PPARγ in MASLD progression. PPARγ expression and activity were increased in murine FFD-model and in hepatocytes of human MASLD/MASH patients, based on single-nucleus RNA-sequencing analysis. PPARγ-deletion conferred protection against diet-induced steatosis, fibrosis, and liver injury by suppressing lipogenic, inflammatory, and fibrogenic signaling. Although de-novo fatty-acid synthesis was only modestly affected and compensated with disease progression, enhancement of lipolysis and suppression of lipid droplet stabilization machinery was persistent. PPARγ-deletion robustly inhibited expression and signaling-activity of TGFβ1, a master regulator of hepatic ¬fibrosis, throughout the progression of MASLD. Importantly, a novel PPARγ-HNF4α regulatory axis in MASLD was identified, with increased HNF4α mRNA/protein expression and activation of its downstream metabolic networks in PPARγ-deficient livers. Further, integration of ChIP-seq and transcriptomic analysis revealed that HNF4α might be co-regulating a major fraction (>70%) of genes under direct control of PPARγ during MASLD. This study provides a comprehensive temporal framework for hepatocyte PPARγ function in MASLD, revealing an antagonistic PPARγ-HNF4α transcriptional network that governs hepatic metabolic fate.

overall_design: Male PPARγflox/flox mice (Jackson Laboratory, stock #004584) at 8 weeks of age received a single intraperitoneal injection of adeno-associated virus AAV8.TBG.PI.Cre.rBG (2.5 × 1011 viral particles/mouse) to generate hepatocyte-specific PPARγ knockout (KO) mice. This vector expresses Cre recombinase under the control of the hepatocyte-specific thyroxine-binding globulin (TBG) promoter. Control littermates received the same dose of AAV8.TBG.PI.eGFP.WPRE.bGH (2.5 × 1011 viral particles/mouse). Both viral preparations were obtained from Addgene (Cre vector: #107787-AAV8; eGFP vector: #105535-AAV8). Following AAV8 injections, both KO and control groups were placed on a “fast-food” diet (FFD; ENVIGO #TD.88137), consisting of high saturated fat (21% by weight; 42% kcal from fat), cholesterol (0.2%), and sucrose (34% by weight), accompanied by fructose-glucose–enriched drinking water (18.9 g/L d-glucose and 23.1 g/L d-fructose) as previously described. Mice were maintained on this regimen for either 2 or 5 months.

first: Shehnaz

last: Bano

first: Matthew

last: Copeland

first: Jia-Jun

first: Anne

last: Orr

first: John

middle: W

last: Stoops

first: Wendy

middle: M

last: Mars

first: Silvia

first: Joseph

last: Locker

first: George

last: Michalopoulos

first: Bharat

last: Bhushan


title: DNA methylation modulation by Azacytidine can restore T cell function and exhaustion in AML.

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

type: Methylation profiling by high throughput sequencing

summary: AML is an aggressive malignancy of the blood and bone marrow associated with poor clinical outcome. Chemotherapy remains the standard of treatment, yet relapse is common, highlighting the need to find alternative therapies. T cell dysfunction and exhaustion are prominent in AML and represent a key barrier to effective immunotherapy. DNA methylation is a major driver of T cell exhaustion and inhibition of de novo methylation can restore T cell function in other disease contexts. Here we investigated the impact of Azacytidine (Aza), an FDA approved hypomethylating agent, on T cell exhaustion in AML. Using a spontaneous AML mouse model and AML patient samples, we find that Aza treatment modulates T cell function. In vivo Aza treatment decreased tumor burden and reshaped CD8+ T cells states, increasing memory subsets and decreasing regulatory T cells (Tregs) frequency in mice. Functionally, Aza treatment overcomes the impaired proliferation in both CD4 and CD8+ T cells in our model.  DNA methylation sequencing reveled hypomethylation and increased expression of stem like precursor gene TCF7 and E2F2, a regulator of cell cycle progression and proliferation. Similar changes in phenotypes are observed in cultures of AML patient samples with Aza. Collectively, we show that Aza remodels epigenetic and functional states in AML and has the potential to reverse T cell exhaustion, with enhanced memory and proliferation capacity. Our work provides a mechanistic framework supporting the rationale of combining hypomethylating agents with T cell based immunotherapies for this lethal disease.

