title: let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq RIPseq]

summary: We identified 581 transcripts enriched ≥2-fold for LIN-28 binding in L1 animals.

overall_design: Animals carrying untagged LIN-28 (N2) or GFP-tagged LIN-28 (lin-28(xe197[lin-28::linker::aid::3xflag::tev::gfp::linker::hibit]) I) were collected at 6 hours after resumption of feeding at 25°C. RNA was extracted in three technical replicates either directly (input samples) or after immunoprecipitation with anti-GFP antibody (IP samples).


title: Effect of HNF1A-MODY on stem cell islets

status: Public on Jun 10 2026

city: Bergen

first: Ulrik

last: Larsen

address: Haukelandsbakken 15

department: Clinical Science

country: Norway

institute: University of Bergen

type: Expression profiling by high throughput sequencing

summary: This project investigates the impact of the hotspot mutation P291fsinsC in HNF1A-MODY (Maturity-Onset Diabetes of the Young) on stem cell-derived islets. RNA sequencing (RNA-seq) was performed on islets differentiated from mutant and control HNF1A-MODY stem cells to study the mutation's effect on gene expression. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms underlying the dysfunction caused by the P291fsinsC mutation during islet development and maturation.

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into the endocrine progentior stage.

first: Lucas

last: Unger

first: Simona

last: Chera


title: Dynamic Cellular Heterogeneity Revealed through a Time-Resolved Single-Cell Atlas in porcine intestinal organoids

city: Sangju-si

first: Tae

middle: Hong

last: Kang

state: Gyeongsangbuk-do

address: Sangju-si 37224, Gyeongsangbuk-do, Republic of Korea

department: Department of Animal Science and Biotechnology

country: South Korea

institute: Kyungpook National University

summary: Intestinal epithelial cells are supported by dynamic cellular heterogeneity, which is critical for maintaining intestinal homeostasis. Recently, intestinal organoid models have been attracting in-vitro platform because they can recapitulate the structural, functional, and cellular complexity of the small intestine. Here, we established porcine intestinal organoids and investigated time-dependent transcriptomic changes using single-cell RNA sequencing.

overall_design: Small intestinal crypts were obtained from three-way crossbred gilt (Landrace × Yorkshire × Duroc) and analyzed using scRNA-seq

first: Tae-hong

first: Sang-in

last: Lee


title: An XRE-Type Regulator in Streptococcus mutans Plays an Important Role in brpA Expression and Oxidative Stress Tolerance Response

city: New Orleans

first: Zezhang

middle: T

last: Wen

state: Louisiana

address: 1100 FLORIDA AVE, Clinical Bldg Room 619

country: USA

institute: LSU Health In New Orleans

summary: Locus SMU.405 encodes a xenobiotic response element (XRE) family transcriptional regulator. This study used a functional genomics approach to explore the role of a XRE-type regulator (SMU.405c) in S. mutans physiology including the expression of biofilm regulatory protein BrpA. Results showed that deletional mutation of xre significantly reduced the ability of the deficient mutant to grow in the presence of methyl viologen, a commonly used oxidative stressor (P<0.001). When challenged in a hydrogen peroxide killing assay, the survival rate of the ∆xre mutant was >2-log less than the parent strain after 60 minutes (P<0.001). Luciferase reporter fusion assays showed that xre deficiency had no significant effect on luciferase expression when it was under the control of the intact brpA promoter, but the reporter activity increased by >6-fold (P<0.001) when the reporter gene was fused to a brpA promoter derivative with deletion of a putative XRE-binding box. EMSA assay showed that recombinant XRE interacted with the brpA promoter, resulting in electrophoretic shift of the promoter probes. In vitro transcription assay also showed that inclusion of XRE caused transcription to fall-off, significantly reducing full-length brpA transcripts. RNA-seq analysis revealed that deficiency of XRE led to altered expression of >102 genes by >2-fold (P<0.05), including 28 with increased expression and 74 with decreased expression. Among the down regulated were genes for DNA repair and oxidative stress tolerance response. These results suggest that XRE (SMU.405c) in S. mutans plays an important role in brpA expression and oxidative stress tolerance response.

overall_design: The allelic exchange xre mutant and its parent strain UA159 were grown in regular BHI broth at 37C in a aerobic chamber with 5% CO2. Total RNAs were extracted from mid-exponential (OD600nm ~0.4) phase cultures and differentially expressed genes in response to xre mutation were identified via RNA-seq.

first: Kassapa

last: Ellepola

first: Lauren C.

last: Guillot

first: Zezhang T.


title: Glutathione is a host-derived cysteine source for Clostridioides difficile

city: Madison

first: Anna

last: Gregory

state: WI

address: 1550 Linden Dr., MSB Rm3435

department: Department of Gastroenterology and Department of Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

summary: Clostridioides difficile is the leading cause of nosocomial diarrhea, afflicting approximately half a million people each year in the USA, burdening both individuals’ quality of life and the healthcare system. In the gastrointestinal (GI) tract, C. difficile must acquire essential nutrients to colonize, establish infection, and persists in a polymicrobial environment. C. difficile is a cysteine auxotroph and the GI tract contains low levels of cysteine, highlighting gaps in our understanding of how C. difficile acquires this amino acid during infection. One possible source of cysteine for C. difficile during infection is glutathione (GSH), tripeptide thiol in mammalian cells. Our data indicate that C. difficile encodes two redundant enzymes (GecA and GecB) that allow it to use GSH as a source of cysteine. Using murine models of C. difficile infection, we also show that C. difficile uses its toxins to increase available GSH in the GI tract during infection. Finally, we show that the ability to utilize GSH gives wild-type C. difficile a fitness advantage over a GSH-deficient mutant in vivo. These findings establish GSH metabolism as a novel strategy of nutrient acquisition that links C. difficile metabolism and virulence and highlight GSH metabolism as possibly impactful target for future therapeutic development.

overall_design: C. difficile WT overnight cultures were back-diluted 1:100 into 15 mL of pre-reduced BDM +/- 25 mM GSH and incubated anaerobically at 37°C until cultures reached mid-log phase (OD600 ~0.20). At mid-log phase, 5 mL aliquots of the cultures were diluted 1:1 in chilled  ethanol:acetone and were stored at −20°C to preserve RNA. Aliquots were centrifuged at 3,000×g for 5 minutes at 4°C. Pellets were washed with 5 mL cold, nuclease-free PBS and then centrifuged at 3,000×g for 5 minutes at 4°C. The supernatant was removed, and remaining pellets were resuspended in 1 mL TRIzol. Resuspended pellets were processed using a TRIzol Plus RNA Purification Kit (Thermo) with on-column DNase treatment, and RNA integrity was confirmed via 2100 Agilent BioAnalyzer and frozen at -80°C.

middle: L

first: Zhe

last: Zhou

first: Mahshid

last: Manouchehri

first: Troy

middle: R

last: Scoggins IV

first: David

middle: M

last: Stevenson

first: Daniel

last: Amador-Noguez

first: Joseph

middle: P

last: Zackular

first: Boone

last: Prentice

first: Stavroula

middle: K

last: Hatzios

first: Andrew

middle: J

last: Hryckowian


title: Retinoic acid regulates macular development in the human retina

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The human retina possesses a region, the macula, specialized for high acuity vision, with a high density of cones and no rod photoreceptors. The mechanisms involved in macular formation are poorly understood. Increasing evidence suggests that retinoic acid (RA) may play a key role in its development. Specifically low RA levels in the macula, maintained by CYP26A1, leads to early cell cycle exit for macular progenitors, and a low rod to cone ratio. To test this model, we performed single cell RNA sequencing on Fetal D57 retina to examine the distribution of RA-associated genes across the central and peripheral retina.

overall_design: We performed multiome (joint single-cell RNA and ATAC sequencing) on a human D57 (Fetal week 8) fetal retina. We dissected the central temporal retina, containing the presumptive macula, and the nasal peripheral regions and processed the two different regions as individual samples.

first: Juliette

last: Wohlschlegel

first: Lew

last: Kaplan

first: Lydia

first: Kayla

last: Arakelian

first: Abbigail

last: Green

first: Aric

last: Prieve

first: Ian

last: Glass

first: Thomas

middle: A

last: Reh


title: Progesterone  receptors drive advanced breast cancer phenotypes including circulating tumor- and stem-like cell expansion in the context of ESR1 mutation [RNA-seq]

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: Endocrine therapy resistance remains a major challenge in the treatment of advanced estrogen receptor positive (ER+) breast cancer. This can be driven by acquired mutations in the estrogen receptor gene (ESR1), such as Y537S or D538G, that primarily emerge in patients with prior aromatase inhibitor therapy and results in constitutive estrogen-independent ER activity.  Progesterone receptors (PR) are important modifiers of ER activity, in part via direct binding. We previously showed that PR mediates expansion of cancer stem-like cell (CSC) populations and promotes tamoxifen resistance in nuclear ER/PR transcriptional complexes. In this study, we sought to define whether PR function changes in the context of ESR1 mutations. PR readily interacted with wild type (WT), but not Y537S or D538G ERs. RNA-seq and ChIP-seq studies demonstrated that ER+ breast cancer models expressing Y537S ER exhibited a distinct response to progesterone. CSC populations were enhanced in Y537S ER+ cells compared to WT ER+ cells. PR knockdown demonstrated that this property required PR expression but was unresponsive to antiprogestins. Moreover, we identified PR-dependent transcriptional programs such as the unfolded protein response (UPR) that can be leveraged to target CSC populations in Y537S ESR1-mutant breast cancer. The UPR activator ErSO, but not UPR inhibitors, blocked expansion of CSCs in WT as well as Y537S ER+ models. Together, our findings demonstrate a critical interplay between PR and mutant ER function and provide insight into PR-driven pathways including hyperactivation of the stress-sensing UPR that can be exploited as potential therapeutic avenues in advanced ER+ breast cancer.

overall_design: For 2D conditions, T47D WT and Y537S ESR1 cells (shGFP and shPR) were plated in triplicate. Cells were hormone-starved for 24h, followed by treatment with E2 (1 nM, 48h) or R5020 (10 nM, 6h). For 3D conditions, cells were plated in triplicate into tumorsphere media in ULA plates and allowed to form for 6 days. RNA extraction was performed using RNeasy Mini Kit (Qiagen). Purity of the total RNA samples was assessed using BioAnalyzer (Agilent) and samples with an RNA integrity score >8 were used for library construction by the University of Minnesota Genomics Core. Libraries were built from individual samples with the TruSeq Stranded mRNA kit (Illumina). 50 base pair paired-end sequencing was performed using Illumina NovaSeq X Plus. On average >15 million reads were sequenced per sample.

