title: eCLIP-Seq of endogenous/exogenous MYC in MCF-7 cells.

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

summary: MYC binds to thousands of promoters and exerts an amplification effect on expression of most genes. Meanwhile, MYC drives tumourigenesis through the regulation of a unique set of cancer-specific targets that differ from its targets in normal cells. The discrepancy in MYC-mediated gene regulation in tumours versus normal cells has not been fully elucidated. In this study, we discovered that MYC protein has a broad RNA binding spectrum including promoter-associated RNAs (paRNAs) and enhancer RNAs (eRNAs). MYC RNA binding peaks colocalize with its DNA binding sites, but they are not dependent on its HLHLZ domain or transactivation domain. By integrating multiple dimensional data sets from cancer cells and tumour samples, we show that the MYC-bound paRNAs and eRNAs can shape MYC chromatin interaction to regulate gene transcription. Finally, we identified and characterized a novel MYC-bound eRNA, which we refer to as MERG1, that plays essential roles in the ERα+ breast cancer tumourigenesis. Mechanistically, MERG1 interacts with MYC and enhances MYC binding to the enhancer and promoter of the GREB1 gene. This process specifically amplifies expression of the MYC target gene GREB1 and accelerates tumour progression. Our study demonstrates that MYC interaction with paRNAs and eRNAs contribute to its specific amplification of gene expression in tumourigenesis.

overall_design: eCLIP-Seq of endogenous, exogenous full-length, and exogenous truncated MYC in MCF-7 cells.

first: Sihan

first: Zehua


title: Constitutive expression of IκBζ promotes tumor growth and immunotherapy resistance in melanoma [mouse RNA-seq]

status: Public on Apr 29 2025

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

type: Expression profiling by high throughput sequencing

summary: Background: IκBζ, a rather unknown co-regulator of NF-κB, is mostly inducibly expressed and can either activate or repress a specific subset of NF-κB target genes. While its role as a transcriptional regulator of various cytokines and chemokines in immune cells has been revealed, IκBζ’s function in solid cancer remains unclear. Methods: We investigated IκBζ expression in melanoma, and assessed its impact on target gene expression, tumor growth, and response to immunotherapy in melanoma cell lines, mouse models, and patient samples. Results: Unlike in other cell types, IκBζ protein was found to be constitutively expressed in a subfraction of melanoma cell lines, and around 35% of melanoma cases. This atypical expression pattern of IκBζ did not correlate with its mRNA levels or known driver mutations, but instead seemed to result from changes in its post-transcriptional or post-translational regulation. Deleting constitutively expressed IκBζ abrogated the activity and chromatin association of STAT3 and p65, leading to reduced expression of the pro-proliferative cytokines IL-1β and IL-6 in melanoma cells. Consequently, loss of tumor-derived IκBζ suppressed self-sustained melanoma cell growth both in vitro and in vivo. Additionally, constitutive IκBζ expression suppressed the induction of the chemokines CXCL9, CXCL10, and CCL5, which impaired the recruitment of NK and CD8+ T-cells to the tumor, causing resistance to α-PD-1 immunotherapy in mice. Furthermore, the expression of tumor-derived IκBζ also correlated with the absence of CD8+ T-cells in human melanoma samples and progressive disease during immunotherapy. Conclusion: We propose that tumor-derived IκBζ could serve as a new therapeutic target and prognostic marker that characterizes melanoma with high tumor cell proliferation, cytotoxic T- and NK-cell exclusion, and unfavorable immunotherapy responses. Targeting IκBζ expression might open up a new therapy option to re-establish the recruitment of cytotoxic cells, thereby resensitizing for immunotherapy.

overall_design: To investigate the functional impact of constitutive IκBζ expression in melanoma, we used CRISR-Cas9 to knock out NFKBIZ (IκBζ) in the IκBζ-expressing D4M-3A melanoma cells


title: Widespread and cell-type-specific transcriptomic reorganization following mild traumatic brain injury

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: Here, we examined the molecular landscape of Traumatic Brain Injury by employing Visium Spatial Transcriptomics on CHIMERA TBI mice.

overall_design: Spatial transcriptomic analysis of the mouse brain following CHIMERA traumatic brain injury.

first: Aditya

last: Swaro

first: Brianna

middle: N

last: Bristow

first: Mehwish

last: Anwer

first: Angela

middle: A

last: Zhang

first: Larissa

last: Kraus

first: Sarah

middle: R

last: Erwin

first: Tara

last: Stach

first: Kaitlin

middle: E

last: Sullivan

first: Riya

middle: K

last: Gandhi

first: Jianjia

last: Fan

first: Wai Hang

last: Cheng

first: Cheryl

middle: L

last: Wellington

middle: S


title: Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancer (RNA-Seq)

status: Public on Apr 30 2025

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

country: USA

institute: Dana Farber Cancer Institute

summary: KAT6A is a histone acetyltransferase that is emerging as a therapeutic target in cancer, including estrogen receptor positive (ER+) breast cancer. We performed CRISPR screens to identify the chromatin adaptor Menin as a regulator of KAT6A inhibitor response. Co-treatment with KAT6A/B and Menin inhibitors had synergistic anti-proliferative effects in ER+, but not ER-, breast cancer lines. Our data revealed that KAT6A and Menin cooperatively regulate ER-driven gene expression and chromatin accessibility via direct effects on ESR1 expression and at ER target genes. KAT6A and Menin co-localize at promoters of ESR1 and ER-driven genes and combined KAT6A/B and Menin inhibition selectively displaced RNA Pol II from chromatin at these loci. Combined KAT6A/B and Menin inhibition was effective in ER+ patient-derived organoids and in models of endocrine resistance. KAT6A/B and Menin inhibitors are currently in clinical trials and have shown manageable toxicity profiles, underscoring the potential therapeutic relevance for ER+ breast cancer.

overall_design: Gene expression changes were assessed in MCF7 and T47D cells after 8h, 48h, and 96h of KAT6A/B inhibition. Additionally, gene expression changes were assessed in MCF7 cells and patient-derived organoids in response to Menin and/or KAT6A/B inhibition.

last: Olsen

first: Charlie

last: Hatton

first: Yanhe

last: Wen


title: Single-cell and spatiotemporal profile of ovulation in the mouse ovary

city: West Lebanon

first: Ruixu

last: Huang

state: New Hampshire

address: 4 Sachem Circle

institute: Dartmouth College

summary: Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, no studies have detailed the precise window of ovulation at single-cell resolution. Here, we performed parallel single-cell RNA-seq and spatial transcriptomics on paired mouse ovaries across an ovulation time course to map the spatiotemporal profile of ovarian cell types. We show that major ovarian cell types exhibit time-dependent transcriptional states enriched for distinct functions and have specific localization profiles within the ovary. We also identified gene markers for ovulation-dependent cell states and validated these using orthogonal methods. Finally, we performed cell-cell interaction analyses to identify ligand-receptor pairs that may drive ovulation, revealing previously unappreciated interactions. Taken together, our data provides a rich and comprehensive resource of murine ovulation that can be mined for discovery by the scientific community.

overall_design: Following ovarian hyperstimulation using human chorionic gonadotropin (hCG), mouse ovaries were collected across the ovulation time course (0h, 4h, and 12h post-hCG) for single-cell sequencing.

first: Caroline

last: Kratka

first: Jeffrey

last: Pea

first: Cai

last: McCann

first: Jack

last: Nelson

first: John

middle: P

last: Bryan

first: Luhan

middle: T

last: Zhou

first: Daniela

last: Russo

first: Emily

middle: J

last: Zaniker

first: Achla

middle: H

first: Alex

last: Shalek

first: Brian

last: Clearly

first: Samouil

last: Farhi

first: Francesca

last: Duncan

first: Britt

last: Goods


title: Constitutive expression of IκBζ promotes tumor growth and immunotherapy resistance in melanoma [human RNA-seq]

first: Matthias

last: Klein

overall_design: To investigate the functional impact of constitutive IκBζ expression in melanoma, we used shRNA to knock down NFKBIZ (IκBζ) in the IκBζ-expressing LOX-IMVI melanoma cells


title: Overexpression of PTHrP in beta cells reveals key effects on endoplasmic reticulum stress

city: Athens

first: Craig

last: Nunemaker

state: OH

address: 228 Irvine Hall

department: Biomedical Sciences

institute: Ohio University

summary: Administration of parathyroid hormone-related protein (PTHrP) has been shown to increase insulin content and secretion in mice. PTHrP also increases beta-cell mass and proliferation. However, the mechanisms for these effects are unknown, and investigations have yet to examine PTHrP in the transcriptome. In this study, we transiently transfected a mouse beta-cell line (MIN6) with either full-length PTHrP or DSred vector. Insulin content and glucose-stimulated insulin secretion were measured, and RNA from the cells after incubating in 20mM glucose was collected. The results showed that PTHrP overexpression increased insulin content and the ratio of insulin secretion between low and high glucose (stimulation index). RNA-sequencing showed that PTHrP overexpression downregulated many genes associated with responses to endoplasmic reticulum (ER) stress such as Hspa40, Dnajc3 and Xbp1. Among enriched KEGG pathways, the ER stress gene pathway was the most strongly downregulated by far, and the most upregulated pathway was for biosynthesis of amino acids required for protein synthesis. These pathways suggest increased rates of protein biosynthesis. qPCR supported RNA-sequencing results for several ER stress genes (Xbp1, Bax, Bip). MIN6 cells transfected with PTHrP also had lower proinsulin-to-insulin ratio, indicting that PTHrP enhanced insulin processing in the ER. Our working hypothesis is that PTHrP augments insulin production and ER efficiency, which is consistent with observations of increased insulin content, decreased proinsulin-to-insulin ratio and reduced ER stress markers in MIN6 cells. In conclusion, our findings suggest a previously unknown role for PTHrP in beta-cell endoplasmic reticulum, which may have therapeutic implications for enhancing insulin production.

overall_design: Transient transfection of MIN6 cells (a murine insulin-secreting cell line) with either full-length PTHrP (MIN6_PT) or DSred vector (MIN6_DS). mRNA samples were collected for RNA sequencing within three days of transfection.

first: Ibiagbani

middle: M

last: Max-Harry

first: Noriko

last: Kantake

first: Kathryn

last: Corbin

first: Thomas

last: Rosol


title: GIPR-Ab/GLP-1 Peptide-antibody Conjugate Requires CNS GIPRs and GLP-1Rs to Engage Anorexigenic Circuitry for Additive Weight Loss in Obese Mice

city: Thousand Oaks

first: Murielle

last: Véniant

state: CA

address: 1 Amgen Center Dr

institute: Amgen

summary: Glucose-dependent insulinotropic polypeptide receptor (GIPR) and glucagon-like peptide 1 receptor (GLP-1R) are expressed in the central nervous system (CNS) and regulate food intake. Here, we demonstrate that a peptide-antibody conjugate that blocks GIPR while simultaneously activating GLP-1R (GIPR-Ab/GLP-1) requires both CNS GIPR and CNS GLP-1R for additive effects on body weight loss in obese, primarily male, mice. Moreover, dulaglutide produces greater weight loss in CNS GIPR KO mice compared to WT mice, and the extent of weight loss achieved with dulaglutide + GIPR-Ab is attenuated in CNS GIPR KO mice. WT mice treated with GIPR-Ab/GLP-1 or CNS GIPR KO mice exhibit similar changes in gene expression related to tissue remodeling, lipid metabolism, and inflammation in white adipose tissue and liver. Moreover, GIPR-Ab/GLP-1 is detected in circumventricular organs in the brain and activates c-FOS in downstream neural substrates involved in appetite regulation. Hence, both CNS GIPR and GLP-1R signaling are required for the full effect of a GIPR-Ab/GLP-1 peptide-antibody conjugate, with loss of CNS GIPR activity potentiating the actions of GLP-1R agonism.

overall_design: RNA-seq profiling of liver and inguinal white adipose tissue in Glpr1 fl/fl and GIPR fl/fl DIO mice with or without treatment of GIPR-Ab/P1; liver and inguinal white adipose in Glp1rWnt1-/- and GIPR syn-/- DIO mice treated with vehicle.

first: Clarissa

last: Liu

first: Matt

last: Kanke

first: Tongyu


title: RNA sequencing of HTNV NP and Gc proteins expressing cells

city: Changchun

first: Yinghua

last: Zhao

address: Dongminzhu street 519

country: China

institute: 1st hosptal of Jinli University

summary: Hantavirus infection has become a public health concern worldwide due to its ability to cause severe diseases in humans. The virulence of Hantavirus is determined by their ability to restrain host innate immune responses, such as type Ⅰ interferon (IFN-Ⅰ) response. Here, we demonstrated that Hantaan virus (HTNV), a prevalent pathogen that causes hemorrhagic fever with renal syndrome in China, can inhibit host IFN-Ⅰ production by manipulating the retinoic acid-induced gene I (RIG-I)-like receptor (RLRs) pathways. In brief, we performed the transcriptome analysis to identify the host factors regulated by nucleocapsid protein (NP) and glycoprotein (Gc) of HTNV, which showed that multiple cellular biological pathways were regulated by NP and Gc, including interferon signaling pathways, neuron differentiation, and response to mechanical stimulus. Further analysis demonstrated that HTNV NP and Gc proteins inhibited IFN-Ⅰ response by targeting MAVS upstream molecules, such as RIG-I and MDA-5. Mechanistically, NP and Gc proteins suppressed RIG-I and MDA-5-induced IFN-Ⅰ production by targeting TRIM25, rather than directly actin on RIG-I and MDA-5. Taken together, our study revealed a cross-talk between HTNV NP or Gc proteins and host innate immune response, which is helpful in the understanding of virus-host interaction in general.

overall_design: To investigate the pathogenesis of HTNV coded NP and Gc proteins, we constructed GFP- and Flag- double-tagged HTNV NP and Gc plasmids for expression in mammalian cells. We transfected the plasmids expressing HTNV NP or Gc into HEK293T cells, and the GFP vector was used as a control. At 24 h post transfection, the GFP-positive cells were sorted and examined by RNA-seq analysis at Majorbio (http://www.majorbio.com/) (n=3).

first: Quan

first: Lihe

last: Che


title: Mouse liver assembloids model periportal architecture and biliary fibrosis [scRNA-seq]

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: Modelling liver disease requires in vitro systems that replicate disease progression1,2. Current tissue-derived organoids fail to reproduce the complex cellular composition and tissue architecture observed in vivo3. Here, we describe a multicellular organoid system composed of adult hepatocytes, cholangiocytes and mesenchymal cells that recapitulates the architecture of the liver periportal region and, when manipulated, models aspects of cholestatic injury and biliary fibrosis. We first generate reproducible hepatocyte organoids with functional bile canaliculi network that retain morphological features of in vivo tissue. By combining these with cholangiocytes and portal fibroblasts, we generate assembloids that mimic the cellular interactions of the periportal region. Assembloids are functional, consistently draining bile from bile canaliculi into the bile duct. Strikingly, manipulating the relative number of portal mesenchymal cells is sufficient to induce a fibrotic-like state, independently of an immune compartment. By generating chimeric assembloids of mutant and wild-type cells, or after gene knockdown, we show proof-of-concept that our system is amenable to investigating gene function and cell-autonomous mechanisms. Taken together, we demonstrate that liver assembloids represent a suitable in vitro system to study bile canaliculi formation, bile drainage, and how different cell types contribute to cholestatic disease and biliary fibrosis, in an all-in-one model.

overall_design: Single Cell RNA profile of hepatocyte (WT), cholangiocyte (nuc-tdTomato) and primary portal mesenchymal cells (Pdgfra-H2BGFP) from dissociated periportal assembloids.

first: Anna

last: Dowbaj

first: Armin

last: Niksic

first: Cedric

last: Landerer


title: Deletion of Bmal1 in Intestinal Epithelium Protects against Colonic Inflammation by Suppressing the Apoptosis Pathway (CUT&Tag)

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The circadian clock has been shown to regulate inflammatory bowel disease (IBD), but the underlying mechanisms remain unclear. Here, we observed that the mice in the active phase of the circadian clock were more tolerant to dextrose sodium sulfate (DSS)-induced colitis, compared to those in the resting phase. Furthermore, we found that the circadian gene Bmal1 displayed a dynamic expression pattern in mouse colonic epithelium during the circadian clock, with a high level in the resting phase and a low in the active phase. Ablation of Bmal1 in the intestinal epithelium reduced inflammatory symptoms in the colon of the DSS-treated mice. The mice with Bmal1 deletion exhibited no obvious disruption on intestinal homeostasis, rather were more resistant to DSS-induced inflammation, with less body weight change, fewer pathological symptoms, and greater epithelial integrity, compared to the control group. Mechanistically, BMAL1 promoted apoptosis by binding to the apoptosis-related genes, such as Bax, P53 and Bak1, and transcriptionally activating their expression. Collectively, our results reveal the Bmal1-centered circadian clock is involved in intestinal repair upon injure. Clinically, targeting Bmal1 function may be a promising approach to treat inflammation-related gastrointestinal tract diseases.

overall_design: To further reveal the underlying mechanism by which Bmal1 governs the progression of colitis, we performed CUT&Tag-seq in mouse colonic organoids.

first: Shan

last: Hua

first: Ze

last: Zhang

first: Zhe

first: Liansheng

first: Shicheng

last: Yu

first: Yanhui

last: Xiao

first: Yuan

first: Siting

last: Wei

first: Ying

last: Xu

first: Ye-Guang


title: Effect of depletion of sin-lncRNA in senescent IMR90 fibroblasts

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Despite the classical view of senescence as passive growth arrest, it is an active process with profound implications for cellular homeostasis. Indeed, senescent cells remain metabolically active to be able to cope with the energetic demand of the senescence program, although the precise mechanisms underlying this metabolic reprogramming are just beginning to emerge. Here we have identified sin-lncRNA, a previously uncharacterized lncRNA, highly specific of senescent cells, and transcriptionally induced by the master regulator of senescence C/EBPβ. While being strongly activated in senescence, sin-lncRNA knockdown reinforces the senescence program by altering oxidative phosphorylation and impairing mitochondrial function. Sin-lncRNA interacts with the TCA enzyme dihydrolipoamide S-succinyltransferase (DLST) to facilitate its proper function. sin-lncRNA depletion increases DLST nuclear translocation, favoring a metabolic shift from oxidative phosphorylation to a glycolytic phenotype. Moreover, while sin-lncRNA expression remains low in highly proliferative cancer cells, it is strongly induced upon cisplatin-induced senescence. Knockdown of sin-lncRNA in ovarian cancer cells results in deficient oxygen consumption and increased extracellular acidification, sensitizing the cells to cisplatin treatment. Altogether, these results indicate that sin-lncRNA is specifically induced in cellular senescence to maintain metabolic homeostasis. Our findings reveal a new regulatory mechanism in which lncRNA contributes to the adaptive metabolic changes in senescent cells, unveiling the existence of an RNA-dependent metabolic network specific to senescent cells.

overall_design: To investigate the function of sin-lncRNA in senescence we depleted sin-lncRNA using siRNAs in 4OHT treated IMR90 for 3 days.  Poly-A selected RNAseq from control or sin-lncRNA knockdown IMR90 senescent cells in triplicates.

first: Elena

last: Grossi

first: Francesco

last: Marchese

first: Jovanna

last: González

first: Enrique

last: Goñi

first: Lukas

last: Bethlehem

first: Alicia

last: Madoz

first: Nicolás

last: Herranz

first: Jesús

last: Gil

first: Marta

last: Montes


title: Selective modulation of gene expression in activated normal human peripheral blood mononuclear cells by store-operated calcium entry blocker BTP2

status: Public on Apr 28 2025

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Rd

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: Calcium is a critical signaling molecule in many cell types including immune cells. The calcium-release activated calcium channels (CRAC) responsible for store-operated calcium entry (SOCE) in immune cells are gated by STIM family members functioning as sensors of Ca2+ store content in the endoplasmic reticulum. We investigated the effect of SOCE blockers BTP2 and CM4620 on human peripheral blood mononuclear cells (PBMCs) polyclonally-stimulated with the mitogen phytohemagglutinin (PHA).

overall_design: To investigate the effect of SOCE blocker BTP2 on human peripheral blood mononuclear cells (PBMCs) stimulated with the mitogen phytohemagglutinin (PHA), we performed bulk RNA sequencing (RNA-seq) and multiplexed single-cell RNA sequencing  to query gene expression at the whole transcriptome level in human PBMCs from four healthy donors.

first: Madhav

last: Mantri

first: Andreas

last: Stephanou

first: Divya

last: Shankaranarayanan

first: Manikkam

last: Suthanthiran


title: Incorporating Metabolic Competence into High-Throughput Profiling Assays

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

summary: One limitation of previous high-throughput transcriptomics (HTTr) chemical screening studies using TempO-Seq is that most of the in vitro models used on those studies lack instrinsic capabilites to metabolize xenobiotics. This study incorporated an in vitro metabolism platform, aliginate immobilization of metabolic enzymes (AIME), into the dosing procedures for HTTr screening to address this limitation. The 384-well, lid-based platform is incubated for 2 hours on standard microplates containing chemicals, metabolic co-factors and cell culture medium to make "conditioned" medium. This medium is used to treat cells rather than treated them with parent chemicals directly, and the AIME platform does not impact downstream procedures for preparation of cell lysates that are compatible with the TempO-Seq assay. The AIME platform was used concurrently in negative or "nomet" (water + alginate) and positive or "met" (hepatic S9 + alginate) metabolic conditions. This proof-of-concept experiment screened three previously studied estrogenic reference chemicals representing three "shifts" with metabolism in the VM7Luc4E2 breast cell line in an estrogen receptor transactivation assay: bioinactivation, bioactivation or no change with metabolism. Our results indicated that the TempO-Seq assay could detect changes in bioactivity with metabolism. The established workflow can be used in future studies to improve human relevance in our chemical screening efforts.

overall_design: The AIME platform was used in a "nomet" and "met" condition in VM7Luc4E2 breast cells. Cells were treated with three estrogenic reference chemicals at eight concentrations, one estrogen receptor active control (17B-estradiol) at one concentration and a vehicle control (DMSO). Each TC plate was split into twelve equal sections that were randomized uniquely, and one of these sections on each plate was analyzed using the human whole transcriptome TempO-Seq assay. One section on three independent assay plates was sequenced per AIME condition.

first: Amanda

last: Jurgelewicz

first: Kristen

last: Breaux

first: Clinton

last: Willis

first: Felix

last: Harris

first: Gabrielle

last: Byrd

first: Joshua

last: Witten

first: Derik

last: Haggard

first: Joseph

last: Bundy

first: Logan

last: Everett

first: Chad

last: Deisenroth

last: Harrill


title: Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors [scRNA-seq]

city: San Francisco

first: Arja

last: Ray

state: California

address: 513 Parnassus Avenue

department: Pathology

institute: UCSF

summary: The anti-tumor function of CD8 T cells is limited through well-established pathways of T cell exhaustion (TEX). Strategies to capture emergent functional states amongst this dominant trajectory of dysfunction are necessary to find pathways to durable anti-tumor immunity. By leveraging transcriptional reporting (by the fluorescent protein TFP) of the T cell activation marker Cd69, related to upstream AP-1 transcription factors, we define a classifier for potent versus sub-optimal CD69+ activation states arising from T cell stimulation. In tumors, this delineation acts an additional functional readout along the TEX differentiation trajectory, within and across TEX subsets, marked by enhanced effector cytokine and granzyme B production. The more potent state remains differentially prominent in a T cell-mediated tumor clearance model, where they also show increased engagement in the microenvironment and are superior in tumor cell killing. Employing multimodal CITE-Seq in human head and neck tumors enables a similar strategy to identify Cd69RNAhiCD69+ cells that also have enhanced functional features in comparison to Cd69RNAloCD69+ cells, again within and across intratumoral CD8 T cell subsets. Refining the contours of the T cell functional landscape in tumors in this way paves the way for the identification of rare exceptional effectors, with imminent relevance to cancer treatment.

overall_design: Adoptively transferred CD45.1; OT-I; Cd69-TFP CD8 T cells were sorted from B78chOVA tumors d12 post transfer into four populations based on the CD69:TFP quadrants (Q1: TFP+/CD69-, Q2: TFP+/CD69+, Q3: TFP-/CD69-, and Q4: TFP-/CD69+). Cells were sorted from 8 tumors grown in separate mice and pooled by quadrants for barcoding and analysis. Sorted cells were separately labeled with lipid and cholesterol-modified oligonucleotides (LMO’s) according to McGinnis et. al. Following 2 washes with PBS + 0.1% BSA, cells were pooled for encapsulation in one lane of a 10X 3’ v3 kit with a target cell number of 18,000.

first: Bushra

last: Samad

first: Alexis

last: Combes


title: Baseline body fat percentage is related with weight and fat mass gain from high-fat overfeeding over a period of 8 weeks

city: santiago

first: Jose

middle: Eduardo

last: Galgani

address: Avda. Libertador Bernardo O´Higgins 340

department: Nutrition, Diabetes and Metabolism

country: Chile

institute: PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

summary: Epidemiological data suggest that lean individuals resist exposure to the obesogenic environment better than those with obesity. To test this, we analyzed the relationship between overfeeding-induced weight and fat mass gains with baseline body mass index (BMI) and body fat percentage. In this controlled intervention study, 34 young men (BMI: 25.5±2.4 kg/m2, body fat [DXA]: 19.3±5.1%) consumed for 8 weeks 40% more energy than needed at weight maintenance. The energy costs of weight and fat mass gain were calculated as the 8-week excess energy consumed (EEC) divided by weight or fat mass gain. Energy expenditure (baseline and after overfeeding) was determined using a metabolic chamber and doubly labeled water. Transcriptomic analysis was conducted from abdominal subcutaneous adipose tissue samples

overall_design:
25 Adipose Tissue RNA samples
BL = baseline, PO = overfeeding-induced weight and fat mass gains

first: Eric

last: Ravussin

first: Pravalika

last: Javvadi

first: Sujoy

last: Ghosh


title: Fes-Deficient Macrophages Prime CD8+ T Cells to Stimulate Anti-tumor Immunity and Improve Immunotherapy Efficacy

city: Kingston

first: Peter

last: Greer

state: ON

address: 18 Stuart St.

department: Sinclair Cancer Research Institute

institute: Queen's University

summary: Homeostatic immunoregulatory mechanisms that prevent adverse effects of immune overaction can serve as barriers to successful anti-cancer immunity, representing attractive targets to improve cancer immunotherapy. Here, we demonstrated the role of the non-receptor tyrosine kinase Fes, abundantly expressed in immune cells, as an innate intracellular immune checkpoint. Host Fes-deficiency delayed tumor onset in a gene dose-dependent manner and improved tumor control, survival, doxorubicin efficacy, and anti-PD-1 therapy sensitization in murine triple-negative breast cancer and melanoma models. These effects were associated with a shift to an anti-tumorigenic immune microenvironment. Fes-deficient macrophages displayed increased Toll-like receptor signaling, proinflammatory cytokine production, antigen presentation to and activation of T cells, leading to increased cancer cell killing in vitro and tumor control in vivo. This study highlights Fes as an innate immune checkpoint with potential as a therapeutic target and a predictive biomarker to guide immune checkpoint inhibitor treatment.

overall_design: Bulk RNAseq analysis was performed on bone marrow derived macrophages isolated from either Fes+/+ (n=3) or Fes-/- (n=3) mice that were either untreated or treated with 1µg/mL of LPS for 4 hours.

first: Brian

last: Laight

first: Natasha

last: Dmytryk

first: Andrew

last: Garven

first: Kathrin

last: Tyryshkin


title: The cytochrome P450 enzyme MpCYP78E1 inhibits meristem initiation and activity in Marchantia polymorpha

city: Vienna

first: Chloe

last: Casey

address: Zimmermannplatz 10

country: Austria

institute: St Anna Children's Cancer Research Institute

summary: Plant shoot branches are formed by the initiation and activation of generative centres known as meristems. In dichotomously branching plants, such as many bryophytes and lycophytes, new meristems are formed when a pre-existing meristem splits into two daughter meristems. These meristems may be active and produce shoot branches or may be inactive. Here, we show that a predictable pattern of active and inactive meristems develops along the thallus in the liverwort Marchantia polymorpha. In conditions where meristem inactivation occurs – such as simulated shade and older plants – one daughter meristem was active and produced a shoot branch, and the other daughter meristem was inactive after dichotomy. The position of the inactive meristem alternated between either side of the plant axis. Using this predictable pattern, we generated transcriptomes of active and inactive meristems. A comparison of these transcriptomes identified the cytochrome P450 monooxygenase, MpCYP78E1, as a novel regulator of meristem activity. MpCYP78E1 reporter expression was higher in active meristems than inactive meristems. More meristems were active in loss of function mutants than wild type, and fewer active meristems developed in gain of function mutants, indicating that MpCYP78E1 inhibits meristem activity. Furthermore, unlike wild type, Mpcyp78e1 loss of function mutants produced supernumerary meristems from the centre of the mature plant body.  We conclude that MpCYP78E1 inhibits both meristem initiation and activity to modulate shoot branching architecture.

overall_design: RNA-seq analysis of pairs of active and inactive M. polymorpha meristems at each of the three stages of meristem inactivation, as well as thallus (non-meristematic) samples

first: Victoria

last: Spencer

first: Magdalena

last: Mosiolek

first: Katharina

last: Jandrasits

first: Natalie

last: Edelbacher

first: Liam

last: Dolan


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. [CUT&RUN]

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, while cone-differentiation factors Thrb, Rxrg, and Mef2c are expressed precociously in cone specification. Functional analyses reveal that Zic3 and Mef2c promote cone specification, acting through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that evolutionary modifications to gene regulatory networks underlie the development of cone-dominant retinas, providing insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

sample_organism:
Mus musculus
Ictidomys tridecemlineatus

platform_organism:
Mus musculus
Ictidomys tridecemlineatus

overall_design: Nuclei were isolated from snap-frozen P5 13LGS and P2 mouse retinas for use in CUT&RUN-sequencing. Two biological replicates were assayed for each species, with each 13LGS replicate consisting of a pool of retinas from two individuals, and each mouse replicate consisting of a pool of retinas from 3 individuals.

first: Kurt

last: Weir

first: Sangeetha

last: Kandoi

first: Roujin

last: An

first: Nicole

last: Pannullo

first: Isabella

last: Palazzo

first: Jared A.

last: Tangeman

first: Jun

last: Shi

first: Steven H.

last: DeVries

first: Dana K.

last: Merriman

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: Deletion of Bmal1 in Intestinal Epithelium Protects against Colonic Inflammation by Suppressing the Apoptosis Pathway

first: Ye-guang

last: Chen

overall_design: Comparative gene expression profiling of RNA-seq data from multiple time points in wild-type mice.

first: Shan

last: Hua

first: Ze

last: Zhang

first: Zhe

first: Liansheng

last: Liu

first: Shicheng

last: Yu

first: Yanhui

last: Xiao

first: Yuan

first: Siting

last: Wei

first: Ying

last: Xu

first: Ye-Guang


title: The disease modeling of Jacob Syndrome reveals an aberrant genome-wide expression modulation from the Y chromosome [RRBS]

city: Thuwal

first: Antonio

last: Adamo

state: Makkah

address: Thuwal 23955-6900 KAUST

department: iological, Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: Male sex chromosome aneuploidies are frequent genetic aberrations in humans characterized by additional X or Y complements in the contest of a 46,XY karyotype. Among male aneuploidies, Klinefelter (KS) and Jacob Syndromes (JS), carrying 47,XXY and 47,XYY chromosomes, respectively, share several clinical features, including sterility, hormonal deficits, neurocognitive delay, and skeletal-muscle defects. In this study, we generated and characterized the inaugural cohort of 47,XYY human induced pluripotent stem cells (iPSCs). We profiled the transcriptome of fibroblasts, iPSCs, and iPSCs-derived neural stem cells (NSCs) to investigate the transcriptional consequences of Y chromosome overdosage across three different cell types. Our data defined subsets of genes sensitive to Y dosage that includes i) non-PAR Y-linked (NPY) genes shared among cell types, ii) genes residing on the X and Y pseudo-autosomal region 1 (PAR1), and iii) autosomal genes that display a mild degree of tissue-specificity. By comparing the expression and identity of PAR1 in KS and JS-derived cells, we confirmed their obligate dosage sensitivity to sex chromosome numbers in a cell type-dependent fashion, and we proved that PAR1 genes are differentially expressed from X and Y chromosomes. We also defined a shared transcriptional signature in X and Y aneuploidies, by comparing sex and autosomal dysregulated genes, that could explain the shared clinical manifestations in JS and KS patients. Furthermore, we demonstrated a regulatory function of NPY genes on their non-PAR homologs on the X chromosome (NPX). By mechanistically linking the expression of X and Y gene pairs, we revealed that NPY genes in overdosage negatively modulate in trans the transcription of their NPX homologs. Finally, we assessed the genome-wide methylation status in cells carrying Y aneuploidies and defined that the additional Y chromosome does not dramatically alter the global DNA methylation status. Our findings expand the knowledge on X and Y chromosome cross-modulation and impact on human gene expression, and suggest that disease modeling of sex aneuploidy through iPSCs may provide an ideal platform for understanding the global effects of aneuploidies in disease-relevant cell types.

overall_design: DNA methylation  profiles of primary fibroblast,iPSC and NSCs derived from 3 Jacob's syndrome patients (47,XYY) and 3 control males (46,XY). For each 47,XYY at least two independent clones  and for each control one clone  were sequenced.

first: Veronica

last: Astro

first: Kelly

last: Cardona-Londoño

first: Lorena

middle: V

last: Cortés-Medina

first: Rawan

last: Alghamdi

first: Gustavo

last: Ramirez-Calderón

first: Fotios

last: Kefalas

first: Jair

last: Dilme-Capó

first: Santiago

last: Radío


title: Oral intake of high fat diet and acidic bile salts may develop carcinogenesis at the esophagogastric junction

city: Sendai

first: Kaname

last: Uno

address: 1-1 Seiryo Aoba-ku

department: Gastroenterology

country: Japan

institute: Tohoku University

summary:
Oral intake of high fat diet and acidic bile salts  may promote the oxidative stress-induced Warburg effect in the tumor
The promotion of the carcinogenesis may be associated with high fat diet-related dysbiosis

overall_design: We utilized microarray analysis of the carcinogenesis in Gan mice between the control group and the HFD+acidic bile salts-intaking group

first: Koichiro

last: Sudo


title: Age-Associated Decline in Autophagy Pathways in the Retinal Pigment Epithelium and Protective Effects of Topical Trehalose in Light-Induced Outer Retinal Degeneration in Mice

city: bristol

first: Gongyu

last: Shi

address: Biomedical Sciences Building, University of Bristol, Tankard's Cl, University Walk

country: United Kingdom

institute: university of bristol

summary: Age is a primary risk factor for chronic conditions, including age-related macular degeneration (AMD). Impairments in autophagy processes are implicated in AMD progression, but the extent of autophagy’s contribution and its therapeutic potential remain ambiguous. This study investigated age-associated transcriptomic changes in autophagy pathways in the retinal pigment epithelium (RPE) and evaluated the protective effects of topical trehalose, an autophagy-enhancing small molecule, against light-induced outer retinal degeneration in mice. Transcriptomic analysis of human RPE/choroid and mouse RPE revealed consistent downregulation of autophagy pathways with age, alongside variable changes as AMD severity progressed. Given the age- and AMD-associated perturbation of autophagy pathways, we examined trehalose treatment in vitro, which enhanced autophagic flux and restored mitochondrial respiratory function in primary murine RPE cells exposed to oxidative stress. In vivo, pre-treatment with topical trehalose improved autophagy-lysosome activity in mouse RPE, demonstrated by elevated LC3B turnover and SQSTM1/p62 degradation. Furthermore, trehalose eyedrops protected mice from light-induced damage to the RPE and photoreceptors, preserving outer nuclear layer thickness, RPE morphology, and junctional F-actin organization. Taken together, the data support that age-related decline and severe dysregulation in autophagy contributed to AMD progression. By restoring autophagic flux, topical trehalose demonstrates therapeutic potential to address early autophagy-related pathological changes in AMD.

overall_design: Murine RPE cells used for RNA-seq were isolated following an established protocol.  Briefly, eyes were enucleated and cleaned using angled scissors to remove any remaining connective tissue. After removing the cornea and lens, the eyecups were incubated at 37°C in hyaluronidase (Sigma-Aldrich) for 45 min, and in Hank’s balanced salt solution with 10 mM HEPES for a further 30 min before retinas were removed via incision. Subsequently, eyecups were incubated at 37°C in trypsin/EDTA for 45 min before being transferred into HBSS with 20% heat-inactivated FCS. Gently shaking facilitated the detachment of RPE sheets, which were further incubated in trypsin/EDTA for 1 min to generate single-cell suspensions. RNA of RPE cells was extracted using the RNeasy Mini kit (Qiagen). The RNA samples were sent to the Genomics Facility at University of Bristol for ScreenTape assessment to ensure RNA integrity (RIN) >7 prior to downstream processes. Library preparation was conducted using Illumina Stranded Total RNA Prep with Ribo Zero Plus (Illumina), followed by sequencing using the Illumina NextSeq 550 platform with 2×75 bp by paired-end reads at a depth of 16 million reads. Galaxy software was used to assess the quality of reads via FastQC, followed by read trimming via Trimmomatic. Reads were then aligned using HISAT2 and quantified using FeatureCounts. Batch correction of the resulting counts from two independent experiments was performed using R Studio v2023.06.1 with ComBat-seq. Following batch correction, the counts were normalized by DESeq2 package and lowly expressed genes (basemean < 20) were excluded. Normalized data of the remaining 14220 genes were processed using iDEP.96 for logarithmic transformation, quality control, and DEG identification.

first: Katherine

last: Cox

first: Neve

last: Read

first: Mohamed

last: Patel

first: Kepeng

last: Ou

first: Zijia

first: Jiahui

last: Wu

first: Suci

last: Cendanawati

first: Jenna

last: Powell

first: Pola

middle: G

last: Oppenheimer

first: Lisa

last: Hill

first: Lindsay

middle: B

last: Nicholson

first: Andrew

middle: D

last: Dick

first: Jian


title: Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors [CITE-seq]

first: Arja

last: Ray

overall_design:
Live CD45+ and CD45- cells were sorted on a BD FACSAria Fusion. CD45+ and CD45- cells were pelleted and resuspended at 1x10^3 cells/ml in 0.04%BSA/PBS buffer before mixing in an 8:2 CD45+:CD45- ratio and loaded onto the Chromium Controller (10X Genomics) to generate 5′ v1.1 gel beads-in-emulsions (GEM). Pooled 8:2 CD45+:CD45- cells were resuspended in Cell Staining Buffer (BioLegend) and stained with a pool of 137 TotalSeq-C antibodies (Table) according to the manufacturer’s protocol before loading onto the Chromium Controller (10X Genomics) for GEM generation. The cDNA libraries were generated using all or a subset of Chromium Next GEM Single Cell 5′ Library Kit for gene expression (GEX), Chromium Single Cell V(D)J Enrichment kit (10X Genomics) for T cell receptor (TCR), and Chromium Single Cell 5′ Feature Barcode Library kit for antibody derived tag (ADT) according to the manufacturer’s instructions. The libraries were subsequently sequenced on a Novaseq S4 sequencer (Illumina) to generate fastqs with the following mean reads per cell: 42,000 (GEX), 34,000 (TCR), and 5,700 (ADT).

Please note that the records have been updated with the re-analysis data on May 21, 2025 as detailed below:

In addition, GSM6552605, GSM6552607, GSM6552609, GSM6552613 from GSE212797 were included in this analysis. The sequencing and processing of these previous samples were the same as the new ones identified here. Identical analysis pipelines were used to analyze these data.
IPIHNSC126_T1_scrna_CD45_enriched_filtered_feature_bc_matrix.h5 (generated from re-analysis of GSM6552605, GSM6552607)
IPIPOOL004_P1_scrna_CD45_enriched_filtered_feature_bc_matrix.h5 (generated from re-analysis of GSM6552609, GSM6552613)

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Bushra

last: Samad

first: Alexis

last: Combes


title: The catalytic domain of SETD1B regulates H3K4me3 breadth and Myc expression in MLL-r leukemia (ChIP-seq_mus)

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

institute: Chiba University

summary: Histone H3 lysine 4 tri-methylation (H3K4me3) is abundant in MLL-rearranged (MLL-r) acute myeloid leukemia (AML) cells, but the enzymes responsible and their roles remain unclear. In this study, we perform a CRISPR-tiling screen against known H3K4 methylation modifiers in MLL-r AML model. We found the non-redundant roles of H3K4 methyltransferase SETD1B for growth regulation in NrasG12D or FLT3-ITD-expressing AML cells that exhibit cytokine-independent growth. The disruption of SETD1B catalytic SET domain causes cell cycle arrest, apoptosis, cell differentiation and a downregulation of gene expression, especially in the MYC pathway. H3K4me3 and SETD1B are distributed to the gene body of Myc, and the loss of SETD1B SET domain result in a significant decrease in H3K4me3 breadth. Overexpression of MYC significantly restores the growth defect and transcriptional perturbation in SETD1B SET domain mutant cells. In the meantime, the expression of MYC does not rescue the reduced H3K4me3 breadth and RNA polymerase II elongation in SETD1B mutant cells. A disruption of H3K4 demethylase KDM5C enhances global H3K4me3 level and promotes the proliferation of AML cell, and partially rescues the defective cell growth of SETD1B SET domain mutant cells. These data indicate that SETD1B is required for both H3K4me3 breadth and Myc expression to support advanced AML cell proliferation. Thus, a thorough understanding of the SETD1B-mediated H3K4me3 breadth will be critical for the development of markers and therapies for leukemia subtypes that are MYC-dependent.

overall_design: SETD1B SET domain in mouse MLL-AF9 / FLT3-ITD expressing leukemia cell was mutated by the specific sgRNA, and single cell clones were established. Myc was exogenously expressed by the additional retrovirus infection into the SETD1B SET domain mutated single cell clone.

first: Shintaro

last: Izumi

first: Takayuki

last: Hoshii


title: The catalytic domain of SETD1B regulates H3K4me3 breadth and Myc expression in MLL-r leukemia (RNA-seq)


title: The disease modeling of Jacob Syndrome reveals an aberrant genome-wide expression modulation from the Y chromosome [RNA-seq]

first: Antonio

last: Adamo

overall_design: Bulk transcriptomic profiles of primary fibroblast,iPSC and NSCs derived from 3 Jacob's syndrome patients (47,XYY) and 4 control males (46,XY). For each 47,XYY patient and for two of the controls, three independent clones have been generated and for each clone two or three independent RNA-Seq libraries have been processed. For  the other two 46,XY controls one single clone was used and at least two independent libraries were sequenced.

first: Veronica

last: Astro

first: Kelly

last: Cardona-Londoño

first: Lorena

last: Cortés-Medina

first: Rawan

last: Alghamdi

first: Gustavo

last: Ramirez-Calderón

first: Fotios

last: Kefalas

first: Jair

last: Dilme-Capó

first: Santiago

last: Radío


title: The catalytic domain of SETD1B regulates H3K4me3 breadth and Myc expression in MLL-r leukemia

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The catalytic domain of SETD1B regulates H3K4me3 breadth and Myc expression in MLL-r leukemia (ChIP-seq_human)

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HA-tagged SETD1B, H3K4me3, H3K36me3, KDM5C and SETD2 in MOLM-13 cells. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3 and H3K36me3 in AML primary samples.


title: Hepatocyte-derived Pumilio1-enriched exosomes inhibit HSC activation by suppressing tropomyosin-4 translation

status: Public on Apr 27 2025

city: Guangzhou

first: Zhiping

last: Wan

state: Guangdong

address: No.600 Tianhe Road, Tianhe District, Guangzhou, China

institute: The Third Affiliated Hospital Of Sun Yat Sen University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) has become the most common chronic liver disease globally. Abnormal crosstalk between hepatocytes and hepatic stellate cells (HSCs) leads to liver fibrosis and aggravates MASLD. We explored the role of the RNA-binding protein Pumilio in this process.

overall_design: Transcriptome sequencing analysis of LX2 cells after PUM1 knockdown. The control group was LX2 cells without knockdown of PUM1.

first: Xiang

last: Cai

first: Xiaoquan

last: Liu

first: Haoqi

last: Chen

first: Xiaoman

first: Xiaoan

last: Yang

first: Qingqing

last: Feng

first: Hong

last: Cao

first: Qiyi

last: Zhao

last: Deng


title: The catalytic domain of SETD1B regulates H3K4me3 breadth and Myc expression in MLL-r leukemia (CUT&Tag)

first: Masaki

last: Fukuyo

first: Shintaro

last: Izumi

first: Takayuki

last: Hoshii


title: Comprehensive serum metabolic snapshots enable diagnosis, prognosis, and monitoring for brainstem gliomas [II]

city: SHANGHAI

first: Ruimin

last: Wang

state: SHANHAI

address: 1954 hUASHAN ROAD

institute: Shanghai Jiao Tong University

summary: Brainstem gliomas (BSG) is a highly malignant central nervous system childhood tumors with a poor prognosis of a 5-year survival rate of < 10%. Metabolism during radiotherapy is a dynamic and precisely programmed process, improving clinical outcomes and guiding therapy decisions of BSG. Here, we for the first time construct diagnostic and prognostic assays of BSG via circulating metabolites based on both cross-sectional study and longitudinal cohort study with 106 BSG patients. We employ nanoparticle enhanced laser desorption/ionization mass spectrometry to characterize high-resolution static and dynamic snapshots of metabolites during BSG radiotherapy. We show that this serological tool reaches the area under the curve of 0.933 for BSG diagnosis in an independent blind test and predicts risk of patients with significant differences (p < 0.05) in prognostic outcomes. We further identify eight distinct temporal patterns of metabolite regulation associated with radiotherapy responses and tracked the metabolic trajectory via dynamic metabolic snapshots throughout radiotherapy process. If further validated, this framework could be extended to derive comprehensive metabolic pictures for cancers including but not limited to BSG.

overall_design: SPF-grade female BALB/c nude mice, aged 4-6 weeks and weighing 18-20 g, were used as experimental subjects in this study, following refinement of the experimental methods based on previous study. All animal care and experiments were approved (#XHEC-F-2023-031) by the Animal Ethics Committee of Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University. To establish the orthotopic intracranial xenograft model, DIPG-XH-01 cells were transduced with lentiviral vectors encoding enhanced green fluorescent protein (eGFP) and firefly luciferase (ffLuc). Positively transduced cells were subsequently sorted by fluorescence-activated cell sorting (FACS) to achieve a purity greater than 95% prior to implantation. Under deep anesthesia, mice were secured on a stereotactic frame, and a cranial burr hole was drilled at stereotactic coordinates relative to the lambda suture: 0.8 mm posterior, 1 mm lateral to the midline, and 4.5 mm depth. A total of 1×10⁶ cells suspended in 3 μL phosphate-buffered saline (PBS) were infused via Hamilton syringe at a controlled rate of 0.3 μL/min. To minimize reflux, the injection needle was retained for 5 minutes post-infusion. Tumor engraftment was validated 72 hours post-surgery by intraperitoneal administration of D-luciferin potassium salt (75 mg/kg; Promega) followed by bioluminescent signal acquisition using the IVIS Spectrum In Vivo Imaging System (PerkinElmer). At the humane endpoint, mice were euthanized. Brain tumor tissue and normal mice brainstem tissues were collected and subjected to RNA sequencing. To establish the subcutaneous tumor model, 3×10⁶ DIPG-XH-01 cells were resuspended in a 1:1 mixture with chilled Matrigel matrix (Corning), maintained on ice throughout preparation. A 100 μL aliquot of the cell-Matrigel suspension was injected subcutaneously into the left dorsal flank of mice using a sterile 25-gauge needle. Tumor volume was measured using a vernier caliper. Radiotherapy was initiated in subcutaneous tumor-bearing mice when the tumor size exceeded 100 mm3. Mice in the radiotherapy group were administered a daily radiation dose of 2 Gy at the tumor site for five consecutive days. Tumor tissues before and after radiotherapy were collected and subjected to RNA sequencing.

first: Keke

last: Li

first: Zhengying

last: Gu


first: Ye-guang


title: The crosstalk between BMP and Wnt signaling establishes the equilibrium of villus length in mammalian small intestine

summary: The precise regulatory mechanisms governing the quantitative balance of epithelial cells in the small intestine have long remained elusive. In this study, we reveal a gradual strengthening of BMP signaling from the proximal to distal segments. Through the utilization of genetically engineered mice, we demonstrate that BMP signaling plays a pivotal role in governing villus length. Furthermore, employing mathematical modeling, we uncover that BMP signaling acts as a cellular positional information sensor, orchestrating cell apoptosis and inhibiting cell proliferation. This collective regulation of cellular processes leads to the observed disparities in villus length between the proximal and distal segments of the small intestine. Notably, BMP signaling inhibits Wnt signaling to control the rate of villus growth, while Wnt signaling reciprocally upregulates BMP to maintain villus length under conditions of excessive proliferation. The spatial crosstalk between BMP and Wnt signaling networks collectively ensures the homeostasis of villus length. Our comprehensive investigation of the key factors underlying the gradient differences in villus length provides crucial insights for a deeper understanding of the functional dynamics of the small intestine.

overall_design: To further substantiate the association between BMP signaling in epithelial cells and villus length variations across different segments of the small intestine, we employed genetically engineered mice to explore the effects of BMP signaling molecules on the length of small intestinal villi

first: Xu

first: Siqi

first: Yuan

first: Xiangyu

last: Kuang

first: Jianxin

first: Pei

last: Yu

first: Ze

last: Zhang

first: Lianzheng

first: Yalong

first: Liansheng

first: Shicheng

first: Mengxian

first: Wanlu

last: Song

first: Meimei

last: Huang

first: Ronghui

last: Tan

first: Huidong

first: Naihe

last: Jing

first: Weizhi

last: Ji

first: Jinsong

first: Lei

first: Ye-Guang


title: The PURB-HOTAIR complex regulates p53-dependent promoter-specific transcriptional activation [CLIP-Seq]

status: Public on Apr 25 2025

city: MANHATTAN

first: Zhangchuan

last: Xia

state: NY

address: 1130 St. Nicholas Ave, Rm 608

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

summary: p53 executes its diverse functions through different transcriptional targets but the precise mechanism of promoter-specific regulation by p53 remains largely unknown. Through biochemical purification, we identify purine-rich element binding protein B (PURB), a dual DNA/RNA-binding protein, which acts as a transcriptional corepressor for p53 in a manner dependent on p53 acetylation status. PURB is overexpressed in human cancers, and its knockdown induces p53-dependent activation of p21 but has no effect on other major promoters such as PUMA and MDM2. In contrast to other p53 corepressors, PURB can recognize a unique DNA element at the p21 promoter, with the loss of this element not affecting p53-mediated transactivation but abrogating the ability of p53 to recruit PURB to the p21 promoter for repression. Mechanistically, PURB requires its sequence-specific binding with long noncoding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) to exert its repressive role. In turn, HOTAIR interacts directly with EZH2 and, bridged by the PURB-HOTAIR complex, p53 can recruit the EZH2 histone methyltransferase to target promoters for transcriptional repression. Further analysis of p53 targets reveals several promoters that may serve as targets for PURB binding, suggesting that this mechanism of PURB-dependent promoter-specific regulation may not be limited to p21. These data establish a mode of lncRNA-mediated regulation of p53 transcription in a sequence-specific manner and reveal a previously unanticipated mechanism for acetylation-mediated promoter-specific regulation through a cis-regulatory element recognized by the PURB-HOTAIR complex.

overall_design: CLIP (Cross-linking and immunoprecipitation)-Seq profiling for PURB-bound RNA from H1299 cells expressing SFB-tagged PURB proetin.

first: Wei

first: Ning

last: Kon

first: Zhenyi

last: Su

first: Jingjie

last: Yi

first: Xu

last: Hua

first: Hui

last: Zhou

first: Zhiguo


title: DDX5 super-enhancer promote vasculogenic mimicry formation and metastasis in nasopharyngeal carcinoma by enhancing ADAM10 transcription [Hi-C]

city: Nantong

first: Tian

address: Xisi Road 20, Nantong, Jiangsu Province

department: Institute of Otolaryngology-Head and Neck Surgery

institute: Affiliated Hospital of Nantong University

summary: Antiangiogenetic therapies (AATs) have limited effects owing to most patients with cancer inevitably developing resistance to them. In this study, data generated using a nasopharyngeal carcinoma orthotopic mouse model in combination with clinical data suggested compensatory vasculogenic mimicry (VM) formation during AATs and the association of VM with poor prognosis of nasopharyngeal carcinoma. Additionally, data-independent acquisition mass spectrometry-based proteomics demonstrated that ADAM10 upregulation contributes to VM. Mechanistically, epigenetic and high-resolution chromatin interaction landscape analyses revealed that while ADAM10 does not interact with either the proximal or distal enhancers, DDX5, a transcription factor of ADAM10, is regulated by long-range looping enhancer-promoter interactions. Further analysis identified transcription factors bound to critical constituents of the DDX5 super-enhancer. Ingenol Mebutate, which docked excellently with DDX5, reversed ADAM10-mediated changes in gene expression, thereby effectively suppressing compensatory VM formation and metastasis and improving prognosis. Collectively, these findings provide insights into the clinical application of AATs.

overall_design: Hi-C is applied to NP69 cell line.

first: Yiwen

last: You

first: Bo


title: Single-cell RNA-seq provides insight into the underdeveloped immune system of germ-free mice

city: Shenzhen

first: Yifei

last: SHENG

address: Complex Building, Beishan Industrial Zone, Yantian District

institute: BGI Research

summary: Germ-free mice feature a profoundly underdeveloped immune system. Despite recent studies that emphasize the role of specific bacteria-derived metabolites in immune cell development and differentiation, it remains unclear how the lack of microbiota leads to immune deficiencies. Here, we performed droplet-based single-cell RNA sequencing to analyze the bone marrow and peripheral blood of both germ-free and specific pathogen-free mice, identifying 25 distinct cell types. Our findings suggest that neutrophil apoptosis in germ-free mice may be associated with the absence of niacin dehydrogenase, which is derived primarily from Pseudomonas. In addition, germ-free mice exhibited elevated excretion of 5’-methylthioadenosine, increased ERK activation induced by reactive oxygen species, and cessation of the bone marrow stromal antigen 2 signaling pathway in germ-free mice. The responses of monocytes and CD8+ T cells to interferon β and interferon γ were reduced in germ-free mice, which explains their increased susceptibility to viruses. Together, we identified a regulatory mechanism that connects immunodeficiency with the absence of microbiota in germ-free mice and validated these findings using multiple techniques.

overall_design: Groups: Compare two conditions (e.g., germ-free (GF) vs. specific-pathogen-free (SPF) mice) Tissues: Collect multiple relevant tissues (e.g., peripheral blood, bone marrow, spleen)

last: Sheng

last: Cheng

first: Yin

first: Qijun

last: Liao

first: Juan

last: Shen

first: Ruizhen

last: Zhao

first: Tailiang

last: Chai

first: Chao

last: Wu

first: Weining

last: Hu

first: Xiang

last: Wei

first: Shanshan

last: Pan

first: Yangrui

first: Rouxi

last: Chen

first: Junpu

last: Mei

first: Hong

first: Lijuan

last: Han

first: Xiaodong

last: Fang


title: KSHV Reprograms Host RNA Splicing via FAM50A to Activate STAT3 and Drive Oncogenic Cellular Transformation

status: Public on Apr 26 2025

city: Pittsburgh

first: Shenyu

last: Sun

address: 5117 Centre Ave, HCC G.1

institute: University of Pittsburgh

summary: RNA alternative splicing is a fundamental cellular process implicated in cancer development. Kaposi’s sarcoma-associated herpesvirus (KSHV), the etiological agent of multiple human malignancies, including Kaposi’s sarcoma (KS), remains a significant concern, particularly in AIDS patients. A CRISPR-Cas9 screening of matched primary rat mesenchymal stem cells (MM) and KSHV-transformed MM cells (KMM) identified key splicing factors involved in KSHV-induced cellular transformation. To elucidate the mechanisms by which KSHV-driven splicing reprogramming mediates cellular transformation, we performed transcriptomic sequencing, identifying 131 differential alternative splicing transcripts, with exon skipping as the predominant event. Notably, these transcripts were enriched in vascular permeability, multiple metabolic pathways and ERK1/2 signaling cascades, which play key roles in KSHV-induced oncogenesis. Further analyses of cells infected with KSHV mutants lacking latent genes including vFLIP, vCyclin and viral miRNAs, as well as cells overexpressing LANA, revealed their involvement in alternative splicing regulation. Among the identified splicing factors, FAM50A, a component of the spliceosome complex C, was found to be crucial for KSHV-mediated transformation. FAM50A knockout resulted in distinct splicing profiles in both MM and KMM cells, and significantly inhibited KSHV-driven proliferation, cellular transformation and tumorigenesis. Mechanistically, FAM50A knockout altered SHP2 splicing, promoting an isoform with enhanced enzymatic activity that led to reduced STAT3 Y705 phosphorylation in KMM cells. These findings reveal a novel paradigm in which KSHV hijacks host splicing machinery, specifically FAM50A-mediated SHP2 splicing, to sustain STAT3 activation and drive oncogenic transformation.

overall_design: RNA-seq profiling of MM cells and KMM cells and their FAM50A knockout cell lines (MM-sgFAM50A-11, MM-sgFAM50A-12, MM-sgFAM50A-14, KMM-sgFAM50A-15, KMM-sgFAM50A-22, KMM-sgFAM50A-28ko).

first: Ling

last: Ding

first: Karla

last: Paniagua

first: Yufei

last: Huang

first: Mario A

last: Flores

first: Shou-Jiang

last: Gao


title: Deletion of Bmal1 in Intestinal Epithelium Protects against Colonic Inflammation by Suppressing the Apoptosis Pathway I

city: Beijing

first: Ye-guang

address: Tsinghua Road, Medical Building

institute: Tsinghua University

summary: The circadian clock has been shown to regulate inflammatory bowel disease (IBD), but the underlying mechanisms remain unclear. Here, we observed that the mice in the active phase of the circadian clock were more tolerant to dextrose sodium sulfate (DSS)-induced colitis, compared to those in the resting phase. Furthermore, we found that the circadian gene Bmal1 displayed a dynamic expression pattern in mouse colonic epithelium during the circadian clock, with a high level in the resting phase and a low in the active phase. Ablation of Bmal1 in the intestinal epithelium reduced inflammatory symptoms in the colon of the DSS-treated mice. The mice with Bmal1 deletion exhibited no obvious disruption on intestinal homeostasis, rather were more resistant to DSS-induced inflammation, with less body weight change, fewer pathological symptoms, and greater epithelial integrity, compared to the control group. Mechanistically, BMAL1 promoted apoptosis by binding to the apoptosis-related genes, such as Bax, P53 and Bak1, and transcriptionally activating their expression. Collectively, our results reveal the Bmal1-centered circadian clock is involved in intestinal repair upon injure. Clinically, targeting Bmal1 function may be a promising approach to treat inflammation-related gastrointestinal tract diseases.

overall_design: To further reveal the underlying mechanism by which Bmal1 governs the progression of colitis, we performed bulk RNA sequencing in colonic epithelial cells isolated from wild-type and Bmal1 cKO mice at 7 days post DSS treatment.

first: Shan

last: Hua

first: Ze

last: Zhang

first: Zhe

first: Liansheng

last: Liu

first: Shicheng

last: Yu

first: Yanhui

last: Xiao

first: Yuan

first: Siting

first: Ying

last: Xu

first: Ye-Guang


title: A Vibrio-Specific T6SS Effector Reshapes Microbial Competition by Disrupting Vibrio Bioenergetics, a Precision Antimicrobial Mechanism

city: Shen Zhen

first: Ming

address: 1088 Xueyuan Blvd, Nan Shan Qu

institute: Southern University of Science and Technology

summary: Type VI secretion systems (T6SS) are widely distributed among Vibrio species, yet their roles in the coexistence of toxigenic and non- toxigenic strains remain unclear. Here, we report a novel orphan T6SS effector-immunity module, TseVs-TsiVs, primarily harbored by non- toxigenic Vibrio cholerae. TseVs exhibits robust vibriocidal activity, specifically targeting susceptible Vibrios (lacking TsiVs). TseVs forms dual-membrane, ion-selective pores that collapse Na⁺/K⁺ homeostasis, resulting in membrane depolarization and ATP depletion. Remarkably, non-Vibrio bacteria evade TseVs through proton motive force (PMF)-dependent resilience, uncovering a previously unrecognized immunity-independent defense strategy. Furthermore, tseVs+ non- toxigenic V. cholerae strains are globally distributed and have dominated in recent decades, highlighting TseVs’s ecological significance in Vibrio population dynamics. By linking TseVs’s bioenergetic assassination to Vibrio population shifts, we demonstrate how T6SS effectors shape microbial genetic diversity. Our findings suggest that TseVs represents a promising model for precision antimicrobial strategies, minimizing collateral damage to commensal microbiota.

overall_design: RNA-seq profiling of V. cholerae C6706 carrying the pBAD33 plasmid and its derivative containing TseVs, grown in LB medium supplemented with 0.2% arabinose

first: Zhao

last: Wang


title: BRAF/MEK Inhibition Induces Cell State Transitions Boosting Immune Checkpoint Sensitivity in BRAFV600E-mutant Glioma

city: Palo Alto

first: Claudia K

last: Petritsch

address: 265 Campus Drive

institute: Stanford University

summary: Resistance to BRAF plus MEK inhibition (BRAFi+MEKi) in BRAFV600E-mutant gliomas drives rebound, progression, and high mortality, yet it remains poorly understood. This study addresses the urgent need to develop treatments for BRAFi+MEKi-resistant glioma in generated mouse models and patient-derived materials. BRAFi+MEKi reveals glioma plasticity by heightening cell state transitions along glial differentiation trajectories, giving rise to astrocyte- and immunomodulatory oligodendrocyte (OL)-like states.  PD-L1 upregulation in OL-like cells links cell state transitions to tumor evasion, possibly orchestrated by Galectin-3. BRAFi+MEKi induces interferon response signatures, tumor infiltration, and suppression of T cells. Combining BRAFi+MEKi with immune checkpoint inhibition enhances survival in a T cell-dependent manner, reinvigorates T cells, and outperforms individual or sequential therapies in mice. Elevated PD-L1 expression in BRAF-mutant versus BRAF-wildtype glioblastoma supports the rationale for PD-1 inhibition in patients. These findings underscore the potential of targeting glioma plasticity and highlight combination strategies to overcome therapy resistance in BRAFV600E-mutant HGG.

overall_design: RNA-seq profiling of murine and patient-derived glioma cell lines and patient 12 before versus after BRAFi+MEKi treatment

first: YL

last: Xing

first: D

last: Panovska

first: JW

last: Park

first: ZP

last: Feng

first: X

last: Ji

first: JMM

last: Levy

first: C


title: The USP11/TCEAL1 complex promotes transcription elongation to sustain oncogenic gene expression in neuroblastoma [RNA-seq II]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: During early transcription, RNA polymerase II (RNAPII) undergoes a series of structural transitions controlled by cyclin-dependent kinases. How protein ubiquitylation and proteasomal degradation control the function of RNAPII is less well understood. Here we show that the deubiquitinating enzyme USP11 forms a complex with TCEAL1, a member of the TFIIS (TCEA)-like protein family. TCEAL1 shares sequence homology with the RNAPII interaction domain of the elongation factor TFIIS, which controls the fate of backtracked RNAPII, and competes with TFIIS for binding to core promoters, potentially preventing excessive backtracking. USP11 protects TCEAL1 from proteasomal degradation and TCEAL1 recruits USP11 to RNAPII. Both USP11 and TCEAL1 promote transcription elongation and maintain expression of RPB8, an essential subunit of all three nuclear RNA polymerases. In neuroblastoma USP11- and TCEAL1-dependent genes define a gene expression program that is characteristic for mesenchymal tumors, which are described to escape from many treatments, suggesting that the USP11/TCEAL1 complex promotes transcription elongation to support a critical oncogenic gene expression program

overall_design: One goal of the study was to (a) compare the gene expression programm upon knockdown of USP11 or USP7 in a mesenchymal cell line with or without the activation of MYCN and (b) investigate changes in gene expression upon TCEAL1 knockdown in a mesenchymal (SH-EP) versus adrenergic (IMR-5) cell line

first: Markus

last: Dehmer

first: Katrin

last: Trunk

first: Gabriele

last: Büchel


title: Co-expression of IL-15 and CCL21 strengthens CAR-NK cells to eliminate tumors in concert with T cells and equips them with enhanced PI3K/AKT/mTOR signal signature

city: Wuhan

first: Xindi

state: Hubei

address: No.1277 Jiefang Avenue

department: Institute of Hematology

institute: Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Chimeric antigen receptor (CAR) natural killer (NK) cell therapy has demonstrated safety and feasibility in clinic; yet, limited efficacy resulted from intrinsic dysfunction and extrinsic depression remains to be addressed. T cells provide a multifaceted complementation to NK cell-mediated response. Here, we designed a novel CD19-targeted CAR-NK armored with secreted interleukin (IL) -15 and CCL21 (15x21 CAR-NK) that are capable of recruiting and cooperating with T cells. These 15x21 CAR-NK cells possess excellent capacities for cytotoxicity, cytokine production, and effector molecule expression in vitro. The cooperation with T cells presents benefits of alleviating mutual exhaustion and boosting the expression of effector molecules/receptors, thus promoting the elimination of tumor cells efficiently. In addition, 15x21 CAR-NK cells were also highly enriched PI3K/AKT/mTOR pathway, associating with downstream pro-survival signaling, anti-apoptosis ability, and mitochondrial fitness. Collectively, our study highlights the intrinsic superiority and extrinsic T-cell cooperative advantages of 15x21 CAR-NK cells, providing a promising strategy for NK-cell based immunotherapy.

overall_design: CAR-NK cells were generated by lentivirus transfecting NK-92 cell line. RNA sequencing was performed for 4 kinds of NK cells, including untransduced NK, CAR-NK, 15 CAR-NK, and 15x21 CAR-NK cells.

first: Heng

last: Mei

first: Yu

last: Hu


title: A trimeric USP11-USP7-TCEAL1 complex stabilizes paused RNAPII to sustain oncogenic transcription [RNA-seq]

summary: During early transcription, RNA polymerase II (RNAPII) undergoes a series of structural transitions controlled by cyclin-dependent kinases. Whether protein ubiquitylation and proteasomal degradation affect the fate of RNAPII at core promoters is less well understood. Here we show that the deubiquitinating enzyme USP11 and its heterodimeric partner USP7 form a trimeric complex with TCEAL1, a member of the poorly understood TCEAL (TCEA/TFIIS-like) protein family. TCEAL1 shares sequence homology with the RNAPII interaction domain of the TCEA/TFIIS elongation factor, which controls the fate of backtracked RNAPII. TCEAL1 stabilizes complexes of USP11 with USP7 and with RNAPII. TCEAL1 is recruited to core promoters upon RNAPII pausing and globally enhances the chromatin association of paused RNAPII. Mechanistically, the USP11/USP7/TCEAL1 complex competes with TFIIS for binding to core promoters and protects RPB8, an essential subunit of RNAPII, from degradation, likely preventing TFIIS-mediated transcript cleavage and RNAPII disassembly. In neuroblastoma and other tumors, TCEAL1-dependent genes define a TGF-beta-dependent gene expression program that is characteristic of mesenchymal and invasive tumor cell types, suggesting that the USP11/USP7/TCEAL1 trimer stabilizes paused RNAPII to support a critical oncogenic gene expression program.

overall_design: Using ChIP-sequencing, we assessed changes in the binding of TCEAL1, TFIIS, total RNA Polymerase II and Ser2-phophorylated RNA Polymerase II to chromatin in SHEP cells under control conditions and after exogenous expression of an OHT-activated MYCN-ER construct. The SHEP cells used in the various different experiments further contained either a Dox-inducible shRNA targeting TCEAL1 or an constitutive exogenous overexpression of HA-tagged TCEAL1 (either wild-type or mutant). In some experiments, SHEP cells were also treated with the CDK7 or CDK9 inhibitors THZ1 or NVP-2, respectively. In addition, poly(A)-RNA-sequencing was used for differential gene expression analysis in SHEP cells with an OHT-activated MYCN transgene and a Dox-inducible shRNA targeting TCEAL1.

first: Peter

last: Gallant

first: Steffi

last: Herold

first: Giacomo

last: Cossa

first: Francesca

last: Conte

first: Jan

last: Koster

first: Florian

last: Sauer

first: Christina

last: Schuelein-Voelk

first: Carsten

last: Ade

first: Raphael

last: Vidal

first: Caroline

last: Kisker

first: Rogier

last: Versteeg

first: Petra

last: Beli

first: Seychelle

last: Vos

last: Buechel


title: Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells [bulk RNA-seq]

city: Barcelona

first: Xoel

last: Mato Blanco

state: Barcelona

address: Doctor Aiguader, 88

department: Neurogenomics

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.

overall_design: To explore whether the mechanisms acting in ASD NSCs are persistent as the cells traverse cortical maturation, control and ASD NSCs were serially passaged with varying FGF2 doses or differentiated, and samples were subjected to bulk RNA-seq.

first: Suel-Kee

last: Kim

first: Alexandre

last: Jourdon

first: Shaojie

last: Ma

first: Andrew

last: Tebbenkamp

first: Fuchen

last: Liu

first: Alvaro

last: Duque

first: Flora

last: Vaccarino

first: Nenad

last: Sestan

first: Carlo

last: Colantuoni

first: Pasko

last: Rakic

first: Gabriel

last: Santpere

first: Nicola

last: Micali


title: The splicing factor Acin1 is essential for embryonic development but has limited effects on muscle structure and homeostasis

city: Toon

first: Mamoru

last: Aoto

state: Ehime

address: 454 Shitsukawa

department: Department of Circulatory Physiology

institute: Ehime University Graduate School of Medicine

summary: Apoptotic chromatin condensation inducer 1 (Acin1) is an RNA-binding protein involved in the regulation of alternative splicing, but its physiological function remains unclear. Global deletion of Acin1 causes embryonic lethality around E11.5, with mutants exhibiting developmental delays and increased apoptosis. Using conditional knockout mice, we found that skeletal muscle myofiber-specific Acin1 knockout mice (Acin1 MKO) are viable and fertile and that Acin1 MKO mice show enlarged myofibers and ongoing muscle damage and regeneration, characterized by increased central nuclei and embryonic myosin heavy chain expression. RNA-seq analysis revealed that Acin1 deletion altered the expression and splicing patterns of genes crucial for muscle function. Notable changes included modified splicing of genes associated with muscle disease and mitochondrial function, often resulting in the expression of gene variants typical of immature or diseased muscle. These findings suggest that Acin1 is essential for embryonic development and has limited effects on muscle structure and homeostasis via its regulation of gene expression and alternative splicing.

overall_design:
In order to study the function of Acin1 in skeletal muscle, we created a skeletal muscle fiber-specific Acin1 knockout mouse.
We isolated RNA from the anterior tibialis muscle of control and knockout mice and performed RNA-seq to analyze gene expression profiling.
We also analyzed the selective splicing events that had changed between control and knockout mice.


title: The USP11/TCEAL1 complex promotes transcription elongation to sustain oncogenic gene expression in neuroblastoma [ChIP-seq II]

first: Martin

last: Eilers

overall_design: One goal of the study was to the occupancy of RNA polymerase 2 and phosphorylated (Ser2), elongating RNA polymerase 2 upon depletion of USP11, and USP7 with/without the activation of MYCN

first: Markus

last: Dehmer

first: Katrin

last: Trunk

first: Gabriele

last: Büchel


title: Resolvin D1–mediated cellular crosstalk protects against MASH [Bulk RNA-seq]

city: Los Angeles

first: Bishuang

last: Cai

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

summary: Recent studies have highlighted the beneficial effect of resolvin D1 (RvD1), a DHA-derived specialized pro-resolving mediator, on metabolic dysfunction-associated steatohepatitis (MASH), but the underlying mechanisms are not well understood. Our study aims to determine the mechanism by which RvD1 protects against MASH progression. RvD1 was administrated to MASH mice, followed by bulk and single-cell RNA sequencing analysis. Primary cells including bone marrow-derived macrophages (BMDMs), Kupffer cells, T cells, and primary hepatocytes were isolated to study the effect of RvD1 on inflammation, cell death, and fibrosis regression genes. RvD1 administration improved MASH features including reducing inflammation, cell death, and liver fibrosis. Mechanistically, RvD1 reduced inflammation by suppressing the stat1-cxcl10 signaling pathway in macrophages and prevented cell death by alleviating ER stress-mediated apoptosis in hepatocytes. Moreover, RvD1 induced Mmp2 and decreased Acta2 expression in hepatic stellate cells (HSCs), and promoted Mmp9 and Mmp12 expression in macrophages, leading to fibrosis regression in MASH. RvD1 reduced stat1-mediated pro-inflammatory response, mitigated ER stress-induced apoptosis, and promotes MMP-mediated fibrosis regression in MASH. Thus, our study highlights the therapeutic potential of RvD1 for MASH.

overall_design: Total liver RNA from MASH+RvD1 mice was extracted for RNA-sequencing

first: Xin

last: Huang


title: A trimeric USP11-USP7-TCEAL1 complex stabilizes paused RNAPII to sustain oncogenic transcription [ChIP-seq]

first: Peter

last: Gallant

first: Steffi

last: Herold

first: Giacomo

last: Cossa

first: Francesca

last: Conte

first: Jan

last: Koster

first: Florian

last: Sauer

first: Christina

last: Schuelein-Voelk

first: Carsten

last: Ade

first: Raphael

last: Vidal

first: Caroline

last: Kisker

first: Rogier

last: Versteeg

first: Petra

last: Beli

first: Seychelle

last: Vos

last: Buechel


title: Defining neuronal responses to the neurotropic parasite Toxoplasma gondii

status: Public on Apr 24 2025

city: Tucson

first: Anita

last: Koshy

state: AZ

address: 1657 E Helen St

institute: University of Arizona

summary: A select group of pathogens infect neurons in the brain. Prior dogma held that neurons were "defenseless” against infecting microbes, but many studies suggest that neurons can mount anti-microbial defenses. However, a knowledge gap in understanding how neurons respond in vitro and in vivo to different classes of micro-organisms remains. To address this gap, we compared a transcriptional dataset derived from primary neuron cultures (PNCs) infected with the neurotropic intracellular parasite Toxoplasma gondii with a dataset derived from neurons injected with T. gondii protein in vivo. These curated responses were then compared to the transcriptional responses of PNCs infected with the single stranded RNA viruses West Nile Virus (WNV) or Zika Virus (ZKV). These analyses highlighted a conserved response to infection associated with chemokines (Cxcl10, Ccl2) and cytokines (interferon signaling). However, T. gondii had diminished IFN-α signaling in vitro compared to the viral datasets and was uniquely associated with a decrease in neuron-specific genes (Snap25, Slc17a7, Prkcg). These data underscore that neurons participate in infection-induced neuroinflammation and illustrate that neurons possess both pathogen-specific and pathogen-conserved responses.

overall_design: RNA seq profiling of E174 cortical neurons harvested from Ai6(RCL-ZsGreen) mice. Ten days post harvest, neurons were either infected with an MOI of 5 of type II (Prugniaud (PRU)) Toxoplasma gondii or left uninfected. RNA was harvested 24 hpi. Three biological replicates were performed for 3 samples of infected, primary cortical neurons and 3 samples of uninfected primary cortical neurons.

first: Hannah

last: Johnson

first: Joshua

last: Kochanowsky


title: Resolvin D1–mediated cellular crosstalk protects against MASH [scRNA-seq]

first: Bishuang

last: Cai

overall_design: Single-cell RNA-seq analysis of liver non-parenchymal cells in mice with Chow-diet and FAT-MASH diet with vehicle and RvD1 treatment.

first: Xin

last: Huang


title: Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells [scRNA-seq]

first: Xoel

last: Mato Blanco

overall_design: To investigate the influence of intrinsic genetic factors on an individual’s early brain development, we newly generated NSCs from iPSCs derived from three idiopathic ASD patients (#375, #384, #434) and three controls (#290, #311, #317). Then, we differentiated NSCs into neurons and performed scRNA-seq 8 days after the differentation induction.

first: Suel-Kee

last: Kim

first: Alexandre

last: Jourdon

first: Shaojie

last: Ma

first: Andrew

last: Tebbenkamp

first: Fuchen

last: Liu

first: Alvaro

last: Duque

first: Flora

last: Vaccarino

first: Nenad

last: Sestan

first: Carlo

last: Colantuoni

first: Pasko

last: Rakic

first: Gabriel

last: Santpere

first: Nicola

last: Micali


title: RNA-seq analysis in hepatocyte-specific Atg7-knockout mice with different p62 mutations

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

institute: Tokyo Women's Medical University

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

overall_design: Refer to individual Series


title: A trimeric USP11-USP7-TCEAL1 complex stabilizes paused RNAPII to sustain oncogenic transcription

first: Martin

last: Eilers


title: A zinc finger-dependent, PRDM13-driven mechanism regulates retinal progenitor cell fate from mouse embryonic stem cells via WNT signaling

city: ANN ARBOR

first: Yuanhao

state: MI

address: 1418 McIntyre st

institute: University of Michigan

summary: The transcriptional regulation underlying eye field (retinal primordium) development requires precise control, yet the mechanisms guiding lineage-specific differentiation within the central nervous system (CNS) remain incompletely understood. Using neuroectoderm (NE) organoids derived from mouse embryonic stem cells, we investigate the role of PRDM13 in eye field specification. We demonstrate that Prdm13 expression inhibits RX+ eye field fate but permits non-eye field NE differentiation, an effect dependent on its first and second zinc finger domains. Prdm13 activates the WNT/β-catenin signaling pathway during differentiation, leading to downregulation of key transcription factors crucial for establishing the eye field. Pharmacological inhibition of WNT signaling abolishes PRDM13-mediated suppression, restoring RX+ eye field differentiation. Our work reveals a previously undescribed PRDM13-WNT signaling axis that regulates lineage-specific neural differentiation of embryonic stem cells.

overall_design: RNA-seq profiling of day 6 mouse eye field/retinal progenitor organoids harboring Dox inducible FLAG-PRDM13 were treated with or without Dox.

first: Brian

last: Basinski

first: Huang

last: Yuanhao

first: Rao

last: Rajesh


title: The prostacyclin receptor PTGIR is a NRF2-dependent regulator of CD8 T cell exhaustion

city: Grand Rapids

first: Russell

last: Jones

address: 333 Bostwick Ave NE

department: Department of Metabolism and Nutritional Programming

institute: Van Andel Insitute

summary: The progressive decline of CD8 T cell effector function, also known as T cell “exhaustion” (Tex), is a major contributor to immune evasion in cancer, yet the molecular mechanisms that promote this decline remain poorly understood. Here, we identify the prostaglandin I2 receptor (PTGIR) as a cell-intrinsic driver of CD8 T cell dysfunction. Transcriptional profiling of dysfunctional CD8 T cells from chronic infection and cancer reveals enrichment of the Kelch-like ECH-associated protein 1 (KEAP1)-Nuclear factor erythroid 2-related factor 2 (NRF2) signaling axis, which mediates cellular adaptations to oxidative stress, in terminally exhausted (Tex-term) CD8 T cells. Increasing NRF2 activity in CD8 T cells (via conditional deletion of KEAP1) promotes increased glutathione production and antioxidant defense yet accelerates the development of terminally exhausted (PD-1+/TIM-3+) CD8 Tex cells in response to chronic infection or tumor challenge. NRF2 promotes the increased expression of PTGIR, a receptor for the circulating eicosanoid prostacyclin, in CD8 T cells. Silencing PTGIR expression restores the anti-tumor function of KEAP1-deficient CD8 T cells. Moreover, lowering PTGIR expression in CD8 T cells both reduces terminal exhaustion and enhances T cell effector responses (i.e. IFN-gamma and granzyme production) to chronic infection and cancer. Mechanistically, PTGIR signaling blunts both bioenergetic metabolism and effector cytokine production in CD8 T cells and promotes a Tex cell signature marked by high expression of interferon-stimulated genes (ISGs). Together, these results identify the prostacyclin receptor PTGIR as an NRF2-regulated immune checkpoint that regulates CD8 T cell fate decisions between effector and exhausted states.

overall_design: bulk RNA-seq profiling of Keap1 KO CD8 T cells treated with iloprost (prostacyclin mimetic; 5 µM) and vehicle (DMSO) for 24h

first: Michael

last: Dahabieh

first: Zhen

last: Fu

first: Rusty


title: RNA-seq analysis in hepatocyte-specific Atg7-knockout mice with different p62 mutations [RNA-seq_S351A]

summary: To investigate global proteome changes dependent on on KEAP1-p62 binding in vivo

overall_design: We performed cytoplasmic proteome profiling.

first: Nozomi

last: Shinomiya

first: Masaaki

last: Komatsu

first: Tomoaki

last: Koga


title: Combined therapy with DR5- targeting antibody-drug conjugate and CDK inhibitors as a novel strategy for advanced MSS and MSI-H colorectal cancer

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

summary: Targeted therapies for advanced microsatellite stable (MSS) subtypes of colorectal cancer (CRC) continue to present significant clinical challenges. Death receptor 5 (DR5/TRAIL-R2) is an apoptotic receptor frequently overexpressed in various cancers. Evidence suggests that DR5-targeting antibody drug conjugates (ADC) show promising efficacy in several cancers. In this study, we demonstrated DR5 as a clinically significant target for CRC by analyzing tissue microarrays from advanced CRC cohorts (473 MSS cases and 36 MSI-H cases), as well as data from a TCGA cohort comprising 418 cases. Our novel clinical-stage DR5-targeting ADC, Oba01, designed to deliver the microtubule-disrupting agent MMAE, shows superior therapeutic efficacy across various CRC cell lines, patient-derived xenografts (PDXs), and corresponding organoids (PDXOs), regardless of their MSS or MSI-H status. Importantly, our functional RNAseq and proteomic analysis of the impact of Oba01 on global gene expression revealed that the cell cycle pathway and cyclin-dependent kinases (CDKs) are mechanistically synergistic targets of the drug's effects. Supporting this idea, we presented solid evidence to show Oba01 and abemaciclib, a FDA-approved CDK4/6 inhibitor for metastatic breast cancer, substantially synergize across various clinically relevant models derived from advanced CRC patients with both MSS and MSI-H status, in both in vitro and in vivo settings. The fact that this synergy spans multiple CDK inhibitors further highlights the potential of combining DR5-mediated delivery of MMAE with CDK inhibition as a novel therapeutic strategy for advanced CRC patients, especially those with the challenging to treat MSS subtype.

first: Dongdong

last: Zhou

first: Er’jiang

last: Tang

first: Wenjun

last: Wang

first: Youban

last: Xiao


title: Mucinous Cystic Neoplasms of the Pancreas and Liver share a similar DNA methylation profile with mucinous ovarian tumors

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

institute: Charité - Universitätsmedizin

type: Methylation profiling by genome tiling array

summary: Mucinous cystic neoplasms (MCN) remain a major riddle in hepato-pancreato-biliary pathology. These cystic tumors are defined by their mucinous epithelium and ovarian-like stroma, with an estimated 10% risk of progression to invasive carcinoma. The origin of the ovarian stroma remains a subject of debate. In this study, we conducted immunohistochemical profiling, targeted DNA sequencing, and genome-wide DNA methylation analysis on a cohort of 15 pancreatic MCNs (MCN-P) and 6 hepatic MCNs (MCN-L). Unsupervised analysis of DNA methylation profiles of pancreatic neoplasms (11 entities and normal pancreatic tissue from 224 unique samples) revealed that MCN-P predominantly forms a distinct group. In the DNA methylation landscape of liver tumors, encompassing 5 tumor types and normal bile duct tissue from 136 unique samples, MCN-L demonstrated a specific methylation profile when compared to all other entities. Furthermore, within the DNA methylation landscape of ovarian tumors—featuring 5 tumor types, normal fallopian tube, and normal ovarian tissue from 90 unique samples—we found that both MCN-P and MCN-L grouped with mucinous ovarian carcinoma and mucinous borderline ovarian tumors. Notably, low-grade MCNs exhibited greater DNA methylation similarities to mucinous borderline ovarian tumors, while high-grade or invasive MCNs were primarily associated with mucinous ovarian carcinomas. When analyzing all samples together (19 tumor types and 4 normal tissue types, n = 430), MCNs similarly grouped with mucinous ovarian tumors and normal ovarian tissue. Additionally, in anetwork analysis of differentially methylated probes indicated that MCN-P and MCN-L share significant methylomic traits, closely resembling mucinous ovarian tumors. In conclusion, our findings highlight that MCN-P and MCN-L are distinct entities in the landscape of pancreatic and hepatic tumors and show DNA methylation profile similarities with mucinous ovarian tumors, suggesting a potential common origin.

overall_design: Analysis of MCN-P and MCN-L FFPE samples through immunohistochemistry, targeted DNA sequencing, and genome-wide DNA methylation profiling. DNA methylation analysis was performed using Illumina Infinium MethylationEPIC v1 BeadChip array.

first: Teodor

last: Calina


title: BRAF/MEK Inhibition Induces Cell State Transitions Boosting Immune Checkpoint Sensitivity in BRAFV600E-mutant Glioma

city: Stanford

first: Claudia

middle: Katharina

last: Petritsch

address: G1115 Lorry. Lokey Stem Cell Research Bl, 265 Campus Drive, Stanford University

overall_design: scRNA-seq analysis of BRAFV600E-mutated HGG was performed using RCAS-BRAF mouse model following BRAFi+MEKi and/or ICI treatment.

first: YL

last: Xing

first: ZP

last: Feng

first: X

last: Ji

first: D

last: Hambardzumyan

first: C