overall_design: After treatment with Aza or PBS for three weeks, CD4 and CD8+ T cells were isolated from spleens of these mice and reduced representation bisulphite sequencing was performed

first: Ravina

last: Pandita

first: Yoko

last: Kosaka

first: Jessica

last: Mulkey

middle: A

first: Lucia

last: Carbone

first: Evan

last: Lind


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [bulk RNA-seq]

first: Fengshen

last: Kuo

overall_design: Bulk RNAseq analysis of flash frozen or FFPE pre-treatment surgically resected tumors from ccRCC patients who later received various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations.

first: Lynda

last: Vuong

first: Abraham

last: Hakimi


title: Glycine-modulating Slc6a20a-ASO restores NMDA receptor function in SHANK2 and SHANK3-mutant mice and cortical organoids

city: Daejon

first: Eunjoon

last: Kim

address: KAIST, Kuseong-dong, Yuseong-ku

department: Dept of biological sciences

country: South Korea

institute: IBS

summary: we report 23237 singel celll transcriptomes from 5 human cortical organoids (hCOs) which was generated from H1 and maintained for 3month.

overall_design: The raw sequencing reads of 23237 cells from 5 organoids were processed using Cell Ranger (version 8.0.1). The reference mouse genome index was built using the GRCh38 human reference genome assembly. Single cell RNA-seq data QC and analysis was performed mainly using Seurat (5.2.0).

first: Mihyun

last: Bae

first: Junyeop

last: Roh

first: Woo-Chang

last: Hwang


title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma [scRNAseq]

overall_design: Advanced ccRCC tumors surgically resected following various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations, were minced, digested, flow sorted for live cells, and analysed by scRNAseq.


title: Transcriptomic analysis of HEK-293 cells subjected to prolonged mild acidification (pH 6.6) and treatment with an SR protein kinase inhibitor (SRPIN340)

city: Moscow

first: Anastasia

middle: Nikolaevna

last: Kazakova

address: Malaya Pirogovskaya

country: Russia

institute: Lopukhin Federal research and clinical center of physical-chemical medicine of Federal medical biological agency

summary: Acidosis, the hallmark of aggressive cancer and chronic inflammation, is associated with altered transcription and alternative splicing. These alterations may be due to the repressed release of transcription and splicing factors from splicing speckles, which are scaffolded by phosphorylated SR-rich proteins. We aimed to partially verify this hypothesis and clarify whether changes in SR solubility caused by acidification and dephosphorylation have any common effects on transcription and alternative splicing. For this, we modelled prolonged (2 d) non-damaging acidosis in non-synchronized HEK-293 cells and compared the transcriptomic changes to those induced by a subtoxic concentration of a specific SR protein kinase inhibitor SRPIN340.

overall_design: We examined bulk RNA-seq data for HEK-293 cells that were: a) treated with SRPIN 340 (10 μM) in Dulbecco's Modified Eagle Medium (DMEM), pH 7.4, for 48 hours; b) treated with an equal volume of DMSO in DMEM (pH 7.4) for 48 hours; c) treated with an equal volume of DMSO in acidified DMEM (pH 6.6) for 48 hours

middle: N

first: Margarita

middle: E

last: Bogomiakova

first: Iuliia

middle: I

last: Pavlova


title: CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL [RNA-Seq fhd286]