first: Thu

last: Truong

first: Noelle

middle: E

last: Gillis

first: rosemary

last: Huggings

first: Julie

middle: H

last: Ostrander

first: Geoffrey

last: Greene

first: Carol

last: Lange


title: Progesterone  receptors drive advanced breast cancer phenotypes including circulating tumor- and stem-like cell expansion in the context of ESR1 mutation

overall_design: T47D WT and Y537S ESR1 cells (shGFP and shPR) were hormone-starved for 48h and then treated with vehicle or R5020 (10 nM, 1h). 1 x 10e6 cells were harvested in ice-cold PBS. Cells were crosslinked in 1% formaldehyde in PBS. Crosslinking was quenched by adding glycine at a final concentration of 125 mM. Crosslinked cell pellets were snap-frozen and stored at -80°C. For each ChIP experimental replicate, 2 x 10e6 crosslinked cells (from 2 crosslinked aliquots) were lysed in lysis buffer with PICS III using sonication (high, 30 seconds on/off, for 5 intervals of 10 minutes). 5% of lysate was reserved for input control and snap frozen to store at -80°C. Lysates were diluted to 1 µg/µl protein based on Nanodrop A280 concentrations and divided into 1 ml aliquots. 5 µg of the appropriate antibodies (phospho-PR [S294] for phospho-PR ChIP, rabbit IgG for phospho-PR negative control) were added to the appropriate lysate aliquots and rotated at 4°C overnight. Protein-chromatin was isolated and eluted using protein G beads (Cytiva Streptavidin Mag Sepharose Magnetic Beads, Thermo Fisher). Eluted ChIP samples were incubated with RNAse A and Proteinase K to reverse the crosslinked protein-chromatin. Input samples and ChIP-DNA were purified using a Qiagen QIAquick PCR Purification Kit, and purified DNA samples were eluted in 30 µl nuclease-free water. ChIP-DNA was quantitated by Qubit (Life Technologies), libraries were generated using the Illumina ChIP-SEQ kit and quality assessed using Bioanalyzer (Agilent). Sequencing was performed on the Illumina NovaSeq X by the University of Chicago Functional Genomics core. Samples were analyzed over 50M clusters per sample, which was variable due to the available library content.

first: Thu R

first: Noelle E

first: rosemary J

first: Nuri A

first: Julie H

first: Geoffrey L

first: Carol A


title: Deciphering HTLV-1-associated Lung Pathology: Inflammation, Monocyte Recruitment and Differentiation Triggered by HTLV-1-exposed Alveolar Epithelial Cells

city: Leuven

first: Clément

middle: Jacques François

last: Heymann

address: 49 Herestraat

department: Microbiology, Immunology and Transplantation

country: Belgium

institute: Rega Institute (KU Leuven, Belgium)

summary: Individuals with Human T-Lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis are prone to pulmonary complications (e.g., bronchiectasis), linked to chronic inflammation. This study assessed the impact of HTLV-1 infection on lung inflammation by analyzing the alveolar transcriptome of A549 epithelial cells following exposure to HTLV-1. Co-culture with HTLV-1-infected MT-2 cells caused transcriptomic changes related to viral response, NF-kB activation, and inflammation. RT-qPCR confirmed elevated expression of the chemokine monocyte chemotactic protein-1 (MCP-1/CCL2) and CSF-1 in A549 MT-2 co-cultures. Increased CSF-1 expression was mechanistically linked to NF-kB signaling, using CRISPR/Cas9 RELA knockout. Supernatant from A549 MT-2 co-cultures triggered chemotaxis and macrophage differentiation of THP-1 and primary monocytes. STRING analysis revealed enrichment in pathways associated with monocyte infiltration and bronchiectasis, aligning with clinical and multi-ancestry GWAS data. Overall, this study highlights HTLV-1's role in driving inflammation and monocyte recruitment in the alveolar epithelium, potentially contributing to viral persistence and immune evasion.

overall_design: Adenocarcinomic human alveolar basal epithelial cells (A549) were stimulated with uninfected and HTLV-1-infected cells. Additional conditions with cells stimulted with filtered cell supernatant, were also included. RNA lysates were obtainned 24h following co-culture (or stimulation with cell supernatant).

first: Mieke

last: Gouwy

first: Robin

last: Hermans

first: Jean-Claude

last: Twiziere

first: Tatiana

last: Assone

first: Jorge

last: Casseb

first: Isaac

last: Racine

first: Isabelle

last: Cleynen

first: Edward

last: Murphy

first: Roberta

last: Bruhn

first: Dominique

last: Schols

first: Evelien

last: Vanderlinden

first: Johan

last: Van Weyenbergh


title: CB001 bioactive compounds improve intestinal immune disorders caused by simulated microgravity and radiation through anti-inflammatory

city: Beijing

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

country: China

institute: beijing institute of radiation

summary: Gastrointestinal discomfort is one of the most common issues during spaceflight, and there is currently a lack of targeted drug treatment strategies. Current research in this area focuses on single-factor modeling, lacking a comprehensive understanding. In the present study, we constructed space flight models based on most important two factors, microgravity and low-dose radiation. Histological, cellular and molecular analyses confirmed the advantage of this dual-factor model in simulating space flight-caused injuries. Upregulated inflammatory and homeostasis disruption were observed in intestines treated by these dual factors. Our data revealed that dual factors enhanced the migration of a Ccr7+ B cells into intestines through upregulating the expression of Cxcr4, which exerted strong activation regulations on leukocytes. We further validated that bioactive compounds of CB001 effectively alleviated intestinal perturbations through recovering the expression of tight junction proteins, suppressing the migration of B cells and downregulating the levels of pro-inflammatory cytokines. Collectively, our work offered CB001 compounds as candidate intervention drug for space flight-induced intestine dysfunctions based on a dual-factor mice model. These data shed lights on special medicine screening for health protection in space flight.

overall_design: Small intestines from two groups were subjected to RNA-seq for dissection of dual fator-induced effects.


title: A single-cell atlas identifies oncogenic transcriptional programs and immune escape mechanisms in hematogolical malignancies [scRNA-seq]

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

summary: Primary cutaneous T-cell lymphomas (CTCL) are a heterogeneous group of extranodal non-Hodgkin lymphomas. Outcomes for patients with advanced-stage disease are suboptimal, as few complete and durable responses are achieved with currently available therapeutic agents. However, improved understanding of oncogenic transcriptional programs in malignant T cells and their engagement with the tumor microenvironment (TME) may unveil therapeutic vulnerabilities. Therefore, we have compiled the largest available scRNA-seq CTCL atlas that includes >2 million skin and blood cells from 116 patients. We identified recurrent transcriptional programs in malignant T cells, a subset of which are associated with GATA-3 dependent transcriptional programs, especially in the setting of large cell transformation and advanced-stage disease. Many of the transcriptional programs identified are therapeutically targetable with clinically available agents, including HDAC, XPO1, JAK/CSF1R, and IKZF1/IKZF3 antagonists. The CTCL TME is dominated by infiltrating and exhausted effector and cytotoxic T cells that are restrained by a robust infiltrate of regulatory T cells (8%), transcriptionally polarized monocytes/macrophages (7%), and cancer-associated fibroblasts. Collectively, these findings have significant implications for the rationale design of combinatorial strategies targeting immune checkpoints, including PD-1. We have identified transcriptional programs, driven by oncogenic transcription factors, and constituents of the TME as therapeutic vulnerabilities in CTCL, and hope that the CTCL atlas constructed will provide a valuable resource for future studies exploiting these therapeutic vulnerabilities.

overall_design:
Skin biopsies with representative tumor were digested to get single cell suspension and used for scRNA-seq. Submitter states that missing raw files are due to patient privacy concerns.

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

first: Ryan

last: Wilcox


title: Dynamics of poised enhancer connectivity upon PRC2 perturbation during the naive-to-primed transition of human pluripotent stem cells

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC Laboratory of Medical Sciences (LMS)

summary: In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associated H3K27me3 histone modifications. In contrast, these poised enhancers (PEs) are scarce in naive hPSCs that model pre-implantation epiblast. PEs form abundant chromosomal contacts with developmental genes, but when these contacts emerge, how their formation relates to enhancer poising and their functional significance remains incompletely understood. Here, we devise high-resolution, PE-targeted Capture Hi-C to generate a comprehensive atlas of PE chromosomal contacts in the time course of hPSC transition from the naive to primed state. In this experiment, we show that PROTAC-induced degradation of Polycomb Repressive Complex 2 (PRC2) early in the transition weakens PE connectivity, while inhibition of its H3K27 methyltransferase activity does not, suggesting a non-catalytic role of Polycomb in supporting PE contacts.

overall_design: To profile contacts involving poised enhancers globally and at high resolution, we devised a Poised Enhancer-targeted Capture Hi-C system (PECHi-C) to enrich Hi-C libraries for poised enhancers-harbouring DpnII fragments using synthetic biotinylated RNAs. These PECHi-C experiments were done in triplicate on HNES1 cells after 5 days of differentiation through the primed state and treatment either with DMSO (control), a PRC2 catalytic inhibitor (UNC1999), or a PRC2 PROTAC degrader (UNC6852).

first: Marina

middle: C

last: Nocente

first: Andrew

last: Malcolm

first: Sarah

last: Elderkin

first: Maria

last: Rostovskaya

first: Peter

last: Rugg-Gunn


title: Dynamics of poised enhancer connectivity upon the naive-to-primed transition of human pluripotent stem cells

summary: In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associated H3K27me3 histone modifications. In contrast, these poised enhancers (PEs) are scarce in naive hPSCs that model pre-implantation epiblast. PEs form abundant chromosomal contacts with developmental genes, but when these contacts emerge, how their formation relates to enhancer poising and their functional significance remains incompletely understood. We devised high-resolution, PE-targeted Capture Hi-C and generate a comprehensive atlas of PE chromosomal contacts in the time course of hPSC transition from the naive to primed state. A subset of PE contacts persist after developmental activation and can mediate long-range gene induction.

overall_design: To profile contacts involving poised enhancers globally and at high resolution, we devised a Poised Enhancer-targeted Capture Hi-C system (PECHi-C) to enrich Hi-C libraries for poised enhancers-harbouring DpnII fragments using synthetic biotinylated RNAs. These PECHi-C experiments were done on human HNES1 cells in the time course of naive-to-primed transition, as well as in cells further differentiated into definitive endoderm (DE) or neuroectoderm (NE). In addition, we also profiled H9 human primed pluripotent stem cells.

first: Monica

last: Della Rosa


title: Poised enhancer chromosomal conformation analysis in unperturbed and CRISPRa-targeted human pluripotent stem cells by 4C-seq

summary: In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associated H3K27me3 histone modifications. In contrast, these poised enhancers (PEs) are scarce in naive hPSCs that model pre-implantation epiblast. PEs form abundant chromosomal contacts with developmental genes, but when these contacts emerge, how their formation relates to enhancer poising and their functional significance remains incompletely understood. In this experiment, we targeted CRISPRa to a candidate PE located between two developmental genes, DLX1 and DLX2, and connected only to DLX1. We found that CRISPRa induced the expression of DLX1, but not DLX2, while 3D chromosomal conformation of the locus remained unchanged, pointing to a role of PE contacts in pre-selecting the target genes for subsequent activation during development.

