title: Inflammation awakens dormant cancer cells by modulating epithelial-mesenchymal phenotypic state [scRNA-Seq]

overall_design: For the samples of day3 or day7 control, Sum159 ITGB4 low clone 1 cells were injected into the lungs of mice through tail vein. At day 6 or day 10, lungs were harvested and dissociated into single cell suspension and sent for scRNA sequencing.  For the samples of day 3 or day 7 bleomycin, Sum159 ITGB4 low clone 1 cells were injected into the lungs of mice through tail vein. 3 days later,  mice were administrated with bleomycin by intratracheal instillation. After 3 days or 7 days of bleomycin administration, lungs were harvested and dissociated into single cell suspension and sent for scRNA sequencing.


title: Transcriptomic Profiling of Small Molecule Atf6 Modulators in the Retina

status: Public on Aug 19 2025

city: Stanford

first: Angela

last: Galdamez

state: California

address: 450 Jane Stanford Way

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: The Unfolded Protein Response (UPR) maintains endoplasmic reticulum (ER) homeostasis and is essential for retinal health. Activating Transcription Factor 6 (ATF6) controls a key UPR branch and upregulates genes that mitigate ER stress. Small molecule modulators of ATF6 have been characterized in cell culture models that increase or decrease the amount of the cleaved, transcriptional activator domain of ATF6 generated from the full-length precursor. However, the effects of these small molecule ATF6 modulators remains unclear in vivo, in part because of the lack of antibodies that robustly detect the cleaved, activated form of ATF6 in model organisms like mice. Here, we used targeted RNA sequencing (RNA-seq) to assess the transcriptional response to intraocular delivery of Ceapin-A7 (an ATF6 inhibitor) and AA147 (an ATF6 activator) in the mouse retina. Using this strategy, we demonstrate that Ceapin-A7 significantly suppressed ATF6 transcriptional targets, whereas AA147 induced ATF6-regulated genes in retinal tissue of the eye. We also show that neither small molecule ATF6 modulator caused retinal cell death, compromised vision, or triggered ER stress by histology, functional testing, and transcriptional analysis. These results identify a transcriptional strategy to sensitively detect and quantify Ceapin-A7 and AA147 modulation of ATF6 in vivo. These findings also identify non-toxic conditions for further in vivo evaluation of small molecule ATF6 modulators in mouse vision loss disease models linked to ER stress.

overall_design: Two small molecule proteostasis modulators were investigated: Ceapin-A7 (ATF6 inhibitor) and AA147 (ATF6 activator), with Tunicamycin as a positive control. At postnatal day 30, C57BL/6J mice were intravitreally injected with each compound (10 μM). For the control treatment, both eyes of each animal were injected with 1 μL of saline containing 0.05–0.1% DMSO. Eyes were collected at 24 hours, 3 days, and 7 days post-injection for safety and efficacy tests. Retinal tissues were analyzed using immunohistochemistry, TUNEL staining, and electroretinography, and Bulk-RNA sequencing.

first: Monica Sophia

last: Aguilar-Diaz

first: Leon

last: Chea

first: Masako

last: Le

first: Soyoung

last: Park

first: Hyejung

last: Min

first: Eun-Jin

last: Lee

first: Jonathan H.

last: Lin


title: H4K16ac is dispensable for mammalian transcriptional control but necessary for a faithful genome duplication program.

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The PRC2 associated factor Epop is required for Hox genes regulation during axial development in mice

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: The Polycomb repressive complex 2 (PRC2) is an essential modulator of gene repression. We previously reported that in mouse embryonic stem cells (mESCs), PRC2 associates with ElonginB/C through EPOP, allowing for low-level expression of target genes. Here we investigate the role of Epop in vivo by generating a mouse knockout model: we show that Epop null mice are viable and fertile, but display highly penetrant posterior homeotic transformations of the axial skeleton. Consistently, Epop depleted embryos present a shift of the anterior boundary of expression of certain Hox genes. Tissue-specific RNA-seq in embryos suggest that the defect in Hox activation originates already at the level of the presomitic mesoderm (PSM). Overall, our findings indicate that Epop is specifically required for correct body patterning along the antero-posterior axis, by preventing premature activation of the Hox genes.

overall_design: 8 paired-end RNA-seq experiments from the posterior part of the tailbud of 4-5 somite-matched E8.5 embryos(WT means wild-type, KO means EPOP KO)

first: Arantxa

last: Gutierrez

first: Ivano

last: Mocavini

first: Luciano

last: Di Croce


title: The developmental emergence and stem cell-based renewal of the intestinal telocyte niche

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

country: China

institute: National Institute of Biological Sciences, Beijing

summary: The intestinal telocytes that reside beneath the intestinal epithelium exert niche-supporting roles for intestinal stem cells (ISCs) and their progenies. They are heterogenous cells compartmentalized along the crypt-villus axis, but the lineage relationships and mechanisms governing the maintenance of this telocyte population remain poorly understood. Through single cell analysis of mouse small intestine development, here we identify a distinct subset of Foxl1+ mesenchymal cells marked by LIM Domain Only 3 (Lmo3), whose emergence at embryonic day E13.5-14.5 precedes the initiation of villus morphogenesis and the appearance of Lgr5+ ISCs. Later on, these villus-associated telocytes undergo proliferation and expansion, extending their presence to both villus and intervillus regions. After birth, the distribution of the Lmo3+ telocytes gradually becomes confined to the isthmus region, where they persist as long-lived cells and slowly give rise to the progenies that migrate either up- or down-wards and differentiate into villus- or crypt-associated telocytes, respectively. The Lmo3+ cells are responsive to intestinal damage and ablation of these cells compromises the epithelial repair process. Thus, the Lmo3+ cells residing in the isthmus region of the adult small intestine represent a population of telocyte stem cells (TeloSCs) that regulate telocyte niche homeostasis and regeneration. The single cell delineation of the ISC niche emergence and the discovery of TeloSCs open up new avenues for understanding the roles of the mesenchymal environment in intestinal development and diseases.

overall_design: Embryonic mouse samples were obtained from timed mating. E0.5d was defined as the morning of the day when the copulatory plug was observed. For embryonic (E12.5d, E13.5d, E14.5d, and E15.5d) samples, several small intestines from many mice were mixed in tissue pooling due to the small sample size, with living cells collected through FACS (Biorad). For the E19.5d samples, small intestines were collected from the middle region of the small intestine from individual mice. For Lmo3_E19.5 samples, Lmo3-CreERT2;Ai6 mice were injected with 120mg/kg tamoxifen each day for three days (E13.5-E15.5), small intestines were then sampled at E19.5d collectively from gravid mice after euthanasia and ZsGreen1+ cells were collected through FACS.

first: Daxin

last: Jiang

first: Guoli

last: Zhu

first: Yongchao

last: Zhang

first: Jiawen

last: Wang

first: Tao

last: Cai

first: Rongwen

last: Xi


title: Multi-omics data reveal the origin of cardiac myxoma

status: Public on Aug 18 2025

city: Chengdu

first: Xiaoping

last: Li

state: Sichuan

address: 32 West 2nd Section, First Ring Road, Qingyang District, Chengdu, Sichuan Province, China

institute: Sichuan Provincial People's Hospital

summary: Cardiac myxoma, the most common primary cardiac tumor, presents significant challenges due to its heterogeneous cellular composition and poorly defined signaling mechanisms. In this study, we applied single-nucleus RNA sequencing (snRNA-seq) to cardiac myxoma and matched normal cardiac tissues to elucidate the tumor’s cellular origin and molecular characteristics. Our analysis provides strong evidence that myxomas arise from endothelial cells. Abnormal endothelial-to-mesenchymal transition (EndMT) contributes to the coexistence of endothelial and mesenchymal phenotypes, while activation of the MET-PTK2 signaling axis appears to drive tumor progression. Pseudotime trajectory analysis revealed dynamic transitions from endothelial-mesenchymal states to metabolically active phenotypes, uncovering distinct myxoma subtypes with potential therapeutic relevance. This study highlights the value of snRNA-seq in resolving the cellular heterogeneity of rare cardiac tumors and provides a molecular framework for developing personalized therapies.

overall_design: Fresh cardiac myxoma and matched normal cardiac tissues were collected from surgical resections. Nuclei were isolated from frozen samples and subjected to single-nucleus RNA sequencing using the 10x Genomics Chromium platform.

first: Shengzhong

last: Liu

first: Wanfeng

first: Huajun

last: Sun

first: Chenqing

last: Zheng

first: Keli

last: Huang

first: Chengming

last: Fan

first: Rensheng

last: Lai

first: Mingzhu

last: Yin

first: Jie

last: Lan

first: Xiushan

last: Wu

first: Longke

last: Ran


title: single-cell RNA-seq dataset of P1 and P7 mice hearts.

city: Oxford

first: Robin

last: Choudhury

address: Level 6 West Wing, John Radcliffe Hospital

department: Department of Cardiovascular Medicine

institute: University of Oxford

summary: The study aims to understand the transcriptomic changes at single-cell level in P1 and P7 mice hearts.

overall_design: Hearts from P1 and P7 mice were harvested, digested and single-cell suspension prepared from them. These were then sequenced using 10X genomics platform.

first: Choudhury

last: Robin

first: Pezzolla

last: Daniela

first: Mohan

last: Kshitij

first: Riley

last: Paul


title: CRISPR/Cas9-mediated suppression of A4GALT rescue endothelial cell dysfunction in a human induced pluripotent stem cell derived fabry disease vasculopathy model

city: Seoul

first: Seung Yun

last: Chae

address: 222 Banpo-daero, Seocho-gu

country: South Korea

institute: The catholic university of korea

summary: This study investigated the efficacy of CRISPR/Cas9-mediated A4GALT suppression in rescuing endothelial dysfunction in Fabry disease endothelial cells (FD-ECs) derived from human induced pluripotent stem cells (hiPSCs). We differentiated hiPSCs (WT (wild-type), WTC-11), GLA-mutant hiPSCs (GLA-KO, CMC-Fb-002), and CRISPR/Cas9-mediated A4GALT-KO hiPSCs (GLA/A4GALT-KO, Fb-002-A4GALT-KO) into ECs and compared FD phenotypes, and endothelial dysfunction. We also analyzed the effect of A4GALT suppression on the reactive oxygen species (ROS) formation, and transcriptome profiles through RNA sequencing. GLA-mutant hiPSC-ECs (GLA-KO and CMC-Fb-002) showed downregulated expression of EC markers and significantly reduced α-GalA expression, increased Gb-3 deposition, and intra-lysosomal inclusion bodies. However, CRISPR/Cas9-mediated A4GALT suppression in GLA/A4GALT-KO and Fb-002-A4GALT-KO hiPSC-ECs increased the expression of EC markers and rescued these FD phenotypes. GLA-mutant hiPSC-ECs failed to form tube-like structure in tube formation assays, and migration of cells into the scratched wound area were significantly decreased. In contrast, A4GALT suppression improved tube formation and cell migration capacity. In GLA-KO hiPSC-ECs, western blot analysis revealed downregulated MAPK, and AKT phosphorylation, while SOD and catalase were upregulated. However, suppression of A4GALT restored these protein alterations. RNA sequencing analysis demonstrated significant transcriptome changes in GLA-mutant EC especially in angiogenesis, cell death and cellular response to oxidative stress, and they were effectively restored in GLA/A4GALT-KO hiPSC-ECs. CRISPR/Cas9-mediated A4GALT suppression rescued FD phenotype and endothelial dysfunction in GLA-mutant hiPSC-ECs, presenting a potential therapeutic approach for FD-vasculopathy.

overall_design: Comparative analysis of gene expression profiles in human induced pluripotent stem cells (hiPSCs), including wild type, GLA-KO, and GLA/A4GALT KO, using Bulk RNA-seq data.

first: Yoo

middle: J

last: Shin

first: Seung

middle: Y

first: Hanbi

last: Lee

first: Xianying

last: Fang

first: Sheng

last: Cui

first: Sun

middle: W

last: Lim

first: Kang

middle: I

first: Jae

first: Can

first: Chul

last: Yang

first: Byung

middle: H

last: Chung


title: HA-PSF-TFE3 bound regions in HA-PSF-TFE3 inducible HK-2 cells

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: PSF-TFE3 is an oncogenic chimeric transcription factor derived from human TFE3-rearranged renal cell carcinoma. To analyze its genome-wide occupancy, we developed HA-tagged PSF-TFE3-inducible HK-2 cell lines, which expresses HA-tagged PSF-TFE3 in a doxycycline-dependent manner. We determined the binding regions of HA-PSF-TFE3 by ChIPSeq.

overall_design: We performed ChIP-seq analysis with an antibody against HA-tag on HA-PRCC-TFE3-inducible HK-2 cell lines.

first: Takanobu

last: Motoshima

first: Kaushal

last: Asrani

first: Yorifumi

last: Satou


title: Sterility in dnd- Atlantic salmon: testicular and ovarian transcriptome

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: The dnd gene is essential for the development of primordial germ cells during early embryogenesis. Temporal silencing of dnd in Atlantic salmon embryos resulted in the loss of gametes and halted further reproductive development, although some males exhibited external signs of maturation. Transcriptome analyses of germ cell-ablated testes and ovaries revealed genes with important roles in reproduction, as well as genes with previously unknown functions in the gonads, for instance, a large set of genes involved in neural system development.

overall_design: Dnd knockdowns were produced by microinjection of “Gapmer” antisense oligonucleotides at the one-cell stage, targeting the dnd mRNA. Embryos, alevins and fry/juveniles were raised under standard hatchery conditions. Sterility/germ cell ablation was assessed by regular histology, in situ hybridization, qPCR and immunohistochemistry of the germ cell marker Vasa/ddx4. Fish were kept at a photoperiod of daily 6 h light (6L:18D) and water temperature of 5–6°C for eight weeks followed by continuous light and 10°C for six weeks according to established protocols of smoltification control. Samples of dnd knockdowns and control fish were collected at the onset of constant light (TP1) and six weeks later (TP3). At TP3, part of fish was stressed by handling and sampled after 24 hours.

first: Krasnov

last: Aleksei

first: Andersen

last: Øivind

first: Tveiten

last: Helge


title: HOXA5-driven transcriptional program in lung development [ChIP-Seq]

city: Québec

first: Lucie

last: Jeannotte

state: QC

address: 2260, boulevard Henri Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

country: Canada

institute: Université Laval

summary: Despite the fundamental role of Hoxa5 in mouse development revealed by the well-characterized phenotypes of Hoxa5 mutant mice, HOXA5-dependent regulatory networks remain ill-defined. We generated a Hoxa5FLAG epitope-tagged mouse line to perform ChIP-seq experiments and uncover genome-wide occupancy of the HOXA5 protein. This was done in the developing lung tissue, in which Hoxa5 plays a predominant role since Hoxa5-/- mouse mutants die at birth from respiratory defects. ChIP-seq allowed us to define an in vivo HOXA5 binding motif and its widespread genome distribution in the embryonic lung. Combined with ATAC-seq assays and epigenetic analyses, HOXA5 targets were identified. They include Hox genes known to show expression changes in lungs from Hoxa5 null mutant embryos. Moreover, several key actors of lung morphogenesis were found to possess HOXA5-binding sites and appeared as potential targets of HOXA5. Impact of the loss of Hoxa5 function on their expression was confirmed by in situ hybridization. These targets include members of the FGF10, SHH, BMP4 and WNT2 signaling pathways. Altogether, these data unveil the crucial role of HOXA5 in the coordinated control of the signaling networks instructing lung development.

overall_design: A FLAG epitope-tagged Hoxa5 knock-in allele was generated to perform in vivo binding assays for HOXA5. To address genome occupancy by HOXA5 during lung formation, we did chromatin immunoprecipitation followed by sequencing (ChIP-seq) for the HOXA5-FLAG protein in lungs from E15.5 Hoxa5FLAG/FLAG mouse embryos using a FLAG antibody.

first: Béatrice

last: Frenette

first: Josselin

last: Guéno

first: Nicolas

last: Houde

first: Jennifer

last: H. Mansfield


title: Glucagon-like peptide-1 receptor agonism is associated with improved lung cancer outcomes and tumor growth control

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

summary: Emerging evidence indicates a reduced incidence of multiple cancers in users of Glucagon-like peptide-1 receptor agonists (GLP-1RAs), drugs widely used for glycemic control and weight reduction that modulate several key regulators of metabolism. We sought to examine their association with non-small cell lung cancer (NSCLC) outcomes in overweight and obese patients and gain mechanistic insights from mouse models. Two clinical cohorts of overweight and obese NSCLC patients—one undergoing surgical resection (n=1,177, 71 GLP-1RA users) and another receiving immune checkpoint inhibitors (ICIs; n=300, 10 GLP-1RA users), were propensity score matched for relevant covariates and analyzed for clinical outcomes. GLP-1RA use was associated with increased recurrence-free survival in overweight and obese patients (HR=0.41 [95%CI=0.16-1.04], p=0.026) after lobectomy. Further, GLP-1RA treatment reduced tumor burden in obese but not normal-weight mice and altered the frequency and phenotypes of leukocyte populations and gene expression patterns in obese tumors, crucial to cancer progression and anti-tumor immunity. Concurrent GLP-1RA and immunotherapy was associated with improved overall (0.41 [0.16-1.01], 0.027) and progression-free survival (HR=0.31, [0.10-0.94], 0.019) for patients with advanced NSCLC. GLP-1RAs may enhance lung cancer-specific clinical outcomes and augment immunotherapy efficacy. Preclinical evidence suggests this effect is obesity-restricted and mediated by immune modulation of the tumor microenvironment.

overall_design: RNA sequencing was performed on excised, subcutaneous KPN1.1 tumors from obese mice treated with GLP-1RA. At the time of mouse tumor harvest, a fragment was flash frozen and was later used for RNA isolation using the miRNeasy mini kit (Qiagen). The sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) kit (Roche Sequencing Solutions), from 500ng total RNA. Following the manufacturer’s instructions, the first step depletes rRNA from total RNA. After ribosomal depletion, the remaining RNA is DNase-digested to remove any gDNA contamination. Samples are then purified, fragmented, and primed for cDNA synthesis. Fragmented RNA is then reverse-transcribed into first-strand cDNA using random primers. The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. Pure Beads (KAPA BIOSYSTEMS) are used to separate the ds cDNA from the second-strand reaction mix, resulting in blunt-ended cDNA. A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments. Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell. Adapter-ligated libraries are amplified by PCR, purified using Pure Beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.). The DNA libraries are quantified using KAPA Biosystems qPCR kit, and are pooled together in an equimolar fashion, following experimental design criteria. Each pool is denatured and diluted to 350pM with 1% PhiX control library added. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge for 100 paired-end sequencing and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

first: Yendamuri

last: Sai

first: Pachimatla

last: Akhil G.

first: Rosario

last: Spencer R.


title: Functional, sustained recovery of hearing in Otoferlin-deficient mice using DB-OTO, a hair cell-specific AAV based dual vector gene therapy

city: Tarrytown

first: Artur

last: Rego-Costa

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc.

summary: Biallelic loss-of-function variants in the Otoferlin gene (OTOF) lead to congenital severe-to-profound sensorineural hearing loss in both humans and in mice. We developed DB-OTO, a hair cell-specific adeno-associated virus (AAV)-based dual-vector gene therapy designed to provide hearing to individuals with OTOF-related hearing loss. DB-OTO is composed of two AAV1 vectors that reconstitute a functional hOTOF gene expression cassette to form the full-length human OTOF isoform 5. A promoter based on the murine Myosin 15 (mMyo15) gene promoter was engineered to restrict the transgene expression to hair cells. The promoter construct was chosen after comparison of multiple variants using a GFP reporter in ex vivo murine explant models, followed by in vivo studies in wild-type mice and in cynomolgus monkeys. Comparison between the 1.0 kb mMyo15 and a ubiquitous promoter driving expression of hOTOFv5 transgene in mice showed that hair cell-specific expression is critical for safe expression of Otoferlin. DB-OTO induced dose-dependent establishment of auditory brainstem response and OTOF expression in inner hair cells over a 10-fold dose range sustained for at least 3 months in a mouse model of OTOF-deficiency. These data supported the initiation of a Phase 1/2 clinical trial of DB-OTO in pediatric patients with OTOF-related hearing loss.

overall_design: single-cell RNA-seq profiling on the cochleae of WT FVB or Otof+/Q828X mice treated with either AAV1-smCBA-OTOF-v5 or AAV1-1.0kb-mMyo15-OTOF-v5 at a dose of 1e11 vg/ear at mean 7.5 weeks of age

first: Yoojin

last: Chung

first: Seth

middle: D

last: Koehler

first: Sarah

last: Cancelarich

first: Tyler

middle: M

last: Gibson

first: Gabriela

last: Pregernig

first: Lars

last: Becker

first: Quynh-Anh

last: Artinian

first: Joseph

last: Goodliffe

first: Ning

last: Pan

first: Tera

last: Quigley

first: Arun

last: Senapati

first: Peter

middle: G

last: Slade

first: Lillian

last: Smith

first: Kathy

middle: S

last: So

first: Xichun

last: Zhang

first: Carleton

middle: E

last: Corrales

last: Weber

first: Lynn

last: Macdonald

first: Brian

last: Zambrowicz

first: Aris

middle: N

last: Economides

first: Christos

middle: A

last: Kyratsous

middle: C

last: Burns

first: Adam

middle: T

last: Palermo

first: Leah

middle: R

last: Sabin

first: John

last: Lee

first: Vassili

last: Valayannopoulos

first: Jonathon

middle: P

last: Whitton

first: Meghan

last: Drummond


title: DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

summary: How neuronal subtypes are generated at distinct times and proportions during human retinal development is poorly understood. Here, we investigated how rod and cone photoreceptor subtypes develop in human retinal organoids. We find that type 3 iodothyronine deiodinase (DIO3), an enzyme that degrades thyroid hormone (TH), is a master regulator of human photoreceptor developmental timing and cell fate stability. DIO3 is highly expressed in retinal progenitor cells (RPCs) and decreases as cells asynchronously differentiate into neurons, progressively lowering TH degradation during development. DIO3 mutant organoids display precocious S cone, L/M cone, and rod development, increased photoreceptor (PR) density, and conversion of S cones to L/M fate. Cell autonomous and non-autonomous mechanisms regulate DIO3 expression to maintain and locally coordinate levels among cells. In a computational model, a mechanism that couples TH levels and fate specification provides robustness to photoreceptor development compared to a probabilistic, cell-intrinsic mechanism. Our findings suggest a population-based mechanism for photoreceptor subtype developmental timing in which the relative proportion of progenitors to neurons decreases over time to relieve degradation of TH signaling, which advances photoreceptor development.

overall_design: Wildtype human retinal organoids or DIO3∆33 human retinal organoids were lysed into a single nuclei suspension and run on the 10x Genomics Chromium Single Cell System platform using the Single Cell Multiome ATAC + Gene Expression chemistry. Libraries were sequenced on Illumina NovaSeq 6000 and processed through the Cell Ranger pipeline using the GRCh38 reference genome.

first: Christina

last: McNerney

first: Kiara

last: Eldred

first: Ian

last: Glass

first: Tom

last: Reh

first: Nate

last: Lord

first: Arturo

last: Hernandez

first: Seth

last: Blackshaw

first: Robert

last: Johnston Jr


title: HOXA5-driven transcriptional program in lung development [ATAC-Seq]

first: Lucie

last: Jeannotte

overall_design: ATAC-seq assays was performed on lungs from E15.5 wt embryos to define open chromatin regions.

first: Béatrice

last: Frenette

first: Josselin

last: Guéno

first: Nicolas

last: Houde

first: Jennifer

last: H. Mansfield


title: Effect of G2E3 knockout and  SUV39H2 knockout  on gene expression and heterochromatin repeats DNA transcription in HeLa cells.

city: Shanghai

first: Yuanyong

last: Huang

state: Shanghai

address: 500 Dongchuan Road, Shanghai,China

department: School of Life Science

institute: East China Normal University

summary: To investigate the correlation between G2E3 and SUV39H2 in regulating gene expression and heterochromatin repeats DNA transcription, we generated G2E3 knockout HeLa cells line and SUV39H2 knockout HeLa cells line by the CRISPR-Cas9 system essentially as described (Ran et al., 2013), and performed gene expression profiling analysis and repeats DNA transcription profiling analysis using data obtained from RNA-seq.

overall_design:
Comparative gene expression profiling analysis and repeats DNA transcription profiling analysis of RNA-seq data for sgG2E3 control HeLa cells, G2E3 knockout HeLa cells and sgSUV39H2 control HeLa cells, SUV39H2 knockout HeLa cells.
sgG2E3 control HeLa cells is a sgRNA stable cell line that has not been cut by Cas9 protein. In our paper, it is marked as Parental control HeLa cells.

first: Quanlong

last: Jiang

first: Jing-Dong

middle: J

last: Han

first: Jiemin

last: Wong


title: Malat1 regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL-2

city: York

first: Fabiano

middle: Sviatopolk-Mirsky

last: Pais

state: Yorkshire

address: Wentworth Way

department: Biology

institute: University of York

summary: Transcriptomic profiling of Malat1-deficient and WT CD4+ T cells at Day 0 (naïve CD4+ T cells) and Day 2 post-induction of differentiation under Th2 conditions. Naive CD4+ T cells isolated from spleens and lymphnodes of female mice. For Th2 polarisation, purified naïve CD4+ T cells (500,000 cells per well) were stimulated with 10 μg/ml plate-bound anti-CD3ε (clone 145-2C11) and 4 μg/ml soluble anti-CD28 (37.51) in RPMI 1640 in flat-bottom 96-well plates in the presence of 25 ng/ml mouse rIL-4 and 5 μg/ml anti–IFN-γ (XMG1.2).

overall_design: Examination of expression profiles of splenic and lymph node  CD4+ T cells from Day 0 (naive) and Day 2 WT and Malat1-/- cells from female mice using Nanopore RNASeq.

first: Dimitris

last: Lagos

first: Mags

last: Gwynne


title: A conserved H3K14ub-driven H3K9me3 for chromatin compartmentalization

summary: To delineate the relationship between G2E3-catalyzed H3K14ub and H3K9me3 in genome-wide, we performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) for H3K14ub, H3K9me3 and H3K4me3 in Parental (sgG2E3) control HeLa cells and G2E3 KO-10 HeLa cells. Our data  demonstrated that G2E3-catalyzed H3K14ub potentiates H3K9 trimethylation (H3K9me3) by SUV39H and is specifically required for SUV39H compartmentalization and H3K9me3 in pericentromeric heterochromatin. Loss ofG2E3 severely impairs not only pericentromeric heterochromatin organization, but also results in aberrant accumulation of SUV39H and H3K9me3 in numerous euchromatin regions and a widespread transcriptional repression (combined with RNA-seq data).

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me3, H3K9me3 and H3K14ub in Parental （sgG2E3）control  HeLa cells and G2E3 knockout HeLa cells.
sgG2E3 control  HeLa cells is a sgRNA stable cell line that has not been cut by Cas9 protein. In our paper, it is marked as Parental control HeLa cells.


title: Inflammation awakens dormant cancer cells by modulating epithelial-mesenchymal phenotypic state [RNA-Seq]

city: Cambridge

first: Jingwei

last: Zhang

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

summary: The awakening of dormant disseminated cancer cells is responsible for the clinical relapses of patients whose primary tumors have been cured months and even years earlier. In the present study, we demonstrate that dormant breast cancer cells lodged in the lungs reside in a highly mesenchymal, non-proliferative phenotypic state. The awakening of these cells does not occur because of a cancer cell-autonomous process. Instead, inflammation and wound-healing of the surrounding tissue microenvironment causes them to shift from a highly mesenchymal to a quasi-mesenchymal phenotypic state in which they acquire stemness and proliferative ability. Once awakened, these cells can stably reside in this quasi-mesenchymal state and maintain their stemness, doing so without ongoing heterotypic signaling from the lung microenvironment. EGFR ligands released by the cells of the injured tissue microenvironment, including notably M2 type macrophages, promote dormant cancer cells to move toward this quasi-mesenchymal state, a transition that is essential for the awakening process. An understanding of the mechanisms of metastatic awakening may lead in the future to treatment strategies designed to prevent such awakening and resulting metastatic relapse.

overall_design: For the samples of Sum159 ITGB4 low clone 1 beomycin treated, Sum159 ITGB4 low clone 1 induced by LM2 and Sum159 ITGB4 clone 3 induced by LM2, cells were injected into the mouse lungs through tail vein. At the end point of the experiment, lungs were harvested and dissociated into cell suspension. Cell suspension containing tumor cells were cultured in petri dishes overnight, and in the next day tdtomato+ tumor cells were sorted by FACS. RNA samples were extracted from the sorted tdtomato+ tumor cells and sent for sequencing.  For the samples of Sum159 ITGB4 high, Sum159 ITGB4 low clone 1 control and Sum159 ITGB4 low clone 3 control, cells were cultured in petri dishes. RNA samples were extracted from these cells and sent for sequencing.

first: Bingbing

last: Yuan


title: NaCl and urea modulate antiviral CD8+ T cell survival, renal accumulation and response to BKV

city: Bonn

first: Sibylle

last: von Vietinghoff

address: Venusbergcampus 1

country: Germany

institute: University Clinic Bonn

summary: Primary human PBMC were treated with allogenic stimulation and elevated NaCl or Urea concentrations. RNA from sorted CD8 Tcells was analyzed for differential expression in high osmolyte environments.

first: Peyman

last: Falahat

first: Adrian

last: Goldspink

first: Lucia

last: Oehler

first: Jessica

last: Schmitz

first: Julia

last: Miranda

first: Islem

last: Gammoudi

first: Jan Hinrich

last: Bräsen

first: Niklas

last: Klümper

first: Olena

last: Babyak

first: Christian

last: Kurts

first: Herrmann

last: Haller

first: Marieta

last: Toma


title: Transcriptomic profiling of whole tumor biopsies of mPDAC patients in Optimize-1

city: Lund

first: Peter

last: Ellmark

address: Scheelevägen 2, Medicon Village

country: Sweden

institute: Alligator Bioscience AB

summary: This dataset was generated to study  the transcriptomic alterations  in tumor tissue of mPDAC patients from the  Optimize-1 (A-20-1013-C-03), with available RNA-seq data and their associations with clinical efficacy endpoints from the 18-months follow up dataset.

overall_design: After collection, samples underwent formalin fixation followed by paraffin embedding (FFPE samples) and were either stored as FFPE blocks or FFPE tissue slides (ten 4µm slides and six 10µm in thickness), according to Optimize-1 study protocol. RNA from FFPE biopsies was extracted and sequenced via Novaseq6000 (Illumina).

first: David

last: Jimenez

first: Hampus

last: Andersson


title: Computational discovery of conserved RNA structures and functional characterization of a structured lncRNA in Leishmania braziliensis

first: Fabiano

last: Pais

summary: Throughout their life cycle, Leishmania parasites, causative agents of the life-threatening leishmaniasis, alternate between the phlebotomine vector and the mammalian host, encountering significant environmental changes that require rapid adaptation in gene expression for survival. In the absence of conventional promoters for RNA polymerase II and given the polycistronic nature of transcription, gene expression regulation in Leishmania occurs primarily at the post-transcriptional level. Although putative regulatory non-coding RNAs (ncRNAs) have been detected in the transcriptomes of L. braziliensis and other trypanosomatids, their functional role remains poorly understood. Recognizing the critical role of RNA structure in cellular systems, we sought to identify evolutionarily conserved RNA structures. We performed a genome-wide alignment of L. braziliensis genome with closely related genomes, predicting 142 conserved RNA structures, among which 38 overlap with previously identified ncRNA transcripts. One of the putative ncRNAs with a conserved structure, a 407-nucleotide long ncRNA (lncRNA45), was previously shown to be differentially expressed across the lifecycle stages of L. braziliensis. Here, we conducted a functional characterization of lncRNA45 using a knockout line, demonstrating that the transcript is crucial for parasite fitness. Reintroduction of the original lncRNA45 sequence restored the fitness of the knockout cell line to parental levels, whereas a sequence carrying a single nucleotide substitution in the structured locus did not. In vitro pull-down assays with both the original and modified versions of lncRNA45 revealed differences in the profile of lncRNA-binding proteins. Our results indicate that lncRNA45 is enrolled cellular processes of L. braziliensis promastigotes, and this activity, along with its interaction with proteins, depends on its secondary structure. This study underscores the importance of structured lncRNAs in Leishmania and advocates for further research into their regulatory roles and therapeutic potential.

overall_design: HA tagged cell lines were submitted to immunoprecipitation by using HA magnetic beads to capture the HA-tagged proteins and the associated proteins and the RNAs. Each immunoprecipitated protein was checked by western blot and submitted to Mass Spec analysis. The associated RNA content was purified and submitted to library preparation followed by RNA-seq .

first: Carolina Ricce

last: Espada

last: Anthon

first: Rubens D M

last: Magalhães

first: José Carlos Quilles

last: Júnior

first: Natalia

last: Monteiro-Teles

first: Fabiano S

first: Lissur Azevedo

last: Orsine

first: Letícia de

last: Almeida

first: Tânia Paula Aquino

last: Defina

first: Adam

last: Dowle

first: Jan

last: Gorodkin

first: Pegine

last: Walrad

first: Angela Kaysel

last: Cruz


title: Lysosomal reduced thiols are essential for mouse embryonic development

status: Public on Aug 17 2025

city: Charlestown

first: Charles

middle: H.

last: Adelmann

address: Mass Gen Hospital, 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary: While it has been appreciated for decades that lysosomes can import cysteine, its significance for whole-organism physiology has remained uncertain. Recent work identified MFSD12 as a transmembrane protein required for cysteine import into lysosomes (and melanosomes), enabling genetic interrogation of this pathway. Here, we show that Mfsd12 knockout mice die between embryonic days 10.5 and 12.5, indicating that MFSD12 is essential for organogenesis. Mfsd12  loss results in the transcription of genes involved in cellular stress and thiol metabolism. Within lysosomes, imported cysteine is largely oxidized to cystine, which is exported to the cytosol by the CTNS (cystinosin) transporter. However, unlike Mfsd12, loss of Ctns is compatible with viability, suggesting that the essential role of MFSD12 lies not in supplying cystine to the cytosol, but in providing reduced cysteine within the lysosomal lumen. Supporting this model, maternal treatment with cysteamine—a lysosome-penetrant thiol—rescued the development of Mfsd12 knockout embryos, yielding viable adult offspring. These findings establish lysosomal thiol import as a critical metabolic pathway and provide genetic tools to further dissect its physiological and biochemical roles.

overall_design: Whole embryo RNA-seq from embryos 10.0-11.0 days post-fertilization.

last: Sabatini

last: Fisher


title: Transcriptomic profiling of IDR CAR-T cells in the CD19 cancer model.

city: New Haven

first: Xinyan

last: Zhang

state: CT

address: 333 Cedar St

institute: Yale University

summary: Chimeric antigen receptor (CAR)-T cell-based therapies demonstrated remarkable efficacies for treating otherwise intractable cancers, particularly B-cell malignancies. However, existing FDA-approved CAR-Ts were limited by low antigen sensitivity, rendering their insufficient targeting to low antigen-expressing cancers. To improve the antigen sensitivity of CAR-Ts, we engineered CARs targeting CD19, CD22, and HER2 by including intrinsically disordered regions (IDRs) that promote signaling condensation. The CARs fused with IDR from FUS, EWS, or TAF15 triggered enhanced membrane-proximal signaling in the CAR-T synapse, which led to an increased release of cytotoxic factors, a higher killing activity towards low antigen-expressing cancer cells in vitro. Moreover, the IDR CAR-Ts induced improved anti-tumor effects in vivo in both blood cancer and solid tumor models. No elevated tonic signaling was observed in IDR CAR-Ts. Together, we demonstrated IDRs as a new tool set to enhance CAR-T cytotoxicity and to broaden CAR-T’s application to low antigen-expressing cancers.

overall_design: PBMCs were isolated from mice blood. Human T cells were sorted for library preparation and single cell RNA sequence.

first: Tobias

last: Hartwich

first: Miranda

last: Mansolf

first: Yang

last: Yang-Harwich

first: Xiaolei

last: Su


title: Computational Tracking of Cell Origins Using CellSexID from Single-Cell Transcriptomes

status: Public on Aug 16 2025

city: Montreal

first: Qian

last: Li

address: 845 Sherbrooke Street West

institute: McGill University

summary: These datasets support the validation and biological application of CellSexID, a computational method for inferring cell origin in sex-mismatched settings using single-cell RNA sequencing (scRNA-seq) data. CellSexID leverages the expression of sex-linked genes to classify individual cells as male or female, providing an in silico alternative to physical labeling. Two scRNA-seq datasets from sex-mismatched chimeric mouse diaphragm models are included: (i) a validation dataset, in which cell multiplexing labels were applied to establish ground-truth cell origin, and (ii) an experimental dataset, analyzed without labels to demonstrate the method’s applicability in unlabeled settings. Together, these datasets provide a resource for benchmarking computational cell origin tracking methods and for studying immune cell populations in chimeric model systems.

overall_design: The chimeric mouse diaphragm validation dataset for CellSexID was generated using sex-mismatched bone marrow chimeras. Female CD45.2 mice underwent whole-body irradiation with diaphragm shielding, followed by transplantation of male CD45.1 bone marrow. Diaphragm macrophages were isolated by FACS, labeled with Cell Multiplexing Oligonucleotides (female: CMO306; male: CMO305), and processed for single-cell RNA sequencing to provide a reference for cell origin classification. The chimeric mouse diaphragm experimental dataset was prepared using the same protocol, except macrophages were not sex-sorted; instead, cells from each mouse were pooled and labeled with a unique Cell Multiplexing Oligonucleotide to enable mouse-specific identification. In the experimental datasets, FACS sorting and cell preparation were performed on four mice per day over two consecutive days (Day 1 and Day 2), yielding a total of eight mice. All libraries were subsequently prepared and sequenced in a single batch.

first: Huilin

last: Tai

first: Jingtao

last: Wang

first: Jiahui

last: Tan

first: Bowen

last: Zhao

first: Ryann

last: Lang

first: Basil

last: Petrof

first: Jun

last: Ding


title: SFPQ-TFE3 gene fusion reciprocally regulates mTORC1 activity and induces lineage plasticity in a novel mouse model of renal tumorigenesis

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

state: MD

address: 1550 ORLEANS

institute: JOHNS HOPKINS MEDICINE

summary: The MiT/TFE family gene fusion proteins, such as SFPQ-TFE3, drive both epithelial (eg, translocation renal cell carcinoma, tRCC) and mesenchymal (eg, perivascular epithelioid cell tumor, PEComa) neoplasms with aggressive behavior. However, no prior mouse models for SFPQ-TFE3-related tumors exist and the mechanisms of lineage plasticity induced by this fusion remain unclear. Here, we demonstrate that constitutive murine renal expression of human SFPQ-TFE3 using Ksp Cadherin-Cre as a driver disrupts kidney development leading to early neonatal renal failure and death. In contrast, post-natal induction of SFPQ-TFE3 in renal tubular epithelial cells using Pax8 ERT-Cre induces infiltrative epithelioid tumors, which morphologically and transcriptionally resemble human PEComas. As seen in MiT/TFE fusion-driven human tumors, SFPQ-TFE3 expression is accompanied by the strong induction of mTORC1 signaling, which is partially amino acid-sensitive and dependent on increased SFPQ-TFE3-mediated RRAGC/D transcription. Remarkably, SFPQ-TFE3 expression is sufficient to induce lineage plasticity in renal tubular epithelial cells, with rapid down-regulation of the critical PAX2/PAX8 nephric lineage factors and tubular epithelial markers, and concomitant up-regulation of PEComa differentiation markers in transgenic mice, human cell line models and human tRCC. Pharmacologic or genetic inhibition of mTOR signaling downregulates expression of the SFPQ-TFE3 fusion protein and rescues nephric lineage marker expression and transcriptional activity in vitro. These data provide evidence of a potential epithelial cell-of-origin for TFE3-driven PEComas and highlight a reciprocal role for SFPQ-TFE3 and mTOR in driving lineage plasticity in the kidney, expanding our understanding of the pathogenesis of MiT/TFE-driven tumors.

overall_design: RNA-Seq analyses of kidneys from a) 15-day SFPQ-TFE3-LSL; KSP-Cre transgenic mice,  compared to controls  b) Tamoxifen-treated, SFPQ-TFE3-LSL; Pax8-ERT-Cre transgenic mice compared to controls and c) PRCC-TFE3-LSL; KSP-Cre transgenic mice compared to controls

first: Kaushal

last: Asrani

first: Adrianna

last: Amaral

first: Juhyung

last: Woo

first: Sanaz

last: Abadchi

first: Thiago

last: Vidotto

first: Kewen

last: Feng

first: Hans

middle: B

last: Liu

first: Mithila

last: Kasbe

first: Masaya

last: Baba

first: Yuichi

last: Oike

first: Patricia

last: Outeda

first: Terry

last: Watnick

first: Avi

middle: Z

last: Rosenberg

first: Laura S

last: Schmidt

first: Marston

last: Linehan

first: Pedram

last: Argani

first: Tamara

middle: L

last: Lotan


title: Transcriptomic profiling of peripheral blood mononuclear cells (PBMC) from patients with Parkinson’s disease (PD), Spinocerebellar ataxia (SCA2) and control subjects

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: To investigate the role of RNA metabolism in Parkinson’s disease in the etiology of Parkinson’s disease, we conducted a global RNA expression profiling in PBMC of PD and SCA2 patients versus controls.

overall_design: Total RNA was extracted from PBMC of patients and controls subjects. All samples included in the study had a RIN>9. One colour Whole Human Genome 60-mer Oligonucleotide 44K microarrays containing ∼41,000 probes and transcripts covering the entire genome (Agilent Technologies) were used to analyse gene expression in PBMC from control subjects and PD cases according to the procedure we previously described (Mutez et al., 2010). Our results highlight RNA metabolism disturbances in PD and SCA2 patients.

first: M

last: Chartier-Harlin

first: A

last: Nkiliza

first: E

last: Mutez

first: C

last: Simonin

first: F

last: Leprêtre

last: Villenet

last: Figeac


title: FCRL3 is an immunoregulatory receptor that restrains the activation of human memory T lymphocytes

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

summary: To characterize the FcRL3+ T cell subset in memory helper CD4+, CD8+, and CD4+ regulatory lymphocytes, we performed RNA-sequencing analysis using T cells, separated by the expression of FcRL3, from the peripheral blood of 5 healthy donors, stimulated for 3h with PMA and ionomycin to induce cytokine expression.

overall_design: Memory helper CD4+, CD8+ and CD4+ regulatory T cells from 5 independent donors were sorted by the expression of FcRL3. Total RNA was extracted from each sample, used for poly-A library preparation following the SMART-seq2 protocol and sequenced with Illumina NOVASeq 6000 platform.

first: Niccolò

last: Bianchi

first: Silvia

last: Monticelli


title: Oxidized Phosphatidylcholines Activate NOX1-Mediated Oxidative Stress Response and Shift Glucose Metabolism in Cardiac Cells

city: Charlottesville

first: Anna

last: Licznerska

state: Virginia

address: 1340 Jefferson Park Avenue, Pinn Hall 5036

department: Pharmacology

institute: University of Virginia

summary: In cardiometabolic syndrome the development of cardiovascular disease is linked with an increase in systemic oxidative stress. The formation of free radical species leads to the oxidative modification of lipids, including phosphatidylcholines (OxPCs), which have been implicated in the progression of cardiovascular diseases in humans. We found that reducing plasma levels of OxPCs in mice by AAV-mediated hepatic expression of an OxPC-targeting antibody fragment (scFv-E06), resulted in significant transcriptional changes in the heart, particularly affecting genes involved in metabolism, redox processes, and fibrosis. To investigate the response of cardiac myoblasts to OxPCs in vitro, we exposed H9c2 cells to a defined mixture of OxPC species (OxPAPC). Treatment with OxPAPC resulted in transcriptional upregulation of key metabolic and redox-regulatory pathways, most notably genes regulated by the Nrf2 pathway, including heme oxygenase 1 (Hmox1). OxPAPC induced reactive oxygen species (ROS) production in H9c2 cells through activation NADPH oxidase 1 (Nox1), which upregulated the production of oxidized glutathione. Key metabolic changes after exposure to OxPAPC included a shift towards the pentose phosphate pathway (PPP) and suppression of glycolysis, resulting in overall decreased ATP production. Furthermore, OxPAPC downregulated oxidative phosphorylation in H9c2 cells through a mechanism involving activation of the MEK–ERK mitogen-activated protein kinase (MAPK) pathway. Together, these data demonstrate that in vitro cardiac myoblasts respond to OxPCs by upregulating redox regulatory pathways and shifts in cellular energy production. Furthermore, we identify NOX1 as a novel mediator of OxPC-induced redox stress that may induce cardiac cell damage in cardiometabolic syndrome.

overall_design: Bulk RNA sequencing on H9c2 cardiac myoblasts that had been treated with 100 µg/ml OxPAPC for 6 hours.

first: Caitlin M.

last: Pavelec

first: Scott

last: Yeudall

first: Clint M.

last: Upchurch

first: Hannah L.

last: Luviano

first: Kyla N.

last: Mucciarone

first: Norbert

last: Leitinger


title: Age-dependent Zap70 expression in thymocyte regulates selection of the neonatal T reg cell repertoire

status: Public on Aug 15 2025

city: La Jolla

first: Gerald

middle: Patrick

last: Morris

state: CA

address: 9500 Gilman Drive

department: Pathology

institute: University of California San Diego

summary: LAT.G135D mutant mice, in which a glycine residue preceding Y136 is replaced with aspartate. This single amino acid change enhances LAT Y136 phosphorylation, leading to increased PLCg1 activation and augmented calcium signaling with little impact on Erk and NF-kB activation.

overall_design: Splenic CD4 and CD8 T cells were isolated from adult wild-type C57BL/6 and B6.LATG135D mice. Bulk TCR sequence anlaysis was performed.

first: Wan-Lin

last: Lo

first: Parker

last: Dow


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [Whole Genome Sequencing]

city: Oxford

first: Alastair

last: Smith

state: England

address: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Genetic alterations alone cannot account for the diverse phenotypes of cancer cells. Even cancers with the same driver mutation show significant transcriptional heterogeneity and varied responses to therapy. However, the mechanisms underpinning this heterogeneity remain under-explored. Here, we find that novel enhancer usage is a common feature in acute lymphoblastic leukemia (ALL). In particular, KMT2A::AFF1 ALL, an aggressive leukemia subtype with a poor prognosis and a low mutational burden, exhibits substantial transcriptional heterogeneity between individuals. Using single cell multiome analysis and extensive chromatin profiling, we reveal that much transcriptional heterogeneity in KMT2A::AFF1 ALL is driven by novel enhancer usage. Using high resolution Micro Capture-C in primary patient samples, we also identify patient-specific enhancer activity at key oncogenes such as MEIS1 and RUNX2, driving high levels of expression of both oncogenes in a patient-specific manner. Overall, our data show that enhancer heterogeneity is highly prevalent in KMT2A::AFF1 ALL and may also represent a mechanism for driving transcriptional heterogeneity in cancer more generally.

overall_design: Whole genome sequencing of KMT2A::AFF1 cell lines

first: Catherine

last: Chahrour

first: Thomas

last: Milne


title: Neutrophil Degranulation is Increased at Seven Days after Human Intracerebral Hemorrhage,   but not at 72 Hours, and Correlates with Decreased miR-3613 and miR-3690

city: Winston-Salem

first: Carl

last: Langefeld

state: NC

address: 525 Vine

institute: Wake Forest University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Intracerebral hemorrhage (ICH) occurs when there s spontaneous, non-traumatic bleeding into the brain and accounts for 50% of stroke-related mortality. We report mRNA-seq and miRNA-seq in the peripheral blood of ICH patients with three serial samples during the first week after the stroke. Twenty-seven ICH patients were enrolled via 24/7 screening and peripheral blood sampled at <24 hours (baseline), 72 hours (+/-12 hours), and 7 days (+/- 2days) from last known normal. mRNA-seq and miRNA-seq were assessed for differential expression (DE) between the time points and pathways identified via enrichment analysis as well as principal component analysis (PCA) were performed. Our analysis found that neutrophil degranulation was the prominent enriched pathway at 7 days after ICH. miR-3613 and miR-3690 are potential regulators of neutrophil degranulation after ICH.

overall_design: A total of 27 ICH patients were enrolled and 3 serial blood samples were collected for <24 hours, 72 hours and 7 days after stroke. After mRNA and miRNA sequencing, differentially expressed (DE) miRNA and mRNA will be tested between 3 time points: 72 hours vs. baseline, 7 days vs. 72 hours, and 7 days vs. baseline will be tested using pathway analysis.

first: Kyle

last: Walsh

first: Miranda

last: Marion

first: DengFeng

last: Li

first: Hannah

last: Ainsworth

first: Amy

last: Zinnia

first: Xiang

last: Zhang

first: Stacie

last: Demel

first: Brady

last: Williamson

first: David

last: Roh

first: Robert

last: Campbell

first: Frederik

last: Denorme

first: Daniel

last: Woo

middle: D


title: Transcriptomic points of departure for 6PPD-Quinone derived from human Caco-2 and HepG2 cells

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

summary: N-(1,3-Dimethyl butyl)-N′-phenyl-phenylenediamine-quinone (6ppd-quinone) is of emerging concern due to its widespread presence and toxicity to aquatic species. The chemical has been detected in human biofluids though little is known about its effects on human tissues.  The objective of this study was to increase understanding of 6ppd-quinone’s potential human health effects by deriving transcriptomic points of departure (tPOD) values in two human cell lines using the TPD-seq workflow. An EC20 for cytotoxicity was calculated for Caco-2 (104µg/L) but not for HepG2 cells. Even in the absence of cytotoxicity, tPOD values (20th gene, 10th percentile, mode) were calculated in Caco-2 (6.5-25µg/L) and HepG2 (0.36-35µg/L) cells.  These ranges capture values from 16 statistical and bioinformatic tests that examined mapping methods (CLC and Deplexer), algorithms (Limma and DESeq2), and filters (log2FC and BMR). The most common and sensitive genes with calculable benchmark doses (BMDs) in Caco-2 (DPF2, CD44,  PGAP1, GDF15, H4C16) and HepG2 (SLC5A3, DKK1, ARG2, PHLDA1, TM4SF1) cells are listed.  Pathway BMDs were also calculated for Caco-2 (systemic lupus erythematosus, 9.7-18µg/L; alcoholism, 9.7-20µg/L; viral carcinogenesis, 9.3-18.1µg/L), and HepG2 (metabolic pathways, 50-60µg/L) cells.  These findings highlight TPD-seq as an efficient workflow to yield quantitative and mechanistic data relevant for human health risk assessment.

overall_design: Caco-2 and Hep G2 cell lines were exposed to 6ppd-quinone at various concentrations to investigate cytotoxicity and transcriptomics effects.

first: Ke

last: Xu

first: Krittika

last: Mittal


title: Different COVID-19 vaccines induce distinct reprogramming of stromal functions in draining lymph nodes

city: Helsinki

first: Bishwa

middle: Raj

last: Ghimire

address: Tukholmankatu 8

department: Institute for Molecular Medicine Finland

country: Finland

institute: University of Helsinki

summary: The non-leukocytic stromal cells of lymph nodes critically regulate immune responsiveness. However, the effects of different SARS-CoV-2 vaccines on stromal cell biology are unknown. We used single-cell transcriptomics to study early responses of stromal cells in draining lymph nodes after immunizing mice with clinically used COVID-19 vaccines, namely Spikevax®, Comirnaty®, Vaxzevria® and Nuvaxovid™. We found that vaccinations lead to robust transcriptomic changes, including vaccine-selective ones, in the different lymph node stromal cell populations priming the lymph node for the upcoming adaptive immune response.

overall_design: Mice were immunized with COVID-19 vaccines and the draining lymph node stromal cells were isolated with enzymatic digestion. Non-hematopoietic cells were enriched using magnetic beads and the negative fraction, i.e. stromal cells was subjected for droplet-based scRNA-seq.

first: Ruth

last: Fair-Mäkelä

first: Marko

last: Salmi


title: The deubiquitinase OTUD7B ameliorates central nervous system autoimmunity by inhibiting degradation of glial fibrillary acidic protein and astrocyte hyperinflammation

city: Hannover

first: Dirk

last: Schlüter

address: Carl-Neuberg-Str. 1

department: Institute for Medical Microbiology and Hospital Hygiene

institute: Medizinische Hochschule Hannover

summary: Astrocytes are central to the pathogenesis of multiple sclerosis; however, their regulation by intrinsic post-translational ubiquitination and deubiquitination is unresolved. This study shows that the deubiquitinating enzyme OTUD7B in astrocytes confers protection against murine experimental autoimmune encephalomyelitis, a model of MS, by limiting neuroinflammation. RNA-sequencing of isolated astrocytes and spatial transcriptomics showed that in EAE OTUD7B downregulates the expression of chemokines in astrocytes of inflammatory lesions, which is associated with reduced recruitment of encephalitogenic CD4+ T cells. Furthermore, OTUD7B was essential for GFAP protein expression of astrocytes bordering inflammatory lesions. Mechanistically, OTUD7B (i) restricted TNF-induced chemokine production of astrocytes by sequential K63- and K48-deubiquitination of RIPK1 limiting NF-κB and MAPK activation and (ii) enabled GFAP protein expression by supporting GFAP mRNA expression and preventing its proteasomal degradation through K48-deubiquitination of GFAP. This dual action on TNF signaling and GFAP identifies astrocyte-intrinsic OTUD7B as a central inhibitor of astrocyte-mediated inflammation.

overall_design: RNA-seq profiling of astrocytes isolated from spinal cords of Otud7bfl/fl and GFAP-Cre Otud7bfl/fl mice at d0 and d15 post immunization with MOG peptide.

first: Kunjan

last: Harit

first: Wenjing

last: Yi

first: Andreas

last: Jeron

first: Jakob

last: Schmidt

last: Beckervordersandforth

first: Emanuel

last: Wyler

first: Artür

last: Manukyan

first: Martina

last: Deckert

first: Helena

last: Radbruch

first: Thomas

last: Conrad

first: Janine

last: Altmüller

first: Markus

last: Landthaler

first: Xu

last: Wang

first: Gopala

last: Nishanth


title: SARS-CoV-2 infection drives local inflammation of the intestinal epithelium in immunocompromised patients with cancer

city: Minneapolis

first: Justin

last: Hwang

state: MN

address: 420 Delaware Street SE

department: Department of Medicine

institute: University of Minnesota

summary: Cancer patients undergoing transplantation-based treatments can develop graft-versus-host disease (GVHD), an inflammatory condition that increases mortality risk. In this study, we analyzed three cancer patients with severe inflammatory disorders following SARS-CoV-2 infection using high-resolution microscopy and spatial transcriptomics on pre- and post-infection GI biopsies. We found that up to 49 days after infection, the duodenal epithelium retained COVID viral elements, showed increased expression of viral receptors, inflammatory genes, and interferon activity, and exhibited tissue scarring. Notably, SERPINA1 was a persistent marker of infection and inflammation, also present in ~600 GI tumor samples, suggesting its role as a broader inflammation marker. These findings indicate that the GI epithelium can serve as a long-term COVID reservoir, potentially driving inflammatory syndromes similar to GVHD. This persistent viral presence may pose additional risks for cancer patients undergoing transplantation, highlighting the need for further investigation into post-COVID inflammatory complications in cancer patients.

overall_design: Spatial transcriptomic analysis was performed on FFPE tumor sections taken from three cancer patients with severe inflammatory disorders pre- and post-SARS-CoV-2 infection.

first: Emil

last: Lou

first: Christine

last: Luo

first: Katherine

last: Ladner

first: Allison

last: Makovec

first: Phillip

last: Wong

first: Jeremy

last: Chacon

first: Eamon

last: Toye

first: Ella

last: Boytim

first: Emily

middle: G

last: Hawkins

first: Anthony

last: Patregnani

last: John

first: Sanyukta

last: Padmanabhan

first: Akshat

last: Sarkari

first: Alison

first: Julia

last: Stuart

first: Andrew

last: Nelson

first: Brian

last: Betts

first: Eliseo

last: Eugenin


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [MCC]

first: Alastair

last: Smith

overall_design: Micro-Capture C for chALL1

first: Nicholas

last: Denny

first: Thomas

last: Milne

first: James

last: Davies


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [ATAC-seq]

overall_design: Accessible chromatin sequencing via ATAC-seq

last: Crump


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [CUT&TAG]

overall_design: CUT&TAG on HSPC-derived KMT2A::AFF1 leukemias

last: Jackson

first: Natalina

last: Elliott

first: Anindita

last: Roy


title: Novel therapeutic strategy targeting STMN1 using chlorambucil-conjugated pyrrole-imidazole polyamide in small cell lung cancer

city: Maebashi

first: Ryohei

last: Yoshikawa

state: Gunma

address: 3-39-22, showamachi,

department: Department of General Surgical Science

institute: Gunma University, Graduate School of Medicine

summary: Introduction Small-cell lung cancer (SCLC) is an aggressive malignancy and its treatment has not progressed over the decades. Stathmin 1 (TMN1) is a cytoplasmic phosphorylated protein that is specific to cancerous tissues and is associated with malignancy. Pyrrole-imidazole polyamide (PIP) compounds decrease gene expression by binding to specific DNA sites and disturbing RNA transcription. In this study, we synthesized a novel Chlorambucil-conjugated PIP compound targeting both the STMN1 promoter and STMN1 DNA sequences (Chb-STMN1 PIP) to evaluate its therapeutic efficacy against SCLC.  Methods We examined the expression of STMN1 in surgically resected lung cancer tissues and cell line database. Suppression of STMN1 by Chb-STMN1 PIP was analyzed using RT-PCR, WB, and CAGE-seq in vitro. The anti-tumor effects of Chb-STMN1 PIP were evaluated in vitro and in vivo.  Results Chb-STMN1 PIP treatment resulted in significant STMN1 suppression and cell viability reduction compared to the Chb alone and Chb-control PIP groups. Administration of Chb-STMN1 PIP to an SCLC xenograft mouse model also showed a tumor reduction effect and significantly suppressed angiogenesis, proliferation potency, and cell viability of SCLC. CAGE analysis indicated that the transcription of STMN1 was suppressed in Chb-STMN1 PIP-treated cells compared to that in control cells.  Conclusions A novel compound, Chb-STMN1 PIP, induced significant anti-tumor effects and suppressed STMN1 expression in SCLC cell lines. Furthermore, SCLC xenograft mouse models show tumor shrinkage and reduced malignant properties. Targeting STMN1 with our developed PIP compound appears to be a novel strategy and promising in SCLC.

overall_design: To investigate the efficacy of Chb-STMN1 PIP for SCLC, we treated H446 with Chb-STMN1 PIP and Control. We extracted RNA from these treated samples, and performed comprehensive gene expression analysis using data obtained from CAGEseq of two samples each for Chb-STMN1 PIP and control.

first: Takayoshi

last: Watanabe

first: Yoichi

last: Ohtaki

first: Toshikazu

last: Bando

first: Hiroshi

last: Sugiyama

first: Takuya

last: Araki

first: Hideaki

last: Yashima

first: Bilguun

last: Erkhem-Ochir

first: Haruka

last: Okami

first: Gendensuren

last: Dorjkhorloo

first: Ikuma

last: Shioi

first: Toshiteru

last: Nagashima

first: Natsuko

last: Kawatani

first: Tomohiro

last: Yazawa

first: Eiji

last: Narusawa

first: Takayuki

last: Kosaka

first: Osamu

last: Kawashima

first: Mitsuhiro

last: Kamiyoshihara

first: John

last: Minna

first: Luc

last: Girard

first: Ken

last: Shirabe

first: Hiroki

last: Nagase

first: Kimihiro

last: Shimizu

first: Takehiko

last: Yokobori


title: Cell-free DNA Methylomics Identify Tissue Injury Patterns in Pediatric ARDS

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

type: Methylation profiling by genome tiling array

summary: Cell-free DNA (cfDNA) is released into the circulation from dead and dying cells, and is elevated in critical illness syndromes including sepsis and acute respiratory distress syndrome (ARDS). Plasma cfDNA has been implicated as a damage-associated molecular pattern (DAMP) that propagates ongoing inflammation. However, the tissue source of circulating cfDNA from different pathological processes has not been fully elucidated, and identification of the cellular origin of cfDNA may provide insight into the mechanisms underlying the early inflammatory response. As cfDNA retains the unique methylation pattern of its tissue of origin, we can leverage cfDNA methylome to map the presumed tissue of origin of these DAMPs. We conducted a pilot study to assess the cfDNA methylation pattern in pediatric ARDS.

overall_design: This was a secondary analysis of a cohort of children with Berlin-defined ARDS from the Children’s Hospital of Philadelphia (CHOP) enrolled between 2014 and 2019, with plasma collected within 24 hours of ARDS onset after obtaining prospective consent from caregivers. In this study, we aimed to include subjects with higher levels of plasma cfDNA to assess the feasibility of our methodology. We randomly selected 24 children with cfDNA levels above the median value and 6 intubated non-ARDS controls. We isolated and quantified cfDNA from plasma, and performed methylation analysis using the Infinium MethylationEPIC and MethylationEPIC v2.0 BeadChip. Processing IDAT files generated from Infinium BeadChip-based data was performed using the openSesame workflow within the SeSAMe package. This workflow effectively addresses critical processing challenges, including signal background correction, dye bias adjustment, inference of color channel swaps, masking of suboptimal signals, and precise extraction of DNA modification levels (beta values).

first: Nadir

last: Yehya


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [ChIP-seq]

first: Alastair

last: Smith

overall_design: Chromatin immunoprecipitation DNA sequencing

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [snATAC-seq]

overall_design: 10x snATAC-seq on primary patient blasts

first: Joe

last: Harman

first: Natalina

last: Elliott

first: Anindita

last: Roy


title: Arsenic regulates ALKBH1 abundance and substrate specificity to promote translation and tumorigenicity

city: Chicago

first: Emma

last: Wilkinson

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Here we show a novel role for arsenic in regulating the abundance and function of the demethylase activity of ALKBH1 in arsenic-induced skin cancer. We demonstrate that ALKBH1 is upregulated in response to acute and chronic arsenic exposure. In chronic arsenic-exposed keratinocytes, ALKBH1 promotes tumorigenicity, as knockdown of ALKBH1 leads to decreased tumorigenicity. ALKBH1 as a demethylase has several substrates and knockdown of ALKBH1 in arsenic-induced keratinocytes lead to increased m6A in mRNA. We identify that ALKBH1 demethylates m6A in vitro in an arsenic-dependent manner. Arsenic binds to the ALKBH1 protein via two cysteine residues to regulate the m6A RNA demethylase activity of ALKBH1. m6A sequencing identifies that ALKBH1 regulates m6A demethylation on the NR2C2 transcript to modulate NR2C2 protein translation in a YTHDF1-dependent manner. Knockdown of ALKBH1 leads to increased NR2C2 expression, which, in turn, leads to decreased mTOR signaling and global translation. Our findings demonstrate a novel role for arsenic in regulating ALKBH1 abundance and activity and add new mechanistic insights into arsenic-induced skin tumorigenicity.

overall_design: m6A-IP-Sequencing of control and ALKBH1-knockdown arsenic-transformed keratinocytes in duplicate

first: Houxiang

last: Zhu


title: A small molecule targets LIC1 to suppress lung tumor growth by inducing autophagy

city: Guangzhou

first: 雷名

last: 吴

address: sun-yat san university

institute: 中山大学药学院

summary: LIC1(DYNC1LI1,DYN), along its homologue LIC2, constitutes subunits of the multiprotein cytoplasmic dynein complex. Although the dynein complex is known to play a role in membrane trafficking, organelle positioning, and microtubule organization, the specific functions of these individual LICs are rarely investigated.Knockdown or small molecule inhibition of LIC1 in NSCLC cells significantly suppressed cell proliferation and induced autophagic cell death.

overall_design: NCI-H1975 and HCC827 non-small cell lung cancer cells mRNA profiles of treatment with 18E(2.5μM,5μM) or siDYN(#1,#2).

first: Sheng

last: Yin

first: Jialuo

last: Huang

first: Leiming

last: Wu


title: Expression data from cultured mouse spermatogonia cryopreserved on the International Space Station (ISS) or on Earth

city: Kyoto

first: Mito

last: Shinohara

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Medical department

institute: Kyoto University

summary: Spermatogonial stem cells (SSCs) undergo self-renewal division to maintain spermatogenesis. In this study, we used SSCs for long-term cryopreservation in space flight. We derived germline stem cell (GS) cultures from DBA/2 mouse testes by supplementing GDNF and FGF2 (Kanatsu-Shinohara et al., 2003, Biol. Reprod. 69, 216-616). GS cells were cryopreserved in the ISS for 6 months. Frozen GS cells were thawed upon return to Earth and their gene expression profiles were analysed.

overall_design: GS cells were established from testes of 2-3 day old mice of the DBA/2 strain as previously described (Kanatsu-Shinohara et al., 2003, Biol. Reprod. 69, 216-616). Cells were cryopreserved for 6 months in ISS or on Earch for 6 months. Total RNA samples were extracted with TRIzol reagent (Invitrogen) and purified using the RNeasy cleanup system (QIAGEN, Valencia, CA). The RNAseq libraries were generated using the  Illumina Stranded mRNA Prep Kit (Illumina, San Diego, CA). Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode. In this dataset, we include the expression data obtained from cultured spermatogonia (GS cells) derived from transgenic mouse line C57BL6/Tg14(act-EGFP-OsbY01) that was bred into DBA/2 background. Each group contains 3 biological replicates.

last: Kanatsu-Shinohara

first: Takashi


title: Differential gene expression in leukemia is driven by enhancer heterogeneity [TOPmentation]

overall_design: Chromatin immunoprecipitation DNA sequencing for the N termius of KMT2A, C terminus of AFF1 and H3K27ac


title: Single-cell RNA-seq of 4T1 breast tumors from mice treated with anti-Siglec-E and/or anti-PD-1 antibodies

city: Shinagawa-ku

first: Kunio

last: Kawanishi

state: Tokyo

address: 1-5-8 Hatanodai

institute: Showa Medical University

summary: Metastasis remains the leading cause of cancer-related mortality, driven by complex interactions within the tumor microenvironment (TME). Tumor-associated macrophages (TAMs) play a pivotal role in metastatic progression, yet molecular diversity and upstream regulators remain poorly defined. Glycoprotein nonmetastatic melanoma protein B (GPNMB), overexpressed in subsets of tumors including triple-negative breast cancer (TNBC), is implicated in epithelial-mesenchymal transition (EMT) and cancer stemness. Recent single-cell RNA-seq studies have identified GPNMB as a marker of immunosuppressive TAMs associated with poor prognosis, but its mechanistic role in TAM polarization in TNBC has remained unclear. Co-culturing monocytic cells with three-dimensional sphere-forming TNBC cells induces their conversion into GPNMB⁺Siglec-9⁺ tumor-associated macrophages (TAMs). Tumor-derived GPNMB promotes monocyte-to-TAM polarization by inducing secondary GPNMB expression in monocytes, establishing a feed-forward amplification loop. Knockdown of GPNMB in TNBC cells significantly inhibits multiple immunosuppressive TAM subtypes, including Siglec-9⁺ TAM and EMT-associated TAM populations, as inferred from scRNA-seq and validated in patient tumors using bulk RNA-seq deconvolution. Distinct sialylation patterns were identified: tumor-derived GPNMB exhibited α2,3-sialylation, whereas macrophage-derived GPNMB exhibited α2,6-sialylation, enabling differential Siglec-9 recognition. Elevated GPNMB and Siglec-9 expression correlated with poor prognosis in TNBC patient cohorts. Importantly, dual inhibition of Siglec-E (murine Siglec-9 ortholog) and PD-1 suppressed IL-6-dependent EMT, reduced tumor stemness, and significantly limited lung metastasis in vivo. The GPNMB–Siglec-9 axis thus represents a critical glyco-immunological checkpoint driving TAM-mediated metastasis, providing a promising therapeutic target in TNBC.

overall_design: Female BALB/c mice (8 weeks of age) were injected with 5 × 104 4T1 cells/50 µL of PBS into the left, fourth mammary fat pad. Tumor development was established in 7 days, with tumor volumes of approximately 70 mm3. Then mice were divided into 4 groups as isotype control, anti Siglec-E antibody monotherapy, anti PD-1 antibody monotherapy, and combination therapy of anti Siglec-E antibody and anti PD-1 antibody (n=6 each) were sacrificed. To obtain single cells, the isolated primary tumors (n=2 each) were minced and dissociated using BD HorizonTM Dri Tumor & Tissue Dissociation Reagent (661563; BD Biosciences) following the manufacturer’s instructions. Red blood cells were then lysed using red blood cell lysis buffer (4333; Invitrogen). Dead Cell Removal MicroBead (130090101; Miltenyi Biotec) was applied to the cells. Then separation using CD326 EPCAM (130061101; Miltenyi Biotec) microbead protocol was performed to separate the epithelial and immune cells.

first: Thuy Linh

last: Dang Cao


title: HIFa isoform specific activation drives cell-type specificity of VHL-associated oncogenesis

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

summary: Cancers arising from dysregulation of generally operative signaling pathways are commonly tissue specific, but the mechanisms underlying this paradox are poorly understood. Based on striking cell-type specificity, we postulated that these mechanisms must operate very early in cancer development and set out to study them in a model of von Hippel Lindau disease. Biallelic mutation of the VHL ubiquitin ligase leads to constitutive activation of hypoxia inducible factors HIF1A and HIF2A and is often a truncal event in clear cell renal carcinoma. We used an oncogenic tagging strategy in which VHL-mutant cells are marked by tdTomato, enabling their observation, retrieval, and analysis early after VHL-inactivation. Our findings reveal markedly different consequences of HIF1A and HIF2A activation, but that both contribute to renal cell-type specific consequences of VHL-inactivation in the kidney. Early involvement of HIF2A in promoting proliferation within proximal tubular epithelium supports therapeutic targeting of HIF2A early in VHL disease.

overall_design: Vhl(KO/flox); Hif1a(flox/flox) (VHKO), Vhl(KO/flox); Epas1(flox/flox) (VEKO) and Vhl(KO/flox); Hif1a(flox/flox); Epas1(flox/flox) (VHEKO) mice carrying the renal tubular epithelium specific Pax8-CreERT2 were dosed with 5x 2 mg tamoxifen and harvested either at an early (1-3 weeks) or late (4-12 months) timepoints after dosing. Cre-mediated recombination marked Vhl and Hif1a and/or Epas1 recombination with the expression of tdTomato. tdTomato-positve cells were retrieved by FACS and subjected to scRNA-seq using the 10X Chromium NextGEM platform.

first: Samvid

last: Kurlekar

first: Joanna

last: Lima


title: Expression data from adult liver of offspring derived from cultured spermatogonia (GS cells) cryopreserved for a 6 months on the International Space Station (ISS) or on Earth.

summary: Spermatogonial stem cells (SSCs) undergo self-renewal division to maintain spermatogenesis. In this study, we used SSCs for long-term cryopreservation in space flight. We derived germline stem cell (GS) cultures from DBA/2 mouse testes (Kanatsu-Shinohara et al., 2003, Biol. Reprod. 69, 216-616). GS cells were cryopreserved in the ISS for 6 months. Frozen GS cells were thawed upon return to Earth and tranplanted into the seminifelous tubules of infertile W mice. Recipients were housed with wild-type C57BL/6 females, and livers of F1 offspring were analyzed for gene expression.

overall_design: In this dataset, we include the expression data obtained from livers of 10 week old offspring derived from GS cells cryopreserved on the ISS or on Earth.   As a control, we also include the expression data from the livers of wild-type BDF1 control mice. Each group contains 6 biological replicates.The liver of adult offspring were homogenised, and total RNA samples were extracted with TRIzol reagent (Invitrogen) and purified using the RNeasy cleanup system (QIAGEN, Valencia, CA). The RNAseq libraries were generated using the  Illumina Stranded mRNA Prep Kit (Illumina, San Diego, CA). Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.


title: scRNAseq of CD8+ T cells from autoimmune encephalitis

city: Lausanne

first: Renaud

last: Du Pasquier

address: Rue Du Bugnon 46

department: Department of Clinical Neurosciences

institute: Lausanne University Hospital - CHUV

summary: Single-cell RNA sequencing in seven anti-Ri autoimmune encephalitis (AIE) patients and three controls showed that neuron-reactive CD8+ T cells are cytotoxic KIR+ CD8+ regulatory T cells. In Ri-AIE, these cells had reduced KIR and IKZF2 (Helios) expression, alongside activated TCR signaling and elevated TNF and IFNG. They also overexpressed TOX, linked to brain-infiltrating cytotoxicity. These findings suggest a loss of regulatory function in KIR+ CD8+ T cells contributes to Ri-AIE pathogenesis.

overall_design: Ex vivo human CD8+ T cells from 11 different samples were isolated from total PBMCs by Magnetic-associated cell sorting (MACS). 8 of these samples originated from patients with Ri AIE (7 samples from patients at time of disease and 1 at remission). 3 of these samples were taken from age-matched donors with non-autoimmune neurological disorders.

first: Sylvain

last: Perriot

first: Samuel

last: Jones

first: Raphael

last: Genolet

first: Amandine

last: Mathias

first: Helen

last: Lindsay

first: Sara

last: Bobisse

first: Giovanni

last: Di Liberto

first: Mathieu

last: Canales

first: Lise

last: Queiroz

first: Christophe

last: Sauvage

first: Ingrid

last: Wagner

first: Larise

last: Oberholster

first: Marie

last: Gimenez

first: Diane

last: Bégarie

first: Stjepana

last: Kovac

first: Virginie

last: Desestret

last: Theaudin

first: Caroline

last: Pot

first: Heinz

last: Wiendl

first: Jerome

last: Honnorat

first: Doron

last: Merkler

last: Gottardo

first: Alexandre

last: Harari


title: Gene expression profile of type 2 innate lymphoid cells (ILC2s) from mouse lungs

city: Beijing

first: Hongjie

last: Chen

address: No.5 Yiheyuan Road

institute: Peking University

summary: Mouse lung ILC2s are a rare cell population. We used bulk RNA-sequencing (RNA-seq) to analyze gene expressions of mouse lung ILC2s

overall_design: Mouse lung ILC2s were isolated by fluorescence-activated cell sorting (FACS) according to certain markers and analyzed using RNA-seq

first: Tingting

last: Liu

first: Jing

last: Yang


title: Altered Cellular Pathways in the Blood of Patients With Guillain-Barre Syndrome

city: Natal

first: Selma

middle: MB

last: Jeronimo

state: Rio Grande do Norte

address: 655 Av Passeio dos Girassois, Capim Macio

department: Tropical Medicine Institute (IMT-RN)

country: Brazil

institute: Federal University of Rio Grande do Norte (UFRN)

summary:
Background and aims: Guillain-Barré syndrome (GBS) is a rare disorder, with a global incidence ranging from 1 to 2 individuals per 100,000 people/year. Infections and vaccines have been implicated as causes triggering GBS. The aim of the study was to identify host genes involved in the pathogenesis of GBS when Zika (ZIKV) and Chikungunya viruses (CHIKV) were introduced in Brazil.

Methods: A case-control study of GBS was performed when ZIKV and CHIKV were introduced into a naïve population. GBS was studied during both acute and postacute phases. RNA sequencing was conducted using whole blood.

Results: GBS typically manifested a week after rash and fever; acute inflammatory demyelinating polyradiculoneuropathy was more frequent. None of the GBS cases had a poor outcome. Serological assays for ZIKV and CHIKV revealed high titers of immunoglobulin G for both viruses in 9 out of 11 subjects. Metatranscriptomic analyses unveiled an increased abundance of reads attributed to Pseudomonas tolaasii and Toxoplasma gondii in the acute phase. Analysis of differentially expressed host genes during the acute phase revealed altered expression of genes associated with axogenesis, synapse assembly, and presynapse organization. Moreover, genes upregulated during acute GBS were primarily related to inflammation and the inflammasome pathways, including AIM2, NLR family genes and LRR-protein genes, and IL-10.

Interpretation: These findings suggest that inflammasome activation via AIM2 could play a role in tissue damage during GBS. Further investigation into the general activation of innate inflammatory responses is warranted to elucidate their potential contribution to the pathology of GBS.

overall_design: Whole blood mRNA samples at Acute and Post-Acute phases of GBS, and wild type (WT)

first: Viviane

last: Nogueira

first: Marília

middle: F

last: Lima

first: Diego

last: Teixeira

first: Mario

middle: E

last: DouradoJúnior

middle: M


title: STING phosphoserine 358 engages IRF3 to activate NF-kB at late endolysosomal compartments

status: Public on Aug 14 2025

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

summary: To map the responsive transcriptome across vertebrates, peripheral blood mononuclear cells (PBMCs) from humans, mice, chickens, turtles, and carp were stimulated ex vivo with cGAMP for 6 h, and  gene expression was quantified by RNA-seq.

sample_organism:
Cyprinus carpio
Gallus gallus
Homo sapiens
Mus musculus
Chelonoidis carbonarius

overall_design: The PBMCs from human, mouse, chicken, turtle, and carp were treated with 50ug/ml cGAMP for 6 hours. Total RNA was extracted and utilized to construct cDNA libraries for subsequent sequencing.


title: Disease specific epigenetic deregulation of enhancers, transposons and polycomb targets in acute promyelocytic leukemia

city: Stockholm

first: Sören

last: Lehmann

address: Blickagången 16

department: the Department of Medicine

institute: Karolinska Institute

summary: Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML), characterized by a fusion between the PML and RARA genes and by a block in the myeloid maturation at the promyelocytic stage. This study investigates the epigenetic landscape of APL by integrating ChIP-seq data on eight histone modifications and RNA-seq in APL as well as non-APL AML. APL showed a distinct chromatin profile that differed from non-APL AML. We describe APL specific changes in H3K27ac, H3K9me3 and H3K27me3 with impact on enhancer activity, repression of transposable elements and Polycomb regulated gene repression. The APL-specific H3K27ac pattern identifies APL-specific enhancer and super-enhancer regions, including a subset of enhancers that are bound by the PML-RARA fusion protein. While chromatin bound specifically by PML-RARA were dominantly active, APL was also characterized by gain of APL-specific heterochromatin states with significant gains of H3K9me3 enriched lamina-associated domains and the transposable elements LINE, LTR and SINE. These findings suggest a unique enhancer and heterochromatin profile in APL, with implications for transcription regulation and treatment response. These findings offer novel insights into the pathogenesis of APL.

overall_design: There was 1 experimental group (ATRA for 72hr)  and one untreated control. The experimental group and control were analyzed in triplicate.

first: Angelica

last: Gamboa-Cedeño

first: Xiangfu

last: Zhong

first: Andreas

last: Lennartsson


title: Epigenetic Programming of Estrogen Receptor in Adipose Tissue by High Fat Diet Regulates Obesity-Induced Inflammation

city: Atlanta

first: Jia

last: Jing

state: GA

address: Decatur St. SE

department: Biology

institute: Georgia State University

summary: Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we showed that DNA methylation, controlled by DNA methyltransferase 1 particularly, is a key determinant of adipose chemotaxis and inflammation. Whole genome DNA methylation profiling with reduced representative bisulfide sequencing (RRBS) analysis revealed that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in white adipose tissue (WAT) of mice. Among these changes there was a significant increase in DNA methylation at the promoter of estrogen receptor α (Esr1), corresponding to the down-regulation of Esr1 expression during HFD. HFD feeding increased the expression of DNA methyltransferase 1 (Dnmt1) and Dnmt3a as well as the binding of DNMT1 and 3a to the Esr1 promoter in WAT of mice. Mice with DNMT1 deficiency in adipocytes (AD1KO) displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge, while D3aKO mice showed a mild metabolic phenotype. The promoter activity of Esr1 promoter enriched with CpG sites was regulated by DNA methylation. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at the Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in mice fed HFD. Our study demonstrates that DNA methylation at the Esr1 promoter plays an important role in regulation of adipose inflammation, which may contribute to obesity-induced insulin resistance.

overall_design: RNA-seq profiling was performed on gonadal fat tissue from floxed control (Dnmt1^fl/fl^) and adipocyte-specific DNMT1 knockout (AD1KO) mice after 18 weeks of high-fat diet feeding. RRBS is aimed at studying adipose tissue DNA methylation changes in mice fed with either a low fat diet or a high fat diet.

first: Bingzhong

last: Xue

first: Hang

last: Shi


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4-positive tissue-resident T-cells in Crohn's disease. (RNA-seq, CD4+ T cell, part1)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: Tissue-resident T-cells (TRM) are deeply involved in immune memory at the site of inflammation. Here, we identified two key transcription factors, RUNX2 and BHLHE40 as regulators of pathologically relevant CD4-positive TRM in the inflamed gut mucosa of Crohn’s disease patients.

overall_design: CD4+ T cells were sorted from mononuclear cells isolated from surgically resected fresh gut specimens by flow cytometry. RUNX2 and BHLHE40 were then knocked down using lentiviral transduction. Infected cells were subsequently re-sorted by flow cytometry, total RNA was extracted using TRIzol reagent, and samples were subjected to bulk RNA sequencing.

first: Mitsuru

last: Arase

first: Mari

last: Murakami

last: Okuzaki

first: Kiyoshi

last: Takeda


title: RNA-seq profiling of macrophage polarization in THP-1 cells co-cultured with GPNMB-knockdown TNBC spheroids

first: Kunio

last: Kawanishi

overall_design:
To investigate the role of GPNMB expressed in TNBCs in macrophage M1/M2 polarization, we established a 3D co-culture system with TNBC spheres and performed RNA sequencing analysis. TNBC cells (Hs578T) were treated with GPNMB and control siRNAs 24 hours prior to sphere formation. Three days later, monocyte-like cells (THP-1) were added directly to the culture of TNBC cell spheres. The optimal co-culture duration was determined to be three days. On the harvest day, the entire co-culture medium was passed through a cell filter to separate the cancer spheres, which accumulated on the filter cap, allowing for the collection and analysis of RNA from the macrophages exclusively.
We conducted a comparative gene expression profiling analysis of RNA-seq data from three distinct cell conditions: (1) "THP-1 control," co-cultured with Hs578T cells transfected with control siRNA; (2) "THP-1 siRNA1," co-cultured with Hs578T cells with GPNMB knockdown using siRNA1; and (3) "THP-1 siRNA2," co-cultured with Hs578T cells with GPNMB knockdown using siRNA2. All data were normalized against the gene expression profile of THP-1 cells cultured alone, without co-culture. We reanalyzed a subset of single-cell RNA-seq samples (GSM5188373, GSM5188379, GSM5188386, GSM5188388, GSM5188393) from GSE169246, which represent tumor-derived myeloid cell populations from triple-negative breast cancer (TNBC) patients. The original libraries were generated using the 10x Genomics Chromium Single Cell 5? platform and processed with Cell Ranger v3.0.0.

Raw UMI count matrices were imported into Seurat v4.3 (R v4.1.2), and quality filtering was applied to exclude cells with fewer than 400 or more than 8,000 detected genes, or with >10% mitochondrial gene content. Normalization was performed using SCTransform, followed by principal component analysis (PCA) and batch correction using Harmony v1.0.

Myeloid cell subsets were identified based on canonical macrophage markers (CD68, CD14, CSF1R, MERTK, CD163, HLA-DRA, VCAN, LYZ), and tumor-associated macrophages (TAMs) were further subclassified using a curated 8-subtype framework including IFN-responsive, regulatory, inflammatory, lipid-associated, angiogenic, resident-like, proliferative, and GPNMB?/SIGLEC9? TAM populations. Cluster-level marker genes were identified using the Wilcoxon rank-sum test, and highly specific, non-overlapping markers were selected to generate a custom TAM signature matrix for digital cytometry.

first: Thuy Linh

last: Dang Cao


title: The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (CUT&RUN)

overall_design: Chromatin profiles in human PBMC-derived CD4 positive T cells overexpressing RUNX2 or BHLHE40 though Lentiviral infection was performed by CUT&RUN Assay using anti-RUNX2 antibody and BHLHE40 antibody, respectively.


title: Biallelic deleterious variants in SNAPIN, a retrograde dynein adaptor, cause a prenatal-onset neurodevelopmental disorder [2]

first: Erica

last: Davis

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

institute: Ann & Robert H Lurie Children's Hospital of Chicago

summary: Fetal brain anomalies identified by prenatal ultrasound and/or magnetic resonance imaging represent a considerable healthcare burden with ~1-2/1,000 live births. To identify underlying etiology, trio prenatal exome sequencing or genome sequencing (ES/GS) has emerged as a comprehensive diagnostic paradigm with a reported diagnostic rate up to ~32%. Here, we report five unrelated families with six affected cases that presented neuroanatomical, craniofacial, and skeletal anomalies, all harboring rare, biallelic deleterious variants in SNAPIN, encoding SNARE-associated protein. SNAPIN is a ubiquitously expressed component of the autophagy-lysosomal pathway that catalyzes retrograde axonal transport and synaptic transmission. To investigate the role of SNAPIN in brain development, we generated zebrafish gene ablation models, which recapitulated human-relevant disease phenotypes. Two independent, genetically stable snapin mutants exhibited pre-adulthood lethality, reduced overall length, disproportionately smaller head size, and altered brain morphology. Transcriptomic profiling of snapin mutant zebrafish heads revealed an early and progressive transcriptomic shift marked by autophagy activation with concomitant downregulation of structural and neurodevelopmental genes. Assessment of brain cellular ultrastructure with electron microscopy and LC3-II immunoblotting revealed retrograde vesicle transport defects, with accumulation of late endosomes and autophagosomes. Together, these findings support SNAPIN as a likely causal gene for a severe neurodevelopmental syndrome and expand the growing list of autophagy-lysosome pathway regulators essential for human brain development.

overall_design: To investigate the impact of snapin dysfunction in an in vivo neurodevelopmental context, we performed transcriptomics studies using RNA isolated from heads of snapin 9bpdel-2bpins homozygous mutants and wild type zebrafish larvae at 33 dpf (three biological replicates each).


title: The role of RUNX2 and BHLHE40 in pathologically relevant  CD4-positive tissue-resident T-cells in Crohn's disease. (CITE-seq, CD4+ T cell) II

overall_design: CD4+ T cells were sorted from mononuclear cells derived from surgically resected fresh gut specimens, peripheral, blood, mesenteric lymph nodes by flow cytometry. Each specimen was labeled with HTO antibodies and subjected to single-cell CITE-seq analysis.


title: Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: By combining chromatin immunoprecipitation (ChIP) with an exonuclease that digests the ends of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies. We introduce a Mammalian-Optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. We validate MO-ChIP-exo by comparing it to previously published ChIP-exo protocols and demonstrate its adaptability to both suspension (K562) and adherent (HepG2, mESC) cell lines. This improved protocol provides a more robust and efficient method for generating high-quality ChIP-exo libraries from mammalian cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Optimization of the ChIP-exo protocol for mammalian cells and current DNA sequencing technologies, resulting in the MO-ChIP-exo protocol. Optimization was mainly performed using the CTCF antibody in K562 cells. Additional testing and validation was performed in HepG2 and mES cells  and with the USF1 antibody.

first: Daniela

middle: Q

last: James

first: Sohini

last: Mukherjee

first: Caiden

last: Cannon