city: Seattle

first: Jay

last: Sarthy

state: WA

address: 1920 Terry Ave

department: Ben Towne Center for Childhood Cancer Research

institute: Seattle Children's Research Institute

summary: Transcription factor (TF) fusion oncoproteins are frequently associated with poor prognosis and remain challenging therapeutic targets. Here we show that the CBFA2T3-GLIS2 (C/G) fusion oncoprotein present in lethal pediatric acute megakaryocytic leukemias (AMKLs) co-opts mSWI/SNF chromatin remodeling complexes, reprogramming regulatory element architecture to sustain aberrant cell cycle progression. The C/G fusion binds to and redistributes mSWI/SNF complexes via the SMARCD1 SWIFT domain and targets complexes to oncogenic enhancers including those bound by ETS family TFs and the G1 cyclin CCND2, a C/G AML-specific dependency. Pharmacologic inhibition of mSWI/SNF-mediated G1 cell cycle phasing via FHD-286 suppresses C/G-driven gene expression programs, induces G1 arrest and apoptosis in cells, and reduces leukemic burden and extends survival in aggressive C/G AML in vivo. These findings define an oncogenic mSWI/SNF–G1 axis in C/G AML and establish a therapeutic framework for targeting chromatin dysfunction-mediated cell cycle aberrancy in high-risk pediatric leukemias.

overall_design: First, mSWI/SNF, histone modifications, and CBFA2T3::GLIS2 fusion protein chromatin binding (CUT&RUN) were profiled in CBF/GLIS+ AML cancer cell lines, as well as cord blood cells transduced with either GFP or CBFA2T3::GLIS2. Additional profiling of accessibility (ATAC-seq, in replicate) and transcription (RNA-seq, in replicate) were conducted in selected cell lines following treatment with DMSO (vehicle), Palbociclib, FHD-286, and combination treatment of Palbociclib and FHD-286.

first: Gabe

last: Boyle

first: Alexander

last: Ying


title: CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL [Cut & Tag cell lines]


title: CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL [ATAC-Seq]


title: LSD1 Attenuates Ferroptosis Sensitivity in Colorectal Cancer Cells via a Demethylase-Independent Manner: An Innovative Antitumor Strategy via Targeted Degradation of LSD1

city: Tianjing

first: Wang

middle: Meng

last: meng

address: Haitang subdistrict

institute: Nankai University

summary: To investigate the global gene expression profiles and identify differentially expressed genes, key signaling pathways, and potential molecular mechanisms underlying compound treatment in human cancer cells, RNA-seq was performed to analyze transcriptomic changes, aiming to provide comprehensive insights into the transcriptome regulation and discover novel biomarkers or therapeutic targets for CRC.

overall_design: Human colorectal cancer cell lines were divided into two groups: control group and experimental 'ENZ' group (treated with LSD1 degrader compound A3). Each group had 3 biological replicates. Total RNA was extracted from cells at 48 hours post-treatment. RNA sequencing was performed on the Illumina NovaSeq 6000 platform with paired-end 150 bp reads. Raw reads were quality controlled and aligned to the human reference genome (GRCh38/hg38). Differentially expressed genes were identified using DESeq2 with thresholds of |log2 fold change| > 1 and adjusted P-value < 0.05. Functional enrichment analysis was performed using GO and KEGG databases.

first: Wenpeng

last: Wang


title: CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL [RNA-Seq]


title: Unleashed condensation by recurrent mutations of an epigenetic regulator promotes cancer

city: Charlottesville

first: Hao

last: Jiang

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University fo Virginia

summary: The pathological mechanisms and significance for the prevalent mutation hotspots in disordered protein regions are poorly understood. ASXL1 is an obligate co-factor for BAP1 in H2AK119 deubiquitination. ASXL1 mutations are very frequent in myeloid malignancies, and are mostly C-terminal truncating mutations concentrated in a specific disordered region of ASXL1. ASXL1 truncations are gain-of-function mutations that promote myeloid malignancies, but the underlying mechanisms remain poorly understood. Here we show that the frequently truncated mutants of ASXL1 possess an intrinsic property of forming phase-separated biomolecular condensates, and this property is normally suppressed by the frequently deleted regions. A disease-mutant of the endogenous ASXL1 in leukemia cells forms dynamic nuclear co-condensates with other endogenous factors important for gene activation. While the ASXL1 disease-mutant can greatly enhance H2A deubiquitination activity of BAP1 in cells and in a purified system, enhance the growth of myeloid leukemia cell growth, and promote hematopoietic colony formation and leukemogenesis in a mouse transplant model by turning on myeloid leukemogenic transcriptional programs, substitution of residues important for condensation disrupted or impaired these abilities, suggesting that the condensation property is crucially important for the ASXL1 mutants in promoting cancer. Moreover, we discover that the conserved negative charges in the highly disordered and frequently deleted region on ASXL1 suppress the condensation of the wild type ASXL1. Charge-neutralizing mutations in this region restores condensation of the full-length ASXL1, and renders the full-length protein capable of promoting leukemogenesis-associated activity and gene expression. Biochemical, biophysical, and simulation analyses suggest the intramolecular interactions normally mask the N-terminal region in engaging intermolecular interactions required for phase separation, and disease truncations escape from the regulatory interactions and unleash the phase separation property to form nuclear hubs to promote expression of tumorigenic gene programs. Finally, by showing a striking correlation of the mutation frequencies with the condensation properties and leukemogenesis activity for a series of human patient mutations, we suggest that dysregulation of condensation is a likely a central mechanism for ASXL1 mutations in promoting myeloid malignancies. This may also be an overlooked mechanism for the prevalent hotspot disease mutations in the disordered proteomes.

overall_design: Explore the RNA-seq profiles of mouse c-Kit+ cells co-transduced with BAP1 and different truncations/mutants of ASXL1 during colony forming cell (CFC) assays.

first: Yansu

last: Song

first: Yi

last: Hao

first: Maria

last: Latac

first: Marta

last: Cykowiak


title: CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL [Cut & Run M-07e]


title: Transcriptomic and epigenomic analysis of WSTF knockdown in colorectal cancer cells [ChIP-Seq]

city: TangShan

first: Wei

last: Fang

state: HeBei

address: 21 Bohai Sea Avenue, Caofeidian New Town

department: College of Life Sciences

institute: North China University of Science and Technology

summary: This study investigates the role of Williams syndrome transcription factor (WSTF/BAZ1B) in colorectal cancer (CRC) progression through multi-omics approaches. WSTF was knocked down in SW620 colorectal cancer cells using siRNA to assess its impact on gene expression and metabolism. Additionally, WSTF overexpression was performed followed by ChIP-seq to identify genome-wide binding sites and direct transcriptional targets. The study aims to elucidate WSTF-mediated regulatory mechanisms and identify potential downstream effectors including GLYCTK in CRC.

overall_design: Cell line: SW620 cells with WSTF overexpression Antibody: Anti-WSTF antibody Control: Input DNA Replicates: 2-3 biological replicates Sequencing: Illumina platform Peak calling: MACS2 against input control

first: Liming

last: Zhou

first: Yan

last: Liu

first: Yuan

last: Yu

first: Jinghua

last: Wu

first: Yufeng

last: Li


title: CB2R Agonism Protects Intestinal Epithelium through β-Catenin/HoxA10 Loop in Radiation Injury

city: 重庆

first: Qianyi

last: Yao

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

summary: Background: Radiation-induced intestinal injury (RIII) represents a significant dose-limiting complication of radiotherapy, characterized by substantial loss of intestinal epithelial cells (IECs). While the activation of cannabinoid receptor 2 (CB2R) is protective in immune‑mediated colitis, the intrinsic role of CB2R in IECs and its potential therapeutic relevance in RIII have not been defined. Methods: An RIII mouse model was established in wild-type and CB2R-/- mice. Small-molecule CB2R agonists were screened for radioprotective efficacy, followed by pharmacological and siRNA-based interrogation of CB2R signaling in intestinal epithelial cell lines and primary mouse intestinal epithelial cells. RNA sequencing and bioinformatics were combined with permeability assays, immunofluorescence, electron microscopy, and molecular analyses of oxidative stress and ferroptosis to elucidate underlying mechanisms. Results: Irradiation induced CB2R expression in the intestinal epithelium, and genetic ablation of CB2R markedly aggravated RIII. A focused pharmacological screen identified a recently synthesized dual‑target compound, CB2R/FAAH modulator‑2 (CF‑2), which combines CB2R agonistic activity with fatty acid amide hydrolase (FAAH) inhibition and significantly mitigated radiation‑induced colonic injury while exerting protective effects on the small intestine and spleen. Mechanistically, CB2R activation attenuated irradiation‑induced ferroptosis and preserved intestinal epithelial integrity. Integrative transcriptomic analyses identified Homeobox A10 (HoxA10) as a critical epithelial‑enriched transcriptional amplifier that reinforced CB2R/β‑catenin signaling through a positive‑feedback loop, thereby enhancing CB2R‑mediated epithelial protection. Conclusions: This study defines an epithelial‑intrinsic CB2R signaling axis in RIII, linking ferroptosis suppression to preservation of intestinal barrier integrity. CF‑2 is positioned as a promising mechanism‑based candidate for radioprotection.

overall_design: Colon tissue samples were collected from 8-week-old male C57BL/6 mice. Animals were randomly assigned to three groups (n=3 per group): Control group (Con): untreated control mice, administered with sterile saline; IR group (IR): mice subjected to 13 Gy abdominal irradiation; IR+CF-2 group (IR+CF-2): mice subjected to the same irradiation and treated with CF-2 at a dose of 7.5 mg/kg via intraperitoneal injection. CF-2 was administered four times: 1 hour before irradiation, and at 24, 48, and 72 hours post-irradiation. All animals were euthanized at 84 hours post-irradiation.

first: Ying

last: Tian

last: Yuan

first: Yongqing

last: Cai

first: Qunfang

last: Yang

first: Lanfang

last: Zhang

first: Yunong

first: Tanjun

last: Wei

first: Qin

last: Ouyang

first: Haigang

first: Xiaoli

first: Tao


title: Laminaria japonica Polysaccharide Mitigates Acute Neuroinflammation in Cerebral Ischemia-Reperfusion Injury

city: zhanjiang

first: tangming

last: guan

address: No. 57, South Renmin Avenue, Xiashan District

institute: Affiliated Hospital of Guangdong Medical University

summary: Cerebral ischemia-reperfusion (I/R) injury triggers acute neuroinflammation, which exacerbates neuronal damage and functional deficits. Laminaria japonica polysaccharide (LJP) has been reported to exert anti-inflammatory and neuroprotective effects, but its molecular mechanisms in I/R injury remain unclear. In this study, we performed transcriptome sequencing on ischemic brain tissues from Sham, Vehicle, and LJP-treated mice to elucidate the molecular mechanisms underlying LJP’s anti-inflammatory actions. Our results show that LJP treatment significantly modulated the expression of key genes involved in inflammatory responses, particularly through the regulation of Csf3-mediated pathways. These findings provide novel insights into the therapeutic potential of LJP for ischemic stroke and identify potential targets for future interventions.

overall_design: RNA sequencing (RNA-seq) was performed on ischemic brain tissues collected from three groups of mice: (1) Sham-operated control group; (2) Vehicle-treated I/R injury group; and (3) LJP-treated I/R injury group. Total RNA was extracted from the tissues, libraries were constructed, and sequencing was conducted to profile gene expression changes. The aim was to identify differentially expressed genes and signaling pathways associated with LJP’s anti-inflammatory and neuroprotective effects.

first: Tangming

last: Guan

first: Siyu

last: Chen

first: Dongbo

last: Jiang

first: Weiming

first: Huayan

last: Wang

first: Kefeng

first: Xin