overall_design: WTC11 iCRISPRa cells with sgRNAs were used to induce the activation of the poised enhancer (ID=280801) located in the DLX1-DLX2 region. 4C-seq experiments are conducted to determine the effect of the activation of this poised enhacer on the 3D proximity contacts.

first: George

last: Lister

first: Isabella

last: Savin


title: Super-enhancer formation in scirrhous gastric cancer-associated fibroblasts, and its presence in fibroblasts in non-cancerous tissues (1)

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

summary: Scirrhous gastric cancer has aggressive clinical courses and is characterized by dominating cancer-associated fibroblasts (CAFs).  We here aimed to explore the molecular basis for scirrhous CAFs and their origin.  Scirrhous CAFs had heavily acetylated super-enhancers, and therapeutic targeting of super-enhancers by a BET bromodomain inhibitor, mivebresib, markedly decreased their migration-promoting activity.

overall_design: ChIP-seq for H3K27ac of cancer-associated fibroblasts from scirrhous gastric cancers and non-scirrhous gastric cancers and normal gastric fibroblasts

first: Yu-Yu

last: Liu

first: Yoshimi

last: Yasukawa

first: Toshikazu

last: Ushijima


title: Recurrent drought stress triggers transcriptional reprogramming and epigenetic modifications in apple seedlings

city: Beaucouze

first: Sandrine

last: Balzergue

address: 42 rue G. Morel

country: France

institute: INRAE

type: Methylation profiling by high throughput sequencing

summary: Developing multiple stress-tolerant crops is the goal of many breeders in the current context of seasonal variability precipitated by the ongoing climate change.  Among the most pressing stress, drought is becoming a major concern in many regions of the world. Plant responses to drought has been studied in many species, including perennial plants such as apple (Malus domestica); however, the effects of recurrent stress and the potential for stress memory, or priming, remain poorly described. Priming reflects the capacity of plants to “memorize” environmental stress experiences and potentially improve their responses to recurring stress. Such information may be retained through epigenetic modifications of DNA and associated histone proteins. This ability could enable training of plants to face future challenges. In this study, we explored the effects of recurrent drought stress on apple seedling morphology and investigated the transcriptomic and epigenetic changes in plants subjected to this treatment. Our results indicate that naïve apple seedlings can be primed upon first exposure to drought stress, and that primed plants respond differently to recurrent stress later in the season. Analyses of differentially expressed genes and differentially methylated regions further indicate that primed plants’ molecular responses differ significantly from plants exposed to drought stress for the first time. Finally, our results suggest that following a winter period, the previously induced priming effect may be partially lost. Overall, our study demonstrates the importance of studying recurrent stress to better understand the memory-associated mechanisms leading to morphological and gene expression alterations in perennial plants.

overall_design: Recurrent Drought Stress (DS) experiments were conducted on 12-week-old seedlings of ‘Golden Delicious’ double haploid 18 (GDDH18). The DS assays were conducted on a total of 163 GDDH18 seedlings, distributed across three biological replicates. Plants were divided into two irrigation regimes: (I) Control group – maintained under well-watered (WW) conditions throughout the experiment; (II) Multiple-DS group – subjected to three drought stress (DS) cycles, each consisting of 3 weeks of drought followed by 3 weeks of rewatering (WW); Leaves and roots were collected for methylation analyses after the first and the third drought périod. In addition, in year n+1, roots and leaves from Control and Multiple-DS plants were also sampled prior to the application of a new stress (Before Stress – BS), after completing one winter cycle.

first: Amanda

last: Malvessi-Cattani

first: Patricia

last: Mallegol

first: Sylvain

last: Hanteville

first: Skander

last: Hatira

first: Béatrice

last: Bonnet

first: Maryline

last: Cournol

first: Anne-Laure

last: Fanciullino

first: Jean-Marc

last: Celton


title: Gene expression analysis of cancer-associated fibroblasts from scirrhous gastric cancers and non-scirrhous gastric cancers

summary: Scirrhous gastric cancer has aggressive clinical courses and is characterized by dominating cancer-associated fibroblasts (CAFs).  We here aimed to explore the molecular basis for scirrhous CAFs and their origin.  The aggressive phenotype of scirrhous CAFs were associated with activation of TGFβ1 and NF-kB, along with increased expression of their downstream genes.

overall_design: RNA-seq of cancer-associated fibroblasts from scirrhous gastric cancers and non-scirrhous gastric cancers


title: Genomic uracil in early embryonic development of Zebrafish

city: Budapest

first: Angela

last: Bekesi

address: Műegyetem rakpart 3.

department: Department of Applied Biotechnology and Food Science

country: Hungary

institute: Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

summary: Uracil incorporation into genomic DNA (U-DNA) can arise under conditions of nucleotide imbalance and may have regulatory consequences. Here, we report an unexpectedly high uracil content in early Danio rerio embryos, which decreases markedly by the time of zygotic genome activation (ZGA). Genome-wide profiling of U-DNA at 2.5 hpf revealed enrichment at specific satellite repeats, including MOSAT, BRSAT1, and SAT-12. These observations suggest that U-DNA and its processing could play roles either in supporting rapid cleavage divisions or in facilitating chromatin remodeling required for ZGA. To test this, we microinjected fertilized eggs with either active or catalytically inactive uracil-DNA glycosylase (UNG), thereby promoting or inhibiting U-DNA removal. Both interventions resulted in embryonic lethality, consistent with disruption of the normal uracil-processing balance and consequent perturbation of ZGA timing. Our findings indicate a potential regulatory function of U-DNA in early vertebrate development.

overall_design: Genomic DNA was isolated from wild-type zebrafish (AB strain) embryos at their 2.5 hpf age, and fragmented to 300-500 bp by sonication. Uracil-DNA enrichment was performed using U-DNA sensor and U-DNA-IP protocol as described previously (PMIDs: 32956035, 26429970). Input and enriched samples were sequenced by Illumina paired-end sequencing (PE-150) on a Novaseq 6000 platform.

first: Milda Blanka

last: Szajkó

first: Viktória

last: Perey-Simon

first: Hajnalka Laura

last: Pálinkás

first: Latifa

last: Kazzazy

first: Máté

last: Varga

first: Beáta

last: G. Vértessy

first: Angéla

last: Békési


title: Interactions between Streptococcus agalactiae, Candida albicans, and human vaginal epithelial cells

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: Group B Streptococcus (GBS) frequently colonizes the vagina asymptomatically where the bacterium interacts with a complex microbial community. During pregnancy, colonization can trigger adverse outcomes and neonatal invasive infection. Using an adapted murine model of vaginal colonization, we show that the human pathobiont Candida albicans supports GBS fitness in the vaginal tract and ascension to the uterus. C. albicans positively associates with GBS across several human studies, and C. albicans and GBS physically interact in a mouse co-colonization model. This co-colonization contributes to GBS persistence in the vagina, cervix, and uterus and facilitates antibiotic evasion. Across clinical isolates, the hyphal form of C. albicans promotes GBS aggregation and adhesion to host epithelial cells. Contact with GBS induces arginine biosynthesis in C. albicans, which drives bacterial virulence gene expression and primes GBS adhesion. These findings show that interkingdom nutrient exchange can increase GBS pathogenic potential and highlight targets for preventative therapies.

sample_organism:
Streptococcus agalactiae
Candida albicans
Homo sapiens

overall_design: We performed RNAseq on human vaginal epithelial cell air-liquid interface cultures, Candida albicans, and Streptococcus agalactiae mono- and co-cultures.

first: Shirli

last: Cohen

first: Arianne

last: Crossen

first: Owen

last: Jensen

first: Melody

middle: N

last: Neely

first: Kirsty

last: Le Doare

last: Nobbs

first: Kyla

middle: S

last: Ost


title: RNAseq analysis of bone marrow plasma cells from Taciflox/flox and Jchain-CreERT2;Taciflox/flox mice

city: Guangzhou

first: Yiming

last: Zhu

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

summary: Durable neutralizing antibodies are essential for vaccine-induced protection and are continuously secreted by bone marrow long-lived plasma cells (LLPCs). The longevity of these cells largely dictates the duration of vaccine-induced immune protection. We perfomred conditional deletion of TACI in PCs to analyze the effect of TACI on bone marow plasma cellls using Jchain-CreERT2;Taciflox/flox mice.

overall_design: Taciflox/flox and Jchain-CreERT2;Taciflox/flox mice were injected once daily with 100 mg/kg tamoxifen in corn oil for 3 consecutive days.Then 10,000 plasma cells (PCs,CD138high B220–) in bone marrow of these mice were sorted using BD FACS Aria Ⅲ. mRNA profiles of sorted bone marrow plasma cells were generated in triplicates by Illumina Platform.

first: Jun

last: Chen

first: Haimei

last: Lv

first: Chunliang

last: Xu


title: Immune checkpoint blockade augments lymphodepleting chemotherapy-induced antitumor immunity by expanding effector CD8+ T cell clones in preclinical models of cancer

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

institute: Weill Cornell Medecine

summary: Cancer treatment using immune checkpoint blockade (ICB) with anti-programmed cell death protein (PD)-1 and anti-cytotoxic T lymphocyte associated protein (CTLA)-4 has been successful. However, primary and acquired resistance limits clinical benefit. To improve the effectiveness of ICB therapies, strategies that reorchestrate anti-tumor immunity through mechanism-based drug combinations are being actively explored. The alkylating chemotherapeutic agent, cyclophosphamide (CTX), has direct tumoricidal and immunomodulatory properties, including the induction of homeostatic proliferation of T cells. Since ICB suppresses inhibitory signals in T cells, we hypothesized that ICB could augment CTX-induced homeostatic proliferation of antigen-specific T cells, thereby resetting the T cell receptor (TCR) repertoire in favor of tumor-specific T cells. Here, we show that a single dose of CTX one day prior to starting aPD-1+aCTLA-4 is sufficient to delay tumor progression in established melanoma and prolong survival in tumor-bearing mice in preclinical models. These effects extended to other lymphodepleting treatments, such as Gemcitabine and radiation therapy. The anti-tumor immune response was mainly driven by the clonal expansion of activated/effector CD8+ tumor infiltrating lymphocytes. Furthermore, combined CTX and aPD-1+aCTLA-4 treatment demonstrated efficacy across additional preclinical tumor models, including colorectal cancer and triple negative breast cancer. Overall, our findings highlight that the combination of CTX and aPD-1+aCTLA-4 represents a clinically relevant approach in the treatment of ICB-refractory tumors.

overall_design: CITEseq and TCR seq profiling for immune cells from B16-F10 tumors of mice treated with IgG, CTX IgG, aPD-1+aCTLA-4, CTX+aPD-1+aCTLA-4 at day 14 after treatment.

first: Mariam

last: George

first: Linda

last: Hamadene

first: Nicholas

last: Ceglia

first: Daniel

last: Hirschhorn

first: Isabell

last: Sculze

first: Lauren

last: Dong

first: Divya

last: Venkatesh

first: Rachana

last: Maniyar

first: Sadhna

last: Budhu

first: Alan

last: Houghton

first: Benjamin

last: Greenbaum

first: Jedd

last: Wolchok

first: Allison

last: Betof Warner

first: Taha

last: Merghoub


title: Recurrent cycles of drought stress led to low transcriptional reprogramming and greater accumulation of epigenetic marks in apple trees

first: Sandrine

last: Balzergue

summary: The differences observed in plant physiology, gene expression, and DNA methylation between two Drought Stress conditions suggest the involvement of a priming mechanism in apple seedlings. Priming, the ability of plants to "remember" environmental stress, can enhance their response to recurrent stress events (Harris et al. 2023). Our data support the idea that an initially naïve plant can be primed after a single drought episode, modifying its response thresholds and regulatory networks, as proposed by Lämke and Bäurle (2017). The progressive reduction in DEGs, dynamic changes in DMRs, and enhanced physiological responses all point toward priming as a key component of drought adaptation in seedlings.

overall_design: Recurrent Drought Stress (DS) experiments were conducted on 12-week-old seedlings of ‘Golden Delicious’ double haploid 18 (GDDH18). The DS assays were conducted on a total of 163 GDDH18 seedlings, distributed across three biological replicates. Plants were divided into two irrigation regimes: (I) Control group – maintained under well-watered (WW) conditions throughout the experiment; (II) Multiple-DS group – subjected to three drought stress (DS) cycles, each consisting of 3 weeks of drought followed by 3 weeks of rewatering (WW).  Leaves and roots were collected for methylation analyses after the first and the third drought périod. In addition, in year n+1, roots and leaves from Control and Multiple-DS plants were also sampled prior to the application of a new stress (Before Stress – BS), after completing one winter cycle.

first: Amanda

last: Malvessi-Cattani

first: Patricia

last: Mallegol

first: Sylvain

last: Hanteville

first: Skander

last: Hatira

first: Béatrice

last: Bonnet

first: Maryline

last: Cournol

first: Anne-Laure

last: Fanciullino

first: Jean-Marc

last: Celton


title: Roles of Msx2 in exogen control: Modulating stem cell niche during the transition from hair shedding to regeneration [RNA-Seq]

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

summary: The exogen phase of the hair follicle cycle, during which club hairs are shed and new hairs emerge, represents a pivotal yet understudied transition marked by structural remodeling and cell fate changes. This study investigates the role of the transcription factor Msx2 in regulating hair anchoring, hair follicle stem cell (HFSC) lineage commitment, and extracellular matrix (ECM) remodeling during exogen. Using Msx2-knockout (KO) mice, we integrated transcriptomic, epigenomic, and functional assays to reveal Msx2 as a key regulator of exogen, critical for maintaining HFSC niche integrity, preserving bulge architecture, and coordinating lineage progression during hair regeneration. By modulating the balance between TGF-β and Wnt signaling pathways, Msx2 ensures proper HFSC activation and prevents premature epidermal differentiation and hair shedding. These findings provide mechanistic insights into the molecular control of hair cycling and highlight Msx2 dysfunction as a potential contributor to hair loss disorders, positioning it as a promising therapeutic target in regenerative dermatology.

overall_design: To elucidate the role of Msx2 in regulating hair follicle stem cell (HFSC) behavior and chromatin dynamics during the exogen phase of the hair cycle, we performed bulk RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) on fluorescence-activated cell-sorted (FACS) epidermal stem cell populations from adult Msx2-knockout (KO) and wild-type (WT) mice. The sorted populations included HFSCs (CD34⁺CD49f⁺Sca-1⁻) and interfollicular epidermal stem cells (EpdSCs; CD34⁻CD49f⁺Sca-1⁺) isolated from dorsal skin. RNA-seq was conducted to profile transcriptional changes resulting from Msx2 deficiency, with a focus on genes involved in adhesion, differentiation, extracellular matrix remodeling, and TGF-β/Wnt signaling. In parallel, ATAC-seq was used to map genome-wide chromatin accessibility and identify differentially accessible regulatory regions, including promoters and distal elements. Combined analysis of RNA-seq and ATAC-seq data enabled the classification of active and repressive regulatory regions. It provided mechanistic insights into the transcriptional control and epigenomic remodeling mediated by Msx2. This integrated approach allowed us to define the transcriptional programs and chromatin landscapes disrupted in the absence of Msx2, and to pinpoint key signaling nodes implicated in HFSC fate transitions and exogen control.

first: Qi Chen

last: Chen

first: Wen-Chien

last: Jea

first: Ting-Xin

last: Jiang

first: Ping

last: Wu

first: Chi

last: Zhang

first: Ji

last: Li

first: Mingxing

last: Lei

first: Cheng-Ming

last: Chuong


title: Roles of Msx2 in Exogen Control:  Modulating the Stem Cell Niche During the Transition from Hair Shedding to Regeneration [ATAC-Seq]

first: Qi


title: Extracellular Vesicle Online Knowledge Explorer (EVOKE) - A guiding tool for the selection of methods to prepare extracellular vesicles from human biofluids II

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

institute: University Ghent

summary: Extracellular vesicles (EVs) exert multiple biological functions which has spurred their development as disease biomarkers and drug delivery vehicles. However, the wide range of EV preparation methods and the complexity of biofluids pose significant challenges for reproducible research and clinical translation. To address this difficulty, we developed the Extracellular Vesicle Online Knowledge Explorer (EVOKE)—a pioneering resource designed to assist researchers in evaluating and comparing EV preparation methods. To establish EVOKE, an international consortium was formed to systematically compare widely used EV preparation methods across diverse biofluids for key performance metrics using trackable reference materials and complementary characterization methods. EVOKE is the first freely accessible resource (www.evoke-tool.org) that guides researchers towards the informed selection of an optimal EV preparation method for a dedicated study goal, currently powered by over 2.4 million data points and amendable to future developments. It offers crucial insights into method-dependent efficiency, specificity, repeatability, and biomolecular variations and activity, ultimately steering informed method selection and reproducibility. In conclusion, EVOKE provides a strong foundation for coping with methodological challenges and advancing the clinical translation of EV research.

overall_design: EVs collected from urine; pooled  healthy donors n=6 and bladder cancer patients n=6; EVs were prepared using 14 preparation protocols with 3 technical replicates


title: The histone modifier KANSL2 is an actionable biomarker in multiple myeloma

city: Berlin

first: Stefan

last: Habringer

address: Hindenburgdamm 30

department: Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

summary: Epigenetic aberrations are key drivers of multiple myeloma (MM), yet targeted therapies exploiting epigenetic alterations have not been established. By integrating clinical and molecular MM patient data sets with an unbiased genetic in vivo screen, we identified KAT8 regulatory NSL complex subunit 2 (KANSL2) as a histone posttranslational modification (PTM)-associated candidate oncogene. High expression of KANSL2 was associated with adverse prognosis in MM patients. Genetic gain and loss of function models identified a protective role of KANSL2 towards genotoxic stress. By transcriptomics, proteomics and quantitative acetylome profiling, we identified a KANSL2-dependent specific molecular program targetable by acetylation-related modifiers. High KANSL2 levels increased sensitivity to the histone deacetylase inhibitor panobinostat and bromodomain and extra-terminal motif inhibitor OTX-015 and their combination. Collectively, we identified KANSL2 to mediate chemotherapy resistance that could be overcome by targeting epigenetic regulators.

overall_design:
RNA sequencing data of MM cell lines with CRISPR-dCas9-CRAB mediated knock-down of KANSL2 and non-targeting control sgRNAs.
ATACseq data of MM cell lines with CRISPR-dCas9-CRAB mediated knock-down of KANSL2 and non-targeting control sgRNAs.

first: Kaiting


title: Transcriptome signatures of SU-Eohyeol pharmacopuncture (SUEHP) in an MPTP-induced Parkinson's disease animal model

city: Daejeon

first: jungim

last: Kim

address: 1672, Yuseong-daero, Yuseong-gu

department: KM Convergence Research Division

institute: Korea Institute of Oriental Medicine

summary: Parkinson’s disease (PD) is a progressive neurodegenerative disorder for which no definitive cure currently exists. The disease is primarily characterized by motor symptoms such as muscle rigidity, bradykinesia, and postural instability, along with a range of non-motor symptoms including pain, depression, sleep disturbances, and cognitive impairment. Given the absence of comprehensive therapeutic approaches that can effectively address both motor and non-motor manifestations of PD, we sought to investigate the potential therapeutic efficacy of SUEHP, a modality derived from traditional East Asian medicine. A mouse model of PD was established via administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), followed by SUEHP treatment administered twice weekly for a duration of two weeks. Based on compositional analysis of the pharmacopuncture formulation, cannabinoid receptor 1 (CB1) and peroxisome proliferator-activated receptor gamma (PPARγ) were identified as potential molecular targets. To assess their involvement, selective antagonists or inhibitors were co-administered. Transcriptomic analysis was subsequently conducted to characterize gene expression alterations associated with SUEHP treatment and to elucidate underlying mechanisms of action.

overall_design: Beginning one week after MPTP injection, SUEHP was administered twice a week for 2 weeks at the GB34 acupoint, a site commonly associated with the amelioration of Parkinsonian symptoms. The gluteal area was used as a control site for comparison. CB1 antagonist or PPARγ inhibitor were co-administered intraperitoneally with SUEHP.

first: Jung-Im

first: Sang-Min

last: Park

first: No-Soo


title: Sequencing analysis of the single-cell transcriptome of Cellulomonas_iranensis

first: Qin

state: Guangdong

address: Wushan road

institute: College of Forestry and Landscape Architecture

summary: We have employed  a single cell sequencing approach using MobiMicrobe platform to study the consister of Cellulomonas iranensis.

overall_design: Cellulomonas iranensis was isolated from the plant fermentation product. Then, the bacterial suspension was subjected to single-cell transcriptome library construction using the single-cell transcriptome library construction platform, and subsequent sequencing analysis was conducted.


title: Transcriptome-wide mapping of m6A in bovine oocytes and preimplantation embryos by SAC-seq [SAC-Seq]

city: Gainesville

first: Zongliang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: RNA N6-methyladenosine (m6A) plays a crucial role in regulating gene expression and early embryonic development. However, the m6A dynamics at single-nucleotide resolution during preimplantation development has not been characterized, and the function of m6A marks in specific transcripts remain largely unexplored. Here, by using SAC-seq, we overcome the limitation of antibody-based m6A profiling and define m6A landscapes in bovine oocytes and pre-implantation embryos at unprecedented level. Notably, we identify a specific m6A site on RPL12 (m6A-RPL12), which was highly methylated at the 8-cell stage. m6A-RPL12 deficient leads to reduced protein synthesis, disrupted expression of translation-related genes, and impaired zygotic genome activation and blastocyst formation. Supplementation with wild-type RPL12 mRNA failed to rescue the developmental arrest, indicating that m6A regulation extends beyond transcript abundance. This study provides invaluable m6A single-nucleotide resolution recourse in early embryogenesis and demonstrates that precise regulation of m6A at selected transcripts can shape early developmental outcomes in mammals.

overall_design: m6A-SAC-seq profiling of the Bovine oocytes (GV, MII stages) and early embryos (2-cell, 4-cell, 8-cell, 16-cell, Morula, Blastocyst). 200cell per stage per replicate were used as a starting material for the SAC-Seq protocol.

first: Rajan

last: Iyyappan


title: Neurotoxicity, α-Synuclein Pathology, and Mitochondrial Dysfunction: A Comparative Study of Three Parkinson’s Disease Mouse Models

city: Shanghai

first: Yifei

last: He

email: crestedibistoki@gmail.com, 21301010016@m.fudan.edu.cn, yumei@fudan.edu.cn, 23211520033@m.fudan.edu.cn

address: 138 Yixueyuan Road

department: Institute of Brain Science

institute: Fudan University

summary: The pathogenesis of Parkinson’s disease (PD) is complex, and it is difficult for a single animal model to fully mimic its pathological features. In this study, a comprehensive analysis of behaviors, PD-like pathologies, and gene and protein expression profiles was carried out in PD mouse models (MPTP-induced, α-Syn A53T transgenic, and MitoPark models). The three PD models showed motor impairments, with MitoPark mice displaying particularly pronounced age-related worsening. Pathologically, they all exhibited nigrostriatal pathway damage but showed differential patterns of glial cell activation. All three PD model mice showed no α-Syn aggregates. However, a few pS129-α-Syn-positive signals were detected in the substantia nigra of α-Syn A53T transgenic mice. Molecularly, RNA sequencing and proteomics revealed significant changes in gene and protein expression, with both unique and common features. Five common differentially expressed genes (Ifi27l2a, Ifitm3, Oasl2, Rtp4, and Ankk1) and two common differentially expressed proteins (Timm8a1 and Sephs1) were identified. Functional enrichment analysis indicated that immune responses, cytokines, and neurotransmitter transport were crucial in PD pathogenesis. Pathway analysis revealed the involvement of ferroptosis in all models, with additional IL-17 pathway activation specifically in MitoPark mice. These findings provide a comprehensive molecular and phenotypic characterization of PD models, offering valuable insights into disease mechanisms and potential therapeutic targets.

overall_design: RNA-seq profiling of the striatum from wild-type mice and three PD mouse models: (i) MPTP-induced model: C57BL/6 mice received acute treatment (15 mg/kg MPTP-HCl i.p. every 2 h for 4 times on day 1) or subacute treatment (20 mg/kg MPTP-HCl i.p. daily for 5 days), with striatal samples collected 3 days after the last administration; (ii) α-Syn A53T transgenic model: striatal tissues were harvested from 12-month and 16-month-old transgenic mice; (iii) MitoPark model: striatum was collected from 5-month-old MitoPark mice.

first: Fang

last: Huang

first: Mei

last: Yu

first: Xiwen

last: Tang


title: ERG preserves endothelial identity to limit atherosclerosis

city: Toronto

first: Kathryn

last: Howe

state: Ontario

address: 101 College Street

department: Biomedical Research (Cardiovascular)

country: Canada

institute: Toronto General Hospital Research Institute

summary: Endothelial function is a critical safeguard against atherosclerosis. At atheroprone sites, the normally protective arterial endothelium can undergo endothelial-to-mesenchymal transition (EndMT), but the timing, contribution, and reversibility of this process during atherogenesis are poorly understood. Here we explored the impact of endothelial identity loss in atheroprogression through modulation of the ETS transcription factor ERG, a principal endothelial identity regulator. Inducible endothelial Erg deletion markedly increased plaque in hypercholesterolemic mice. Endothelial-lineage tracing and single-cell transcriptomics revealed that ERG loss induced profound dedifferentiation, followed by mesenchymal fate acquisition and migration and expansion of EndMT cells into the plaque, which interacted with pro-atherosclerotic macrophages and smooth muscle cells. Endothelial identity loss also promoted early disruption of junctional signaling and barrier, leading to enhanced lipid uptake, and foam cell accumulation in typically atheroresistant regions. Investigation of ERG in human atherosclerosis identified reduced chromatin accessibility and expression in plaques, where endothelial cell transcriptional changes paralleled murine Erg deletion. Restoration of ERG in cultured EndMT cells reversed mesenchymal and restored endothelial cell gene regulatory programs. These findings implicate ERG downregulation as a novel driver of endothelial dysfunction in atherosclerosis, reinforce the link between EndMT and atheroprogression, and highlight ERG as a mechanism to restore endothelial identity.

overall_design: Following atherosclerosis induction with injection of AAV8-PCSK9 and 4 or 12 weeks of high-cholesterol diet, aortic intimal cells were isolated from ERG EC-KO or control mice and analyzed using scRNA-seq. The experiment contains 4 samples: week 4 ERG control; week 4 ERG EC-KO; week 12 ERG control; week 12 ERG EC-KO.

first: Steven

last: Botts

first: Jason

last: Fish


title: DUX4 activates a transcriptional network involving Krüppel-like factors KLF17 and KLF18 [KLF17_KLF18_OE]

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: DUX4 is a critical regulator of gene expression during human embryonic development and is the driver of facioscapulohumeral muscular dystrophy (FSHD). In this study, we demonstrate that DUX4 induces expression of Krüppel-like factor 18 (KLF18), which is necessary for the subsequent activation of KLF17 and a subset of genes induced in the DUX4 transcriptional network. Loss of KLF18 partially disrupts the DUX4 transcriptional network in both muscle cells and human embryonic stem cells, including genes associated with zygotic genome activation. KLF18 binds to the promoter regions of many of the genes it regulates but also requires DUX4 expression to transcriptionally activate many of its targets, indicating a feed-forward regulatory mechanism. While KLF17 and KLF18 have high homology in the zinc-finger DNA binding domain, human KLF18 contains a region with a variable number of tandem repeats (VNTRs) of fourteen amino acids predicted to form a beta-solenoid-like protein structure that is absent in rodent homologs and variably present in other species. Multiple structural variants consisting of different numbers and positions of repeat deletions are present in the human population, although initial studies do not show evidence of functional differences among the most common variants. These studies identify KLF18 as a key transcription factor in a feed-forward transcriptional network regulating early embryonic genes and the pathological DUX4 program in facioscapulohumeral dystrophy.

overall_design: Myoblasts were transiently trasnfected with KLF17, KLF18, or GFP expression vectors then harvested for RNA sequencing 48 hours later

first: Danielle

last: C. Hamm

first: Aidan

last: B. O’Donnell

first: Sean

last: R. Bennett

first: Richard

last: J. L. F. Lemmers

first: Patrick

last: J. van der Vliet

first: Silvère

last: M. van der Maarel

last: J. Tapscott


title: DUX4 activates a transcriptional network involving Krüppel-like factors KLF17 and KLF18 [ChIP-Seq]

summary: Sean, R. Bennett

overall_design: ChIP-seq was performed on either MB135-iDUX4ca WT or MB135-iDUX4ca 3xFLAG using a 3xFLAG antibody.


title: Single cell RNA-sequencing of EC lineage tracing mice

city: New Haven

last: Citrin

address: 10 Amistad St

institute: Yale University

summary: In order to ascertain how EC gene expression is heterogenous and changes throughout atherosclerosis, the aorta of mice fed a western diet for 8 weeks was processed for single cell RNA-sequencing.

overall_design: Mice were injected with PCSK9-AAV8 and fed a western-type diet for 8 weeks. The aorta was harvested and processed into a single cell suspension. tdTomato+ (EC) and tdTomato- (non-EC) were separated by FACS, and then recombined to enrich the EC. Cell suspensions were then submittted for scRNAseq.

first: Yajaira

last: Suarez


title: Endothelial miR-33 protects from atherosclerotic lesion initiation and acute inflammation

summary: Human aortic endothelial cells (HAEC) were treated with TNF, or TNF and LDL, in order to determine how cholesterol loading  influences HAEC inflammatory responses to TNF. Cells were also transfected with a miR-33 mimic to determine which of the LDL-mediated perturbations are dependent on cholesterol-induced miR-33 dysregulation. From these analyses, we determined that miR-33 is able to rescue a signifcant portion of the genes dysregulated in hypercholesteremic inflammation compared to normocholesteremic inflammation.

overall_design: RNA-seq analysis of transcriptomic changes that occur in Human Aortic Endothelial Cells (HAEC) under inflammatory and/or lipid-laden conditions, with or without miR-33 mimicry.


title: RNA-seq of B-cell lymphoma treated with Ibrutinib and CAR T cells

city: Taipei

first: Yi-Lin

last: Chiu

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

summary: This dataset presents RNA sequencing (RNA-seq) data from human B-cell lymphoma HT tumors established in immunodeficient mice. Tumors were treated with ibrutinib (IB), CD19-directed chimeric antigen receptor T cells (CAR T cells), or a combination of both. The study aimed to investigate transcriptomic changes and treatment-related gene expression differences induced by monotherapy or combination therapy. These data provide insight into the molecular responses to IB and CAR T-cell treatment in vivo and may help elucidate mechanisms underlying therapeutic synergy.

overall_design: Human HT B-cell lymphoma cells (1.5 × 10⁷) were implanted subcutaneously into male CAnN.Cg-Foxn1nu/CrlNarl mice (4 weeks old). When tumors reached ~100 mm³, animals were randomized to four treatment arms:(i) vehicle control, (ii) ibrutinib (25 mg kg⁻¹ day⁻¹, oral gavage), (iii) intratumoral CD19-directed CAR-T cells (5 × 10⁶ cells), or (iv) the combination of ibrutinib and CAR-T. Tumor size was monitored twice weekly; mice were euthanized if volumes exceeded 2000 mm³. At the study endpoint, tumors were excised and total RNA was extracted with QIAzol/RNeasy. Strand-specific libraries were prepared by Genewiz and and sequenced on an Illumina NovaSeq 6000 platform using 2×150 bp paired-end mode. FastQC was used for read-quality assessment, adapters and low-quality bases were trimmed, and transcript abundance was quantified against the Ensembl GRCh38 (release 114) transcriptome using Salmon v1.10.0 and kallisto v0.46.1.

first: Xin-Jie

last: Lu

first: Hsing-Fan

last: Lai


title: Determination of transcriptomic changes associated with freezing-temperature stress in Arabidopsis plants grown in soil pots

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: We report the gene expression profiles of Arabidopsis seedlings treated with or without ethanol under freezing-temperature stress condition.

overall_design: Arabidopsis seedlings were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle. Fourteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 6 days. After ethanol pretreatment, the pots were subjected to freezing temperature treatment at -4.0 °C onvernight by a low-temperature incubator. During the freezing temperature stress treatment, the pots were electrically rotated in the incubator to avoid the local effect. After the treatment, the pots were returned to the growth room and maintained for the indicated time periods.

first: Daisuke

last: Todaka

first: Kentaro

last: Nakaminami

first: Maho

last: Tanaka

first: Satoshi

last: Takahashi

first: Do

last: Quynh

first: Junko

last: Ishida

first: Kyoko

middle: Y

last: Mogami

first: Atsushi

last: Nagano

first: Motoaki

last: Seki


title: Methylome profiling of SetDB1 deficient ESCs reveals coordinated epigenetic cross-talk during pluripotency

city: Nijmegen

first: Nick

last: Bovee

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

summary: DNA methylation profiling using whole-genome bisulfite sequencing of conditional SetDB1 knockout (KO) mouse embryonic stem cells (ESCs). Induction with 4-hydroxytamoxifen (4-OHT) facilitated the deletion of Setdb1 floxed exons 15 and 16, resulting in loss of SetDB1. Methylomes were profiled in wildtype (WT) serum- and 2i-cultured ESCs, and on multiple days after inducing SetDB1 depletion. Study also includes methylome profiles of ESCs undergoing simultaneous SetDB1 depletion and 2i-adaptation.

overall_design: DNA methylation profiling using whole-genome bisulfite sequencing in timecourse following SetDB1 depletion in serum- and 2i-cultured mouse ESCs.

first: Stefan

last: Hoogland

first: Ehsan

last: Habibi

first: Siebren

last: Frölich

first: Arie

last: Brinkman

first: Klaas

last: Mulder

first: Joop

last: Jansen

first: Matthew

last: Lorincz

first: Henk

last: Stunnenberg

first: Hendrik

last: Marks


title: Determination of transcriptomic changes associated with freezing-temperature stress in Arabidopsis plants grown in agar plates

first: motoaki

last: seki

overall_design: Thirteen- or 11-day-old seedlings were treated with gaseous ethanol for 1 d or 3 d, respectively.

first: Kentaro

last: Nakaminami

first: Daisuke

last: Todaka

first: Maho

last: Tanaka


title: Repurposed fludarabine alleviates type 1 diabetes through the dual effects on dendritic cell activation and β cell ferroptosis

city: wuhan

first: shan-jie

last: Rong

address: wuxian road tongji hospital research buliding

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

summary: Type 1 diabetes (T1D) imposes a substantial burden on patients yet effective therapies to halt disease progression are lacking. Immunomodulatory strategies that suppress autoreactive immune response and preserve pancreatic β cell function are essential for improving long-term therapeutic outcome. Herein, we repurposed fludarabine, a clinically applied drug, in the T1D setting. Fludarabine treatment markedly alleviates inflammatory immune activation and β cell destruction. Moreover, fludarabine induces tolerogenic dendritic cell (DC) phenotype through chemical reprogramming. The protective effect of fludarabine-treated DCs was further corroborated by adoptive transfer experiment. Mechanistically, fludarabine directly binds to STAT1 and disrupts its interaction with the aryl hydrocarbon receptor (AHR), thereby facilitating AHR nuclear translocation. Activated AHR transcriptionally upregulates anti-inflammatory and anti-ferroptotic programs, conferring a tolerogenic DC phenotype and protecting β cells from stress-induced ferroptosis. Collectively, our findings identify fludarabine as a promising immunometabolic therapeutic candidate that restores immune tolerance and enhances β cell resilience, which could be a viable approach against T1D in clinical settings.

overall_design: We initially induced DC_WT and DC_Flu from WT mice, the prepared BMDC were pretreated with LPS (100 ng/mL) for 24 h. Then total RNA was extracted using Trizol reagent (#9108, Takara, Japan) according to the manufacturer’s procedure. RNA sequencing was performed on the NovaSeq X Plus platform using the Illumina NovaSeq Reagent Kit. Raw sequencing reads were first subjected to quality control using FastQC, to ensure data integrity. Clean reads were then aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) aligner. Transcript abundance was quantified using feature Counts, which provides read counts for each gene. The read counts were normalized to account for library size and other technical variations using the DESeq2 package. Differential expression analysis was then performed to identify genes with statistically significant changes in expression between conditions. Among the six samples, a minimum of a one-fold difference in log 2 expression and FDR adjusted P value < 0.05 were considered as expression differences.

first: Shanjie

first: Chunliang

last: Yang

first: Fei

last: sun

first: Tiantian

last: Yue

first: Qilin

last: Yu

first: Congyi

last: Wang


title: lncRNA-operated stem cell fate control: RPS3 organizes the in situ Gm16751-Zhx3 interactome to program spermatogonial differentiation [Long RNA-Seq]

first: Ji

last: Wu

state: Shanghai

address: No. 800, Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Long non-coding RNAs (lncRNAs) play pivotal regulatory roles in mammalian male gametogenesis. Advances in high-throughput technologies have demonstrated that lncRNAs orchestrate robust, flexible, and context-specific gene regulatory networks through dynamic interactions with proteins, DNA, and RNA, modulating transcriptional and post-transcriptional processes. However, the mechanistic role of in situ lncRNA-mRNA interactions in spermatogonial stem cell (SSC) differentiation remains poorly understood. In this study, we employed RIC-seq (RNA in situ conformation sequencing) and LongRNA-seq to systematically identify a functional interaction between lncRNA Gm16751 and Zhx3 mRNA during SSC differentiation, which was further visualized via a Circos plot. Mechanistically, we demonstrated that Gm16751 enhances the mRNA stability of Zhx3, thereby promoting SSC differentiation. Furthermore, mass spectrometry analysis revealed that RPS3 (Ribosomal Protein S3) serves as a critical RNA-binding protein (RBP) that bridges the interaction between Gm16751 and Zhx3, ultimately stabilizing Zhx3 mRNA and modulating SSC differentiation. Our findings provide novel mechanistic insights into the lncRNA-mRNA regulatory axis in SSC differentiation and establish a foundation for understanding the molecular etiology of male germ cell developmental disorders and spermatogenic dysfunction.

overall_design: LongRNA-seq profiling the transcriptome changes of mouse spermatogonial stem cells and their differentiation, including linear mRNA,  lncRNA, and circRNA

first: Weijun

last: Gao

first: Wenzhi

last: Ma


title: Glutathione S-transferase Theta 2 causes drug resistance by inhibiting arsenic trioxide-induced ferroptosis in pancreatic ductal adenocarcinoma

city: HangZhou

first: Rong

last: Chen

state: Zhejiang

address: Fuchun Road

department: College of Pharmacy

institute: Zhejiang Chinese Medical University

summary: Currently, chemotherapy remains a key treatment modality for pancreatic ductal adenocarcinoma (PDAC). However, the emergence of drug resistance limits the chemotherapeutic efficacy. Ferroptosis inhibition plays a significant role in chemotherapy resistance. This study investigates the potential mechanisms of PDAC resistance to arsenic trioxide (ATO) and explores the role of GSTT2 in chemotherapeutic resistance. PDAC cells showed ATO resistance due to inhibition of drug-induced ferroptosis, which was validated in vivo and in vitro. Inhibition of nuclear factor erythroid 2-related factor 2 (Nrf2) did not restore ferroptosis. Transcriptomic analysis showed that GSTT2 is significantly upregulated in ATO-resistant cells, suggesting it is a key factor in drug resistance. GSTT2 is highly expressed in ATO-resistant cells compared to ATO-sensitive cells. Silencing GSTT2 enhances the sensitivity of resistant cells to ATO. Further studies indicate that GSTT2, a downstream target of Nrf2, regulates the expression of glutathione peroxidase 4 (GPX4) and ferritin light chain (FTL). Silencing GSTT2 can enhance drug sensitivity by activating ferroptosis in drug-resistant cells. Our study identifies the Nrf2-GSTT2-GPX4 ferroptosis regulatory axis, demonstrating that GSTT2 is a negative regulator of ATO-induced ferroptosis. The development of therapeutic strategies targeting the Nrf2-GSTT2-GPX4 axis will open new avenues for combating resistance to chemotherapy in PDAC.

overall_design: Transcriptome sequencing on tumor tissues from orthotopic xenograft mouse models bearing AsPC-1 or BxPC-3 cells, with or without ATO treatment.


title: lncRNA-operated stem cell fate control: RPS3 organizes the in situ Gm16751-Zhx3 interactome to program spermatogonial differentiation [RIC-Seq]

overall_design: RNA in situ coformation-seq profiling the in situ RNA-RNA interaction changes of mouse spermatogonial stem cells and their differentiation.


title: Transcriptomic Analysis to Elucidate Key miRNAs and Signaling Pathways Involved in the Promotion of Periodontitis by Hypertension

city: Nanning

first: xiaoping

last: su

state: Guangxi

address: shuangyong road

institute: guangxi medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify key miRNAs that promote the progression of periodontitis in the context of hy-pertension through high-throughput sequencing, rat models of periodontitis and periodontitis combined with hypertension were established, with healthy rats serving as the control group. Periodontal tissues from each group were collected for small RNA sequencing. Subsequently, differential miRNAs were analyzed in the periodontitis with hypertension group compared to the control group, as well as in the periodontitis with hypertension group compared to the periodontitis group.

overall_design: Three groups were established – a periodontitis model group, a periodontitis with hypertension model group, and a healthy rat control group. Gingival tissues from each group were harvested for miRNA sequencing.

first: Haiqing

last: Liao

first: Cuiping

last: Li

first: Zhiqing

last: Feng

first: Chenrui

last: Fan

first: Jialei

last: Xu

first: Lufei

first: Xiaoping

last: Su


title: Transcriptomic Analysis to Elucidate Key Genes and Signaling Pathways Involved in the Promotion of Periodontitis by Hypertension

summary: To identify key genes and metabolites that promote the progression of periodontitis in the context of hypertension through transcriptomic analyses. Rat models of periodontitis and periodontitis combined with hypertension were established, with healthy rats serving as the control group. Periodontal tissues from each group were collected for transcriptomic sequencing. Subsequently, differential mRNA, lncRNA and circRNA were analyzed in the periodontitis with hypertension group compared to the control group, as well as in the periodontitis with hypertension group compared to the periodontitis group. Gene Ontology and KEGG enrichment analyses were performed, and a joint analysis of differential genes and metabolites was conducted. The differential genes and metabolites were primarily enriched in the pathways of arginine biosynthesis, cysteine and methionine metabolism, and biosynthesis of amino acids. Hypertension may promote the development of periodontitis by altering interferon-inducible genes-related pathway.

overall_design: Three groups were established – a periodontitis model group, a periodontitis with hypertension model group, and a healthy rat control group. Gingival tissues from each group were harvested for transcriptomic sequencing.


title: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor [scRNAseq]

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor We characterized mPB CD34+ cell population dynamics (n=2 donors) by single cell RNA sequencing (scRNAseq) during 8 days of expansion culture using commercial serum-free media (Miltenyi Bioscience) in the presence of the epigenetic modifier UM171 and early acting cytokines (SFT6: stem cell factor, 100ng/mL; flt3 ligand, 100ng/mL; thrombopoietin, 50ng/mL; interleukin 6, 50ng/mL). Cultured cells were transduced with a lentiviral vector expressing a marker gene, to simulate a gene therapy context. CD34+ cells from donor 1 were analyzed before culture, on day 4 and on day 8 of expansion. For donor 2, in addition to the CD34+ bulk expansion culture, part of the CD34+ cells were FACS-sorted into subpopulations enriched in primitive HSPC (CD34+CD38-), committed granulocyte-monocyte progenitors (GMP) or megakaryocyte-erythrocyte progenitors (MEP), and subsequently expanded for 7 days.

first: Erika

last: Zonari

first: Matteo Maria

last: Naldini

first: Bernhard

last: Gentner


title: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor [bulkRNAseq]

summary: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor. We characterized mPB CD34+ drug products and their ex-vivo expanded samples (4 and 7 days) cell populations (n=2 patients from 10.1056/NEJMoa2106596) and transduction efficency by single cell RNA sequencing (scRNAseq) using commercial serum-free media in the presence of the epigenetic modifier UM171 and early acting cytokines (DP: refers to 10.1056/NEJMoa2106596; for cultured samples at day4 and day 7: SFT6: stem cell factor, 100ng/mL; flt3 ligand, 50ng/mL). Cells of DP and its expanded samples were transduced with a lentiviral vector expressing the IDUA gene. WPRE transcript quantification was used as surrogate of LV IDUA expression to evaluated transduction efficiency.

overall_design: CD34+ cells were expose to small molecules UM171 and SR1 during culture. For details see manuscript.

first: Beatrice

last: Martini


title: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor [MPS_scRNAseq]

overall_design: We characterized mPB CD34+ drug products and their ex-vivo expanded samples (4 and 7 days) cell populations (n=2 patients from 10.1056/NEJMoa2106596) and transduction efficency by single cell RNA sequencing (scRNAseq) using commercial serum-free media in the presence of the epigenetic modifier UM171 and early acting cytokines (DP: refers to 10.1056/NEJMoa2106596; for cultured samples at day4 and day 7: SFT6: stem cell factor, 100ng/mL; flt3 ligand, 50ng/mL). Cells of DP and its expanded samples were transduced with a lentiviral vector expressing the IDUA gene. WPRE transcript quantification was used as surrogate of LV IDUA expression to evaluated transduction efficiency.


title: Single-cell RNA Sequencing of Human Embryonic Stem Cells Reveals Immediate and Deferred Transcriptomic Responses to ATRA Toxicity Across Cell Sub-populations

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

summary: Identifying chemical-mediated molecular signatures may provide nuanced insights into early developmental processes, characterized by plasticity, rapid growth, and differentiation. This requires increased resolution of the multiple cell states and trajectories that are present at this stage. Cell-based models can facilitate higher-throughput evaluation and screening of potential developmental toxicants. In this study, we used single-cell RNA sequencing to characterize the transcriptomic signatures of the H9 human pluripotent stem cell (hPSC) maintained under pluripotency and treated with 30 nM all-trans retinoic acid (RA), a developmental morphogen, for 6 and 72 hours. In addition, we evaluated the molecular effects of RA on hPSCs over an undirected differentiation course for 14 days, to characterize retinoic acid-associated cell transition states. For both pluripotent (6- and 72-hrs) and undirected differentiation (14-day) exposure paradigms, transcriptional responses to RA were observed and compared to gastrulation markers of altered developmental trajectories. At 14 days in differentiation media, we observed cell clusters representing differentiation into multiple cell-types. This transcriptomic data could be utilized to identify and screen chemicals for developmental toxicity.

overall_design: In this study, we leveraged the resolution of scRNA-seq to characterize short-term exposure-mediated molecular signatures during early embryogenesis. We sought to identify developmental toxicant-associated biomarkers that could be applied towards high-throughput chemical screens. To this end, we treated an hPSC cell line (H9) with all-trans retinoic acid (RA), a well-established pan-developmental morphogen and teratogen, for 6 and 72 hours, and used scRNA-seq to define RA-modulated transcriptomic profiles in pluripotent/progenitor cell states. We identified RA-mediated signatures starting at 6 hours of treatment. In addition, we assessed the effects of RA on undirected differentiation of H9s for 14 days, to elucidate RA-mediated cell states and molecular pathways that may be enriched or diminished compared to untreated cells.

first: Chorley

last: Brian N.

first: Gallegos

last: David

first: Park

last: Sarah


title: Evaluation of Season and Sex specific Differential Gonadal Transcriptomics in Himalayan Snow trout Schizothorax plagiostomus

city: West Lafayette

first: Harish

last: Kothandaraman

state: Indiana

address: 201S University St

department: Purdue Institute for Cancer Research

institute: Purdue University

summary: Despite wide presence of Schizothorax plagiostomus in cold-water bodies of central Asian mountains it is highly neglected Himalayan ichthyofauna. Here we have performed de novo RNA-sequencing in adult S. plagiostomus gonads captured from natural habitat of Garhwal Himalaya [during three distinct maturational stages (pre-spawning, spawning and post-spawning) for both sexes] and compared the season and sex specific differential transcriptomic profiles

overall_design: Gonad RNA Sample

first: Indrashis

last: Bhattacharya

first: Shriya

last: Purohit

first: Partigya

last: Sharma

first: Sachin

last: Kothiyal


title: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor

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

overall_design: Refer to individual Series


title: Hypoxia differentially affects coronary vessel formation during heart development

city: Oxford

first: Sophie

last: Payne

address: Old Road Campus

department: Department of Physiology, Anatomy & Genetics

institute: University of Oxford (UK, Oxford)

summary: The coronary vessel system is a dense and diverse network of arteries, veins and capillaries formed by endothelial cells from a variety of sources. While hypoxia is a known stimulus for angiogenic sprouting, the exact mechanisms by which hypoxia - and resultant increased VEGFA - influences vessel growth in the heart are not clearly delineated. We used a genetic mouse model to mimic hypoxia through ectopic stabilisation of myocardial HIFα. This enabled us to study the consequences of hypoxia without vascular depletion. Changes in coronary ECs in these hearts relative to littermate controls were assessed by single cell RNA-sequencing. This identified increased angiogenic gene expression and a shift towards a non-proliferative, migratory tip cell phenotype.

overall_design: Mouse embryos were harvested from a single litter at embryonic day (E)13.5, following the timed mating of a Phd2fl/fl;Nkx2.5-Cre male with a Phd2fl/fl;RosaYFP female. Expression of the reporter YFP gene indicated presence of CRE activity, and genotypes were later confirmed by PCR. Hearts were dissected from 4 Phd2fl/fl;Nkx2.5-Cre embryos and 4 control Phd2fl/fl embryos, with the atria and outflow tracts removed. Each heart was processed as a single sample for the scRNA-seq experiment. Hearts were dissociated and enriched for endothelial cells using fluorescence activated cell sorting (FACS), before library preparation and scRNA-seq analysis.

first: Susann

last: Bruche

first: Dorota

last: Szumska

first: Alice

last: Neal

first: Mark

middle: D

last: Preston

first: Sarah

last: De Val


title: Neural stem cells epigenomes and fate bias are temporally coordinated during corticogenesis [Methyl-Hi-C]

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

summary: The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell transcriptomics and chromatin accessibility, together with genome-wide profiling of DNA methylation and 3D chromosomal contact across mouse corticogenesis (E13–E18) to elucidate cell fate transitions. We reveal using metacell flow analysis that neural stem cells (NSC) progressively shift from an intermediate progenitor–biased state toward an astrocytic lineage and that his process is accompanied with DNA methylation programming and chromosomal insulation changes. A model integrating transcription factor motif affinities with epigenetic features, identifies key regulators of cis-regulatory element (CRE) activation. In vivo reporter assays further decouple the intrinsic regulatory potential of CREs from context-dependent synergistic activation. Collectively, our findings uncover temporal epigenomic reprogramming that underlies the evolving differentiation potential of NSC, providing insights into the intrinsic and extrinsic mechanisms that pattern cortical lineages.

overall_design: scRNA-seq and scATAC-seq were performed on the somatosensory cortex of mouse embryos at E13, E15, E16, E17 and E18. Methyl-Hi-C was carried out on neural stem cells (NSC) (Pax6+ cells) isolated from the somatosensory cortex at E13, E15, E16 and E17. Additionally, in utero electroporation for massively parallel reporter assay (MPRA) was performed in the somatosensory cortex at E12, E13, E14, E15 and E16 and MPRA was subsequently conducted on NSC (Pax6+ cells) and intermediate progenitors (IPC) (Tbr2+ cells) isolated 24 hours after each respective time point.

first: Yonatan

last: Shapira

first: Florian

last: Noack

first: Silvia

last: Vangelisti

first: Faye

last: Chong

first: Aviezer

last: Lifshitz

first: Amos

last: Tanay


title: Neural stem cells epigenomes and fate bias are temporally coordinated during corticogenesis [scATAC-seq]


title: Neural stem cells epigenomes and fate bias are temporally coordinated during corticogenesis [scRNA-seq]


title: Loss of Ambp ameliorates MASLD progression via generating protective ROS and activating PPAR signaling pathway

city: Zhan Jiang

first: Xiaoyu

last: Li

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

summary: Background: Metabolic dysfunction-associated steatotic liver disease  (MASLD) is a widespread and severe hepatic disease, affecting approximately 30% of the global population. Despite its prevalence, the precise pathophysiological mechanisms underlying the development of MASLD remain incompletely elucidated. Previous investigations have revealed that A1M exerts regulatory effects on endoplasmic reticulum stress and oxidative reactions within hepatocytes, thereby affecting liver homeostasis. However, the roles of AMBP, the precursor of A1M and Bikunin, in the pathogenesis and progression of MASLD remain inadequately characterized. Methods: In this study, we analyzed the AMBP expression across multiple MASLD related Gene Expression Omnibus (GEO) datasets. Utilizing zebrafish ambp-/- and mouse Ambp-/- mutants subjected to high-fat diet (HFD) feeding, we assessed hepatic lipid accumulation. Additionally, we measured reactive oxygen species (ROS) levels, glutathione peroxidase 4 (Gpx4), and malondialdehyde (MDA) expression, and performed RNA sequencing in HFD-fed ambp-/- zebrafish. The roles of ROS were further investigated using the ROS inhibitor N-acetylcysteine (NAC) and the PPARα-specific inhibitor GW6471. Results: Our finding revealed that ambp deficiency mitigated the occurrence of MASLD under HFD conditions. Mechanistically, ambp deficiency induced the production of cytoprotective ROS, which subsequently activated the PPAR signaling pathway, thereby inhibiting oxidative stress and enhancing the mitochondrial fatty acid β-oxidation. Conclusions: Collectively, our results demonstrate that AMBP serves as a critical regulator of MASLD pathogenesis. Inhibition of AMBP might be a promising therapeutic approach for the treatment of MASLD.

overall_design: We extracted the total RNA from the livers of WT and ambp-/- zebrafish subjected to HFD feeding

first: Lei

last: Zhou

first: Mei

last: Wu

first: Jingjing

last: Zhang


title: Effect of HNF1A-MODY on stem cell islets [PGP-1]

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

institute: University of bergen

summary: This project investigates the impact of the hotspot mutation P291fsinsC in HNF1A-MODY (Maturity-Onset Diabetes of the Young) on stem cell-derived islets. RNA sequencing (RNA-seq) was performed on islets differentiated from mutant and control HNF1A-MODY stem cells to study the mutation's effect on gene expression. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms underlying the dysfunction caused by the P291fsinsC mutation during islet development and maturation.

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into the posterior foregut. The Sonic Hedgehog (SHH) pathway was manipulated using purmorphamine at the start of the stage to assess its effect on the differentiation process and evaluate the impact of the mutation on this developmental stage.

first: Simona

last: Chera


title: Expression data from  outer molecular of mouse hippocampus after entorhinal lesion

city: Frankfurt

first: Jessica

last: Schlaudraff

address: Heinrich-Hoffmann-Straße

institute: Klinische Neuroanatomie

summary:
After lesion of the entorhinal cortex, expression changes occur in the denervated dentate gyrus.
We used microarrays to examine gene expression changes underlying reorganization processes and identified down and upregulated genes during different time points after lesion

overall_design: Entorhinal lesion leads to denervation of the dentate gyrus.After time points of 1, 3, 7, 14 and 28 days after lesion, tissue of the outer molecular layer was specifically isolated layer-specific via laser microdissection and microarray was performed with isolated RNA.


title: Expression data from granule cell layer of mouse hippocampus after entorhinal lesion

overall_design: Entorhinal lesion leads to denervation of the dentate gyrus.After time points of 1, 3, 7, 14 and 28 days after lesion, tissue of the granule cell layer was specifically isolated layer-specific via laser microdissection and microarray was performed with isolated RNA.

first: time

last: course


title: SP6 safeguards human multipotent trophoblasts from DNA damage-induced ageing by shaping DNA-PK complex

city: Guangzhou

first: yulong

last: zhong

state: Guangdong Province

address: 1838 Guangzhou Avenue North

department: physiology

institute: Southern Medical University

summary: The placenta can be threatened by DNA damage caused by genotoxic events. However, how placental trophoblasts coordinate cell type-restricted mechanisms in response to DNA damage and how they maintain genome stability remains elusive. We previously reported that the transcription factor SP6 regulates the fate of human cytotrophoblasts (CTs) and trophoblast stem cells (TSCs). Here, we demonstrate that SP6 interacts with DNA-PKcs in CTs and TSCs to shape the phosphorylation pattern of this kinase for DNA damage repair (DDR), a role that is independent of its transcriptional activity. Lack of SP6 leads to the inactivation of DNA-PKcs, defects in DNA-PK complex assembly and DDR, and eventually cell senescence. Moreover, pharmaceutically or genetically targeting OTUB1-SP6 regulatory axis, which controls the dynamic turnover of cellular SP6 during DDR, can reset the susceptibility of CTs or TSCs to genotoxic stress-induced DNA damage. Taken together, these findings identify a CT- or TSC-specific DDR mechanism, and we propose a potential druggable target for mitigating DNA damage and cell senescence-related human placental diseases.

overall_design: Performing in situ ChIP-seq on SP6 to specifically study the impact of DNA damage on the SP6 binding regions.

first: Xuefei

last: Gao

first: Shanshan

last: Ai

first: Yulong

last: Zhong


title: Epigenetic Subtypes of High-Grade T1 Bladder Cancer Reveal Intra-Tumor Heterogeneity and Distinct Interactions with Tumor Microenvironment

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

summary: High-Grade T1 (HGT1) Non-Muscle Invasive Bladder Cancer (NMIBC) is a clinically heterogeneous disease, characterized by unpredictable treatment responses and limited tools for recurrence prediction. Although molecular classification efforts have been made, patient stratification still primarily relies on clinicopathological features, which offer limited clinical precision. In this study, we integrated chromatin profiling in bulk with single-nuclei(sn) RNA-seq, immunohistochemistry and spatial transcriptomics to define epigenetic subtypes of HGT1, characterize their heterogeneity, and investigate tumor–microenvironment interactions. Our findings reveal distinct chromatin profiles differentiating urothelial (URO) and micropapillary (MP) histological variants of high-risk HGT1. We identified three epigenetic states: two within the URO group, luminal-like inflammatory (LLI) and basal-like (BL), and a separate signature unique to MP tumors. Single-cell and spatial resolution approaches validated intratumoral heterogeneity and provided insight into subtype-specific microenvironmental contexts. Notably, ∼40% of URO tumors exhibited spatially distinct coexisting LLI and BL components. BL regions showed enrichment for angiogenesis and hypoxia pathways and were preferentially located near vascular stroma, while LLI regions showed to be located at the core of the tumor. MP tumors featured a markedly different microenvironment, characterized by diverse populations of cancer-associated fibroblasts (CAFs) and M2-polarized macrophages intermingled with tumor cells, suggesting a more immunosuppressive niche which could account for their worse clinical outcome. URO tumors, by comparison, showed a more immune-excluded phenotype. These findings provide a detailed molecular and spatial map of bladder cancer heterogeneity, highlighting how distinct epigenetic subtypes and histological variants are associated with tumor architecture and microenvironmental interactions. Our data underscore the need for subtype-specific therapeutic strategies to more effectively address the complexity already existing at HGT1 bladder cancer.

overall_design:
We started from 10 sections 10 μm thick that were washed 3 times with xylenes to remove paraffin, rehydrated in an ethanol/water series. The tissue was resuspended in lysis buffer as previously described and sonicated for 5 minutes using a Covaris E220 instrument (setting: 140 peak incident power, 5% duty factor, and 200 cycles per burst) in 1 ml adaptive focused acoustics (AFA) fiber millitubes. Soluble chromatin (5 μg) was immunoprecipitated with 10 μg H3K27ac (Diagenode catalog number C15410196)) antibody (Ab).
NMIBC clinical samples were selected from the Hospital del Mar-Parc de Salut Mar-Biobank, Barcelona, Spain. Nuclei isolation was performed using a modified version of a protocol originally developed for frozen specimens (Cejas and Long, 2022), optimized for FFPE material. Paraffin was removed through sequential xylene washes, followed by tissue rehydration in a graded ethanol series ending in distilled water. After centrifugation, the tissue pellet was resuspended in a dissociation buffer composed of phosphate-buffered saline (PBS, 896.5 µL), Liberase TM (38.5 µL at 6.5 U/µL), Collagenase D (40 µL at 100 mg/mL), and RNase inhibitor (25 µL at 40 U/µL). Samples were incubated at 37°C for 1 hour in a thermomixer to facilitate enzymatic tissue dissociation. Following dissociation, samples were washed with PBS, centrifuged, and the resulting pellet was resuspended in 300 µL of a lysis buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. The suspension was incubated overnight at 37°C in a thermomixer to ensure complete lysis and nuclear release. After incubation, 700 µL of 0.1% Tween-20 RSB buffer was added before passing them through a 40 µm cell strainer to remove debris. The nuclei could then be counted on the Countess II before proceeding to pelleting them down by centrifugation at 1,250 × g for 10 minutes at 4°C using a fixed-angle rotor. Approximately 10,000 nuclei per sample were processed for single-nucleus RNA sequencing using the 10x Genomics GEM-X Flex Gene Expression protocol. Libraries were prepared, multiplexed, and sequenced as 150 bp paired end reads on the Illumina NovaSeq XP platform.

first: Xie

last: Yingtian


title: The cGAS-STING pathway is an in-vivo modifier of genomic instability syndromes

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Genomic instability is one of the primary hallmarks of aging, promoting inflammation via interferon signaling, senescence, apoptosis, and cancer. To functionally explore the relationship between genomic instability and aging, we developed genetic models for DNA repair disorders in the naturally short-lived African turquoise killifish. Specifically, we mutated the Ataxia Telangiectasia (ATM) and the Bloom Syndrome (BLM) genes. Both ATM and BLM are autosomal recessive syndromes, which are characterized by overlapping and distinct aging-related phenotypes. We show that these models replicate human disease phenotypes, including infertility, short stature, reduced lifespan, cytoplasmic DNA fragments, and activated interferon signaling. Finally, we demonstrated that mutating cGAS, a sensor of dsDNA fragments, which is upstream to interferon, rescues specific degenerative phenotypes in ATM fish.  Together, our findings propose the cGAS–STING pathways as a promising in-vivo target for ameliorating disease phenotypes linked to genomic instability.

overall_design: Livers and brains from killifish were used, and each group varied by sex (males or females), age, and genotype (wild-type, atm mutant, atm&cgas double mutant, or blm1 mutant).

first: Marva

last: Bergman

first: Uri

last: Goshtchevsky

first: Tehila

last: Atlan

first: Gwendoline

last: Astre


title: Single-cell transcriptomics reveals markers of regulatory T cell dysfunction in Gestational Diabetes Mellitus

city: London

first: Panicos

last: Shangaris

address: Waterloo Road

institute: King's College London

summary: Gestational Diabetes Mellitus (GDM) is a common pregnancy complication and the role of regulatory T cells (Tregs) in this disease is ambiguous. This study aims to determine the aberrant transcriptional landscape in Tregs from GDM patients and controls. We identify gene expression programmes dysregulated in GDM Tregs and assess their utlilty as GDM biomarkers in bulk mRNA.

overall_design: Single cell RNA sequencing was performed on CD4+ T cells and Tregs isolated by FACS from peripheral blood mononuclear cells.

first: Mensah

last: Nana

first: Shangaris

last: Panicos