title: Genome-wide mapping of formaldehyde-induced DNA-protein crosslinks reveals unique patterns of formation and transcription-coupled removal in mammalian cells

city: Minneapolis

first: Colin

last: Campbell

state: MN

address: 3-130 Nils Hasselmo Hall

department: Pharmacology

institute: University of Minnesota

summary: DNA-protein crosslinks (DPCs) form following exposure to various alkylating agents including environmental carcinogens, cancer chemotherapeutics, and reactive aldehydes. If not repaired, DPCs can interfere with key biological processes such as transcription and replication and activate programmed cell death. A growing body of evidence implicates nucleotide excision repair (NER), homologous recombination, and other mechanisms in the removal of DPCs. However, the effects of genomic context on DPC formation and removal have not been comprehensively addressed. Using a combination of next generation sequencing and DPC enrichment via protein precipitation, we show that DPCs induced following exposure to formaldehyde are non-randomly distributed across the human genome, based on chromatin state. The data further show that the efficiency of DPC removal correlates with transcription at loci transcribed by RNA polymerase II. Data presented herein indicate that efficient removal of chromosomal DPCs requires both the Cockayne syndrome group B gene as well as ‘downstream’ TC-NER factor xeroderma pigmentosum group A gene. In contrast, loci transcribed by RNA Polymerase I showed no evidence of transcription-coupled DPC removal. Taken together, our results indicate that complex interactions between chromatin organization, transcriptional activity, and numerous DNA repair pathways dictate genomic patterns of DPC formation and removal.

overall_design: DPC seq was performed on HT1080 cells, both WT and XPA-KO, treated with +/- 400 μM formaldehyde for two hours. The DPC seq was done in triplicate (for WT cells: control  vs. treatment) and in duplicate (for WT vs. KO: control vs. treatment vs. recovery)

first: Duha

last: Alshareef

first: Micah

middle: D

last: Gearhart


title: RAG recombinase expression discriminates the development of natural killer cells

status: Public on Jul 25 2025

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

country: Germany

institute: University of Tuebingen

type: Expression profiling by high throughput sequencing

summary: V(D)J recombination initiated by recombination-activating gene (RAG) endonucleases is a crucial process for the generation of diversified antigen receptors of T and B lymphocytes but regarded dispensable for the generation of innate natural killer (NK) lymphocytes that lack clonotypic receptors. However, a fraction of human and murine NK cells derives from RAG-expressing progenitors, which have non-productive rearrangements within their Ig and TCR loci. An impact of V(D)J rearrangements on maturation and function of NK cells has been suggested by mouse and human models. We studied the impact of RAG expression ontogeny on NK cell maturation and function by using RAG-fate mapping reporter permanently labeling NK progenitors and mature NK cells.

overall_design: To explore the impact of potential rearrangements on NK cell maturation, RAG-fate mapping reporter human induced pluripotent stem cell (iPSC) lines were generated by introduction of RSS-invEGFP constructs (an inverted EGFP cassette flanked by two recognition signal sequences (RSS)) into the AAVS1 locus using CRISPR/Cas9. Reporter iPSC lines were subsequently differentiated into hematopoietic stem progenitor cells (HSPC) and NK cells in vitro (protocol published by Euchner et al., Front Immunol, 2021). GFP+ and GFP- NK cell progenitors were sorted using FACS after week 1, week 2, and week 3 of NK cell differentiation. RNA-Seq analysis was performed on 3 replicates of each sample and time point.

first: Kerstin

last: Felgentreff

first: Jasmin

last: Sprissler

first: Nicolas

last: Casadei

first: Michaela

last: Pogoda

first: Laurence

last: Kuhlburger

first: Stefan

last: Czemmel

first: Eva-Maria

last: Rump

first: Ulrich

last: Pannicke


title: Glucocorticoid-induced alterations of skeletal stem cell-based processes

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

country: USA

institute: UC Davis

summary: Glucocorticoid (GC) induced osteoporosis (GIOP) and osteonecrosis remain a significant health issue with few approved therapies that can treat the bone loss and dysfunction of skeletal vasculature. Therefore, we aimed to investigate the cellular and molecular processes by which GCs affect osteogenesis and angiogenesis, as well as how treatment with parathyroid hormone (hPTH 1-34) modifies these effects in a mouse model of GIOP. GC treatment reduced bone mass through decreased bone formation by skeletal stem cells (SSCs) while also increasing osteoclast mediated resorption. Concomitantly, endothelial cells were increased in numbers but displayed distorted phenotypical features. However, hPTH treatment prevented GC induced changes in osteogenesis and angiogenesis. Transplantation studies of SSCs combined with molecular analysis by single cell RNA-sequencing and functional testing of primary human cells tied GC-induced skeletal changes to altered stem and progenitor cell differentiation dynamics. This in turn perpetuated reduced osteogenesis and vascular malformation through direct SSC-endothelial crosstalk mediated at least in part by Basigin. In accordance, the conditional heterozygous deletion of Basigin in the skeletal lineage as well as antibody-mediated blockade of Basigin during GC treatment prevented detrimental bone loss. Intriguingly, aging also increases skeletal Basigin levels. When administered to 2-year-old mice, anti-Basigin therapy reinstated bone remodeling to significantly improve bone mass independent of sex. These findings, while helping to explain the cellular and molecular basis of GC induced bone loss, provide new therapeutic vantage points for GIOP and potentially other conditions associated with bone loss.

overall_design:
To study the effects of glucocorticoids on bone biology, Methylprednisolone 5 mg 60-day release pellets and vehicle were (cat#SG-241, Innovative Research of America, Sarasota, FL, USA) implanted under the skin of mice near the lumbar spine at day 0, and pellets were maintained for 58 days or removed after 28 days as indicated. Human parathyroid hormone 1-34 (hPTH 1-34) was purchased from Sigma (cat#:P3796), and the treatment was administered subcutaneously at 5 μg/kg/day, 5x/week for four consecutive weeks. There were a total of four groups of mice receiving subcutaneous release pellets of: (1) Placebo (Control), (2) Methylprednisolone (GC), (3) Methylprednisolone removal (GC removal), (4) Methylprednisolone (GC) + hPTH 1-34 (GC+PTH).For renal capsule transplantation experiments cells from three-month old male GFP reporter mice (C57BL/6-Tg(CAG-EGFP)1Osb/J; JAX: 003291) were transplanted into male B6 mice (C57BL/Ka-Thy1.1-CD45.1; JAX: 000406).
For single cell analysis femur bones were processed, digested, and prepared for FACS. Single cell solutions of each treatment group were then pooled (n=5 per group) and equal amounts of 1x10e6 PI-Ter119-CD45- and CD45+ cells were sorted into the same collection tube for each grouup containing FACS buffer. Cells were then processed with 10X Chromium Next GEM Single Cell 3ʹ GEM kit (10X Genomics Inc, v3.1) according to manufacturer’s instruction. Alternatively, cells were harvested from separate experiments of renal capsule grafts of groups (1), (2) and (4). To that end, renal capsule transplantations in the anaesthetized mouse a 5-mm dorsal incision was made and the kidney was exposed manually. Then, a 2-mm incision was created in the renal capsule using a needle bevel, and 5,000 FACS-purified mouse SSCs resuspended in 2 μl of Matrigel were transplanted beneath the capsule. The kidney was re-approximated manually and incisions were closed using sutures and staples. At time of surgery, mice were randomly divided into the three groups. Mice either received subcutaneous placebo or Methylprednisolone pellets as described above. One group additionally was treated with intermittent hPTH 1-34. Grafts were collected after 21 days and processed for single cell RNA-sequencing as described above.

first: Nancy

middle: E

last: Lane

first: Charles

middle: K

last: Chan


title: Affect of Aramchol on TGFβ stimulated H69 Cholangiocytes

status: Public on Jul 23 2025

city: Richmond

first: Grayson

middle: Welch

last: Way

email: waygw@vcu.edu, waygw@outlook.com

state: Virginia

address: 1217 E Marshall Street Room 534

department: Microbiology and Immunology

institute: VCU

summary: Cholestatic liver diseases, such as primary sclerosing cholangitis (PSC), are characterized by biliary fibroinflammation. Transforming growth factor-β (TGFβ) activated cholangiocytes release signals that recruit immune cells to drive inflammation and activate myofibroblasts to deposit the extracellular matrix (ECM). TGFβ regulates stearoyl-CoA desaturase (SCD) in stimulating lipid signaling. However, the role of SCD or its inhibitor, Aramchol, has not been investigated in biliary fibroinflammation. Here we used human transformed H69 cholangiocytes that were treated with TGFβ (10ng/mL) with and without Aramchol acid (30µM) overnight. RNA-seq analysis showed significant inhibition of TGFβ-induced hepatic fibrosis pathways while upregulating peroxisome proliferator-activated receptor (PPAR) signaling by Aramchol.

overall_design: RNA-seq profiling of human H69 cholangiocytes stimulated with TGFβ (10ng/mL) with and without Aramchol acid (30uM) overnight.

first: Sayed Obaidullah

last: Aseem

first: Jing

last: Wang

first: Huiping

last: Zhou


title: Intermittent Hypoxia Induces Cognitive Dysfunction and Hippocampal Gene Expression Changes in a Mouse Model of Obstructive Sleep Apnea

city: Tokyo

first: Yuki

last: Uchida

state: Shinagawa

address: 1-5-8 Hatanodai

department: Department of Physiology

country: Japan

institute: Showa University School of Medicine

summary: Obstructive sleep apnea syndrome (OSAS) is characterized by cycles of decreased blood oxygen saturation followed by reoxygenation due to transient apnea. Cognitive dysfunction is a complication of OSAS, but its mechanisms remain unclear. 8-week-old C57BL/6J mice were exposed to intermittent hypoxia (IH) to model OSAS, and cognitive function and hippocampal gene expression were analyzed. Three groups were maintained for 28 days: IH group (oxygen alternating between 10-21% in 2-minute cycles, 8 hours/day), sustained hypoxia group (SH) (10% oxygen, 8 hours/day), and control group (21% oxygen). Behavioral tests and RNA-seq analysis were performed. While Y-maze results showed no differences, the IH group demonstrated impaired memory and learning in passive avoidance tests compared to control and SH groups. RNA-seq revealed specific changes in learning/memory-related genes and oxidative stress response genes in the IH group. RT-qPCR showed decreased Lars2, Hmcn1, and Vstm2l expression in the IH group. Pathway analysis showed the suppression of the KEAP1-NFE2L2 antioxidant pathway in the IH group vs. SH group. Our findings demonstrate that IH may cause cognitive dysfunction through oxidative stress and suppressed antioxidant defenses. IH-specific downregulation of Lars2, Hmcn1, and Vstm2l may contribute to OSAS-related cognitive impairment.

overall_design: To investigate the effects of intermittent hypoxia on cognitive function, hippocampal gene expression in mice was analyzed using RNA-seq.

first: Kenta

last: Miyo

first: Ryota

last: Nakano

first: Shotaro

last: Kamijo

first: Masahiro

last: Hosonuma

first: Yoshitaka

last: Yamazaki

first: Hikaru

last: Isobe

first: Fumihiro

last: Ishikawa

first: Hiroshi

last: Onimaru

first: Akira

last: Yoshikawa

first: Shin-Ichi

last: Sakakibara

first: Tatsunori

last: Oguchi

first: Takuya

last: Yokoe

first: Masahiko

last: Izumizaki


title: Regulatory T cells epigenetically reprogrammed from autoreactive effector T cells mitigate established autoimmunity

city: Boston

first: Xudong

last: Li

state: MA

address: 150 Harrison Avenue, Jaharis 523a, M&V 702 Building

department: Immunology

institute: Tufts University

summary: Reprogramming autoreactive CD4⁺ effector T (Teff) cells into immunosuppressive regulatory T (Treg) cells represents a promising strategy for treating established autoimmune diseases. However, the stability and function of such reprogrammed Tregs under inflammatory conditions remain unclear. Here, we show that demethylation of core Treg identity genes in Teff cells yields lineage-stable Effector T cell Reprogrammed Tregs (ER-Tregs). A single adoptive transfer of ER-Tregs not only prevents autoimmune neuroinflammation in mice when given before disease onset but also arrests its progression when administered after onset. Compared to Foxp3‑overexpressing Teff cells, induced Tregs from naïve precursors, and endogenous Tregs, ER‑Tregs provide superior protection against autoimmune neuroinflammation. This enhanced efficacy stems from their inherited autoantigen specificity and selectively preserved effector‑cell transcriptional programs, which together bolster their fitness in inflammatory environments and enhance their suppressive capacity. Our results establish epigenetic reprogramming of autoreactive Teff cells as an effective approach to generate potent, stable Tregs for the treatment of refractory autoimmune conditions.

overall_design: Ex vivo RNA-seq profiling of ER-Tregs and nTreg at day 7 after CFA/MOG immunization of recipient mice.

first: Tyler R

last: Colson

first: James J

last: Cameron

first: Hayley I

last: Muendlein

first: Mei-An

last: Nolan

first: Jamie L

last: Leiriao

first: James H

last: Kim

first: Alexander N

last: Poltorak


title: BMI1 regulates human erythroid self-renewal through both repressive and activating chromatin associations [RNA-seq]

status: Public on Jul 28 2025

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

summary: To assess transcriptional consequences of BMI1 overexpression, we performed RNA-seq in SREs and iSREs.

overall_design: RNA-seq in sorted SRE and iSRE cells (overexpressing Bmi1).

first: Jayme

last: Olsen

first: Kathleen

last: McGrath

first: Michael

last: Getman

first: Kristin

last: Murphy

first: Hyun

last: An

first: Vincent

middle: P

last: Schulz

first: Ah

middle: R

first: Bin

last: Zhang

first: Taylor

last: Schofield

first: Julien

last: Papoin

first: Lionel

last: Blanc

first: Paul

last: Kingsley

first: Connie

last: Westhoff

first: Patrick

middle: G

last: Gallagher

first: Stella

last: Chou

middle: A

first: James

last: Palis


title: L-2-hydroxyglutarate modulates ferroptosis through Nrf2/Slc7a11 and Atf4/Chac1 axes in hepatocellular carcinoma

status: Public on Jul 26 2025

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Liver tumors undergo profound metabolic reprogramming to support survival, proliferation, and metastasis. Through a metabolic library screen combined with network-level integration of transcriptomic and metabolomic data, we identified a regulatory role of L-2-hydroxyglutarate dehydrogenase (L2HGDH) and its substrate, L-2-hydroxyglutarate (L2HG), on ferroptosis in hepatocellular carcinoma (HCC), which exhibits a metabolic environment prone to L2HG accumulation. Mechanistically, L2HG was found to promote chromatin accessibility at ferroptosis-related gene loci. Specifically, L2HG conferred protection against ferroptosis by enhancing cystine uptake via NRF2/SLC7A11 activation, while concurrently sensitizing cells to ferroptosis through glutathione degradation via ATF4/CHAC1 induction. The ferroptosis-protective effect of L2HG was dependent on NRF2, the ablation of which restored near-normal metabolic profiles in a spontaneous liver tumor mouse model. These findings suggest that the metabolically accumulated L2HG plays a dual role in modulating both ferroptosis resistance and sensitivity, thereby influencing liver tumorigenesis. Targeting these metabolic axes may provide novel strategies for ferroptosis-based antitumor therapies.

overall_design: RNA-seq were conducted for the HCC cell lines Hep3B and SNU398, treated with 1 mM TFMB-L2HG, cultured with HPLM medium for 48 hours before RNA purification with the PureLink RNA Mini Kit (Invitrogen). ATAC-seq was conducted for Hep3B cells with or without TFMB-L2HG treatment using the ATAC-seq kit (Active Motif) according to the manufacturer’s instructions. Metabolic scale CRISPRa screen was conducted in HuH7 cells expressing dCas9-VPR and transfected with lentiviral packaged to target metabolic genes using the library (Addgene, #187080). The virus infected HuH7 cells were treated with 5 μM Imidazole ketone erastin to induce ferroptosis for 14 days. The genmic DNA from initial and final populations were subjected to PCR amplification and deep-sequenced using an Illumina HiSeq 2500 platform. Sequencing reads were aligned to the reference sgRNA library, and sgRNA abundance was quantified. Results were reported as percent total sgRNA reads.

first: Caixia

last: Xi

first: Junfeng

last: Pang


title: A time-resolved framework for the recruitment of mRNP processing and assembly factors to a site of transcription

status: Public on Jul 24 2025

city: Davis

first: Ben

last: Montpetit

state: CA

address: One Shields Avenue

institute: University of California, Davis

summary: Processing and packaging of messenger ribonucleoprotein (mRNP) particles involve complex, coordinated interactions between nascent transcripts, RNA binding proteins (RBPs), and other associated factors. Despite the critical role of co-transcriptional mRNP assembly in gene expression, the temporal dynamics of this process are not well understood. Here, a live cell imaging assay is reported in S. cerevisiae to quantitatively detect recruitment of endogenous fluorescently tagged proteins to a transcriptionally active locus. Protein recruitment to an inducible integrated gene array composed of twenty-five transcriptional units is detected by colocalization with lacO repeats. Using arrays with two different promoters and the same coding sequence (GFA1), arrival times for a variety of mRNP processing and assembly factors were quantified. These analyses revealed Yra1, Cbp80, and Yhs7 as pioneering assembly factors. Notably, Yra1 recruitment occurs independently of the THO complex, with early localization supported by Cbp80 and the RNA recognition motif (RRM) of Yra1. Altogether, this work establishes the first comprehensive temporal framework for understanding protein recruitment during co-transcriptional mRNP assembly, providing mechanistic insights into the dependencies of Yra1 recruitment.

overall_design: RNA-seq profiling of WT and pCUP1-GFA1 25x array strains over hour time-course following treatment with 500 uM Copper Sulfate. Samples collected at 0, 5, 10, 15, 20, 25, 30, 45, and 60 minutes.

first: Theresa

last: Wechsler

first: Ryuta

last: Asada

first: Andrew

middle: N

last: Dominguez

first: Rachel

first: Julia

last: McCormick

first: Kalyn

last: Concepcion


title: Acetylated microtubules refine cytomegalovirus interactions with and remodeling of host chromatin [TT-seq]

city: Chicago

first: Derek

last: Walsh

state: Illinois

address: 303 East Chicago Avenue, Ward 6165

department: Microbiology Immunology

institute: Northwestern University

summary: Human cytomegalovirus extensively alters nuclear organization and the cellular transcriptome, yet our understanding of these events remains relatively limited. Here, chromatin conformation capture reveals that cytomegalovirus dramatically alters chromosome organization at both large-scale and local compartment levels. Nascent transcriptomics further reveals the extent to which transcriptional changes correlate with compartment changes, while also uncovering infection-induced read-in and read-through events that result in the expression of normally repressed neuronal genes in infected fibroblasts. Moreover, we find that viral genomes preferentially localize to the most abundant and euchromatic compartments of the host, further dysregulating transcription of subsets of host genes. Finally, we show that microtubule-derived forces on the nucleus regulate viral interactions with host chromatin as well as local compartment interactions, which in turn influences infection-induced transcriptional reprogramming. Combined, our findings reveal the extent to which HCMV alters chromatin organization and transcriptional activity, along with the contribution of microtubules to these processes.

overall_design: Nascent Transcriptional profiling of wildtype (siControl) NHDF cells and their knockdown derivatives (siSUN1 and siATAT1) using independent siRNAs at 72hr, 96hr, and 120hr timepoints, both in mock and MOI5 conditions.

first: Celeste

last: Rosencrance


title: Tlr9 expression protects against Tlr7-dependent exocrine gland and systemic disease manifestations in primary Sjögren’s disease in a sex-biased manner

city: Dallas

first: Chengsong

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary:
Primary Sjogren’s disease (pSD) is a systemic autoimmune disease. Currently, the causes of pSD remain unknown, and no curative therapies are available. Prior studies by our group showed Tlr7 activation was an important driver of pSD in females. Since
Tlr7 is regulated by Tlr9, we hypothesized that ablation of Tlr9 would exacerbate disease in a Tlr7-dependent manner. To this end, we generated pSD mice that lacked systemic expression of either Tlr9 (NOD.B10 Tlr9-/-) or both Tlr7 and Tlr9
(NOD.B10 Tlr-DKO). The objective of this study was to determine if Tlr9 mediated sex-biased disease and whether this was dependent on the expression of Tlr7.

sample_organism:
Mus musculus
blank sample

overall_design: We analyzed sera from 5 female and 5 male mice of each of the following strains: NOD.B10, NOD.B10 Tlr9 KO, NOD.B10 Tlr-DKO. All mice were aged to the clinical disease stage (26 weeks of age).

first: Jill

middle: M

last: Kramer


title: Acetylated microtubules refine cytomegalovirus interactions with and remodeling of host chromatin [Hi-C]

overall_design: High-throughput chromosome conformation capture (Hi-C) during HCMV infection in fibroblasts at 72, 96 and 120hrs. Hi-C was also performed in wildtype (siControl) NHDF cells and their knockdown derivatives (siSUN1 and siATAT1) at 72hr during infection at an MOI of 5.


title: Acetylated microtubules refine cytomegalovirus interactions with and remodeling of host chromatin [CUT&Run]

overall_design: CUT&RUN profiling of H3K9me3 and H3K4me3 in mock fibroblasts and HCMV infected conditions (MOI5) at 96hrs


title: Acetylated microtubules refine cytomegalovirus interactions with and remodeling of host chromatin [RNA-seq]

overall_design: Transcriptional profiling of wildtype (siControl) NHDF cells and their knockdown derivatives (siSUN1 and siATAT1) using independent siRNAs at 72hr and 96hr timepoints, both in mock and MOI5 conditions.


title: Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing

city: Raleigh

first: Linda

last: Hanley-Bowdoin

state: NC

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

institute: North Carolina State University

summary: The application of high-throughput sequencing to cellular transcriptome profiling (RNA-seq) has enabled significant advances in our understanding of gene expression in plants. However, conventional RNA-seq data reports mainly cytoplasmic transcript abundance rather than actual transcription rates. As a result, it is less sensitive to detect unstable and low-abundance nuclear RNA species, such as long non-coding RNAs, and is less directly connected to chromatin features and processes such as DNA replication. To bridge this gap, several protocols have been established to profile newly synthesized RNA in plants and other eukaryotes. These protocols can be technically challenging and present their own difficulties and limitations. Here we analyze newly synthesized nuclear RNA metabolically labeled in vivo with 5-ethynyl uridine (EU-nuclear RNA) in maize (Zea mays L.) root tips and compare it to the entire nuclear RNA population. We also compare both nuclear RNA preparations to conventional RNA-seq analysis of cellular RNA. The transcript abundance profiles of protein coding genes in nuclear RNA and EU-nuclear RNA were tightly correlated with each other (R2=0.767), but quite distinct from that of cellular RNA (R2=0.170 or 0.293). Nuclear and EU-nuclear RNA reads are frequently mapped across entire genes, including introns, while cellular reads are predominantly mapped to mature transcripts. Both nuclear and EU-nuclear RNA exhibited a greater ability to detect both protein coding and non-coding expressed genes.

overall_design: To estimate transcriptional activity, we used the cell-permeable uracil analog, 5-ethynyl uridine (EU) to label newly synthesized RNA of maize B73 root tips in vivo, and compared the EU-labeled RNA to the total nuclear RNA.

first: Leigh

last: Mickelson-Young

first: Emily

last: Wear

first: William

middle: F

last: Thompson

first: Lorenzo

last: Concia


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: Spatial Transcriptomics of  9-month old mouse brain tissue

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Analysis of steady-state mRNA levels in mouse brain hippocampus tissue at 9 months from wild-type C57BL/6J, Dp16, 5xFAD, and 5xFAD-Dp16 mice.

overall_design: Comparison of wild-type (n=1), Dp16 (n=1), 5xFAD (n=1), and 5xFAD-Dp16 (n=1) mice.

first: Paula

last: Araya

first: Caitlin

middle: C

last: Winkler

first: Kelly

last: Sullivan


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from 6-month old mouse brain cortex tissue ± JAK1/3 inhibition with tofacitinib

summary: Analysis of steady-state mRNA levels in mouse brain cortex tissue at 6 months from wild-type C57BL/6J, Dp16, 5xFAD, and 5xFAD-Dp16 mice.

overall_design: Comparison of sham-treated wild-type (n=5), Dp16 (n=3), 5xFAD (n=4), and 5xFAD-Dp16 (n=4) versus tofacitinib-treated wild-type (n=5), Dp16 (n=5), 5xFAD (n=6), and 5xFAD-Dp16 (n=4) mice.


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from 6-month old mouse brain hippocampus tissue ± JAK1/3 inhibition with tofacitinib

summary: Analysis of steady-state mRNA levels in mouse brain hippocampus tissue at 5 months from wild-type C57BL/6J, Dp16, 5xFAD, and 5xFAD-Dp16 mice.


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from 9-month old mouse brain hippocampus tissue

overall_design: Comparison of wild-type (n=4), Dp16 (n=4), 5xFAD (n=4), and 5xFAD-Dp16 (n=4) mice.


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from 5-month old mouse brain cortex tissue

summary: Analysis of steady-state mRNA levels in mouse brain cortex tissue at 5 months from wild-type C57BL/6J, Dp16, 5xFAD, and 5xFAD-Dp16 mice.


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from 5-month old mouse brain hippocampus tissue


title: Blood samples taken under anaesthesia can be used as a source of non-diseased controls for immune-based assays.

status: Public on Jul 22 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: This study includes only the whole blood (bulk) RNAseq data from tempus tubes described below; a full abstract for the overall study is provided. Recruiting very young, healthy children to serve as age-matched controls in research settings presents substantial ethical and practical challenges. One potential approach to address this issue is to recruit healthy children who are referred for elective procedures under general anaesthesia. However, infants are typically anaesthetised using volatile anaesthetics before a cannula is inserted to administer additional drugs. Consequently, blood samples are accessible after the onset of a drug-induced coma. As prolonged exposure to inhaled anaesthetic agents is known to have immediate immune modulatory effects which could bias any comparisons between samples taken while awake and under general anaesthesia, we set out to investigate whether immune changes could be observed in samples collected immediately after gas induction in children undergoing elective dental procedures. The composition and transcriptional profile of whole blood immune cells were evaluated by multiparameter flow cytometry and bulk RNA-sequencing, respectively. Cryopreserved PBMCs were used to study changes in the phenotype of activated CD4+ T cells by single-cell RNA-sequencing analysis using the 10x genomics platform. We report that inhaled anaesthetic induction using a combination of nitrous oxide and sevoflurane has minimal effect on the immune system composition and transcriptional profile and does not alter the phenotype of activated CD4+ T cells stimulated with Staphylococcal Enterotoxin B (SEB). However, we did observe changes in absolute cell counts. Therefore, blood samples collected during elective procedures under general anesthesia may offer a valuable opportunity for recruiting healthy children for research studies, depending on the planned tests.

overall_design:
This study recruited a total of ten individuals referred for elective dental procedures under general anaesthesia between three and six years of age. On the day of the procedure, prilocaine cream was applied for at least 15 minutes on both antecubital fossae to facilitate the insertion of a 22G cannula in the cephalic or medial cubital veins. Analgesic cryogenic ethyl chloride spray was used after skin preparation and ultrasound guidance employed if the vein could not be seen or felt. A first blood sample was taken before any administration of anaesthetic gases (pre-SEVO). Parents were asked to confirm consent for an inhalational induction at that point. A mix of nitrous oxide and oxygen was then used, increasing progressively the concentration of sevoflurane to 8%. Once the child was asleep, the nitrous oxide was turned off and a second blood sample was taken via the cannula (post-SEVO)

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

first: Clara

last: Domingo-Vila

first: Evangelia

last: Williams

first: Megan

last: Smithmyer

first: Basilin

last: Benson

first: Lauric

last: Ferrat

first: Sefina

last: Arif

first: Michelle

last: Hudson

first: Becky

last: Dobbs

middle: B

last: Johnson

last: consortium

first: Iain

last: Yardley

first: Cate

last: Speake

first: Richard

last: Oram

first: Timothy IM

last: Tree

first: Benjamin

middle: J

last: Blais


title: NaCl stress in Citrus sinensis

city: Kunming

first: mengjie

last: Zhang

address: Qingyun Street Panlong District

country: China

institute: southwest forestry university

summary: NaCl stress in Citrus sinensis

overall_design: Citrus sinensis seeds in the same physiological state were collected for the cultivation of tissue culture seedlings, and samples were obtained from the obtained tissue culture seedlings by treating them with 2% NaCl for 14 days, with three replicates for each treatment.


title: Transcriptomic analysis of ovarian cancer cells after drug administration and tRNA transfection at 10 and 24 hours

city: Tsuruoka-shi

first: Yuki

last: Iimori

address: 246-2 Kakuganji Aza, Mizukami

institute: Keio University

summary: SLFN11 sensitizes cancer cells to DNA-damaging agents (DDAs) by cleaving and reducing tRNALeu(TAA). In this study, we investigated how the reduction of tRNALeu(TAA) contributes to cell death under Camptothecin (CPT) treatment. RNA-seq and proteome analyses were performed to assess the global effects of tRNALeu(TAA) transfection. The results suggest that tRNALeu(TAA) influences the expression of proteins essential for proteostasis, particularly those involved in ubiquitin-dependent proteolysis, at the protein level rather than the mRNA level. These findings indicate that SLFN11 plays a crucial role in proteostasis by regulating tRNAs, and thus determines cell fate under DDA treatment.

overall_design: RNA-seq analysis of ovarian cancer cells (TOV-112D cells) was performed at 10 and 24 hours after treatment under the following three conditions to assess transcriptomic changes: 1: Treatment with transfection reagent followed by treatment with DMSO 2: Treatment with transfection reagent followed by treatment with 100nM Camptothecin 3: Treatment with transfection reagent and 10nM tRNALeu(TAA) followed by treatment with 100nM Camptothecin

first: Akio

last: Kanai


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from 9-month old mouse brain cortex tissue

first: Matthew

last: Galbraith

summary: Analysis of steady-state mRNA levels in mouse brain cortex tissue at 9 months from wild-type C57BL/6J, Dp16, 5xFAD, and 5xFAD-Dp16 mice.

first: Paula

last: Araya

first: Kelly

last: Sullivan


title: Triplication of HSA21-encoded genes modulates Alzheimer's Disease-related phenotypes in vivo via interferon signaling

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

overall_design: Refer to individual Series


title: Transglutaminase 2 regulates ovarian cancer metastasis by modulating the immune microenvironment

city: Ottawa

first: Barbara

last: Vanderhyden

state: Ontario

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: Ovarian cancer is the most lethal gynecological malignancy. Deepening our knowledge of the interactions within the tumor microenvironment (TME) is important for discovering new targeted treatment strategies. Transglutaminase 2 (TG2) is a protein implicated in many biological and pathophysiological processes, including promoting tumor progression in ovarian cancer. Its role in disease progression has been studied in ovarian cancer cells; however, its role in the ovarian TME is less understood. Using the ID8 Trp53-/- Brca1-/- and KPCA.B syngeneic mouse models of ovarian cancer, we defined the contribution of TG2 in the TME to the metastatic process. Lack of TG2 in the TME prolonged survival in the ID8 Trp53-/- Brca1-/- metastatic model. Through extensive analysis of the immune composition in both the primary tumor and metastatic ascites in the ID8 Trp53-/- Brca1-/- model, we discovered that the lack of host TG2 resulted in decreased frequency of immunosuppressive tumor-associated macrophages, and increased frequency of T cells, NK cells, and B cells. RNA sequencing of the primary tumors with or without TG2 present in the TME, revealed an enrichment of pathways related to B cell activation and regulation, highlighting a crucial role for TG2 in modulating B cells to enhance survival in the ID8 Trp53-/- Brca1-/- model. Taken together, our findings highlight the importance of TG2 in the TME for ovarian cancer metastasis, potentially through the activation of humoral immunity.

overall_design: RNA-sequencing of primary tumors collected from ID8 Trp53-/- Brca1-/- tumor bearing WT and Tgm2-/- mice 6 weeks post implantation.

first: Dalia

last: Ibrahim

first: Sarah

last: Nersesian


title: Dengue virus susceptibility in Aedes aegypti tied to natural cytochrome P450 variants

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: The mosquito Aedes aegypti serves as the primary vector for dengue virus (DENV), a human pathogen responsible for infecting hundreds of millions of people globally each year. Natural populations of Ae. aegypti show significant variability in their ability to become infected with DENV, which is largely governed by mosquito genetic factors. Previous studies suggest that genes encoding digestive enzymes, such as trypsins, and canonical antiviral immune genes may contribute to this variation 5-10. However, the specific causal gene variants underlying DENV susceptibility in Ae. aegypti are unknown. Here, we identify a gene encoding a cytochrome P450 (CYP4G15) whose genetic variants drive differences in DENV susceptibility in a natural Ae. aegypti population. CYP4G15 is transiently overexpressed in the midguts of DENV-resistant mosquitoes early in infection. Knockdown of CYP4G15 expression increases DENV susceptibility, while transgenic overexpression enhances resistance. A naturally occurring CYP4G15 variant with an 18-base-pair deletion in its promoter shows reduced expression and confers higher DENV susceptibility. The identification of CYP4G15 as a factor underlying DENV susceptibility in Ae. aegypti is unexpected because cytochrome P450 enzymes are typically associated with metabolism. Our finding challenges the long-standing focus on canonical immune pathways and opens new avenues for understanding antiviral defense and DENV transmission in mosquitoes.

overall_design: Bakoumba mosquitoes were infected with DENV-1 via an experimental infectious bloodmeal. At 24 and 48h post bloodmeal, midguts were dissected and subjected to RNA extraction. A qPCR quantifying viral RNA was performed to determine the infection status of each midgut. At each time, 8 infected and 8 non-infected midguts were selected for RNA sequencing.

last: Merkling

first: Odile

last: Sismeiro

first: Rachel

last: Legendre

first: Louis

last: Lambrechts


title: Hyperfunctioning MYC selectively redirects expression programs during human plasma cell differentiation III

city: York

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

summary: MYC acts as a rheostat during plasma cell (PC) differentiation, linking B-cell activation to cell growth and division. Tight control over MYC is an essential feature of the network controlling differentiation. Deregulation of MYC is common in aggressive B-cell neoplasms, driving cellular transformation, and is often accompanied by apoptotic protection conferred by BCL2. Here we assess how acutely enforced MYC and BCL2 deregulation impacts on the ability of human B-cells to complete PC differentiation. In the context of a permissive state for PC differentiation such acute deregulation does not suffice to transform human B-cells. Instead MYC drives a sequence of metabolic and growth-related expression programs while suppressing the transition to immunoglobulin secretion and thus establishes an aberrant differentiation state. The ability of MYC to establish this aberrant state depends on MB0 and MBII of its transactivation domain. Dependence on MBII is profound and can be resolved to conserved residue W135.

overall_design: RNA-seq profiles of human naïve B-cells differentiated from day 0 to day 20 plasma cells, from 3-4 healthy donors, with transductions of retroviral constructs that explored MYC/BCL2 overexpression in the context of different MYC mutations.

first: Reuben

last: Tooze

first: Panagiota

last: Vardaka


title: Priming of Naïve Melanoma and HIV-specific Human CD8+ T Cells by the Immuno-STAT Immunostimulatory Protein Framework

status: Public on Jul 21 2025

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

institute: St. Jude Children's Research Hospital

type: Methylation profiling by high throughput sequencing

summary: Adoptive cell transfer (ACT), an increasingly used immunotherapeutic approach for the treatment of cancer and infectious diseases, typically infuses antigen-specific CD8+ T cells obtained after ex vivo stimulation with patient-derived dendritic cells (DC) loaded with defined peptides. However, broader use of this approach is limited by logistical complexity, variability, cost, and inconsistency in cell quality. To overcome these limitations, we developed a dimeric protein scaffold-based antigen-presentation platform, Immuno-STAT (IST), which delivers peptide-specific TCR activation and costimulatory signaling to robustly expand highly functional antigen-specific CD8+ T cells. We demonstrate that delivering TCR and CD28 signals by IST selectively activates and expands highly functional cytotoxic CD8+ T cells from the naïve CD8+ T cell repertoire specific for the melanoma-associated MART-1 antigen and the HIV-associated SL9 antigen. While naïve MART-1-specific CD8+ T cells were expanded by both MART-1-peptide loaded DC and MART-1-specific IST, naïve SL9-specific CD8+ T cells were expanded only by SL9-specific IST and not by SL9-peptide loaded DC. By enabling ex-vivo expansion of naïve antigen-specific T cells without generation of autologous DC, IST may overcome the practical hurdles limiting the wider use of ACT and expand its use as a therapeutic strategy for both cancer and infectious disease.

overall_design: 6 replicates of UNSTIM samples, 4 replicates of MART DC samples, 4 replicates of MART IST samples, 4 replicates of SL9 IST samples

first: April

last: Mueller

first: Harris

last: Goldstein


title: Hyperfunctioning MYC selectively redirects expression programs during human plasma cell differentiation II


title: Identification of reactive CpGs and RNA expression in early COVID-19 through cis-eQTM analysis  reflecting disease severity and recovery [Bisulfite-Seq]

city: Ulsan

first: Jong

last: Bhak

state: Ulju-gun/Eonyang-eup

address: 50 UNIST-gil,

department: Biomedical Engineering (BME)

country: South Korea

institute: Korean Genomics Center (KOGIC)

summary: Multi-omics analyses of severe COVID-19 cases are crucial in deciphering the complex interplay between genetic and epigenetic factors. Here, we present an analysis of Expression Quantitative Trait Methylation (eQTM) to investigate the complex interplay of methylation and gene expression pattern during the acute phase of severe COVID-19.  We identified 16 differentially expressed genes and 30 nearby differentially methylated CpG sites. Six key genes—SRXN1, FURIN, IL18RAP, FOXO3, GCNT4, and FKBP5—were either up-regulated or down-regulated near hypomethylated CpG sites.  These genes are associated with viral infiltration, immune activation, lung damage, and oxidative stress-related multi-organ failure, which are the hallmarks of severe COVID-19. Interestingly, during the recovery phase, methylation and gene expression levels returned to baseline, underscoring the rapid and reversible nature of these molecular changes. These findings provide insight into the dynamics of epigenetic and transcriptomic shifts according to the infectious stage, supporting potential prognostic and therapeutic approaches for severe COVID-19.

overall_design: DNA Methylation experiments on (i) COVID-19 hospitalized patients across multiple time points from acute phase to recovery and (ii) COVID-19 convalescent individuals at a single or few time points.

first: Hyojung

last: Ryu

first: Kyungwhan

last: An

first: Yoonsung

last: Kwon

first: Yeonsu

last: Jeon

first: Sungwon

first: Hansol

last: Choi

first: Yeo Jin

last: Kim

first: Sunhwa

first: Ok Joo

last: Sul

first: Eun-Seok

last: Shin

first: Seung Won

last: Ra


title: Hyperfunctioning MYC selectively redirects expression programs during human plasma cell differentiation I

first: Matthew

first: Reuben


title: Identification of reactive CpGs and RNA expression in early COVID-19 through cis-eQTM analysis  reflecting disease severity and recovery [RNA-seq]

overall_design: RNA-seq experiments on (i) COVID-19 hospitalized patients across multiple time points from acute phase to recovery and (ii) COVID-19 convalescent individuals at a single or few time points.


title: Hyperfunctioning MYC selectively redirects expression programs during human plasma cell differentiation


title: NOX4/NOX1 dual inhibition in cholangiocarcinoma as an effective approach to target TGF-beta protumorigenic actions in cancer associated fibroblasts

city: Salamanca

first: Javier

last: Vaquero

address: Campus Miguel de Unamuno, SN

department: CIC-IBMCC

country: Spain

institute: CSIC

summary: Transforming growth factor beta (TGF-β) signalling has become an attractive therapeutic target, due to its pro-tumorigenic actions on epithelial cells and its immunosuppressive effects in the tumour microenvironment. In intrahepatic cholangiocarcinoma (iCCA), a highly aggressive malignancy of the biliary tract with poor prognosis, the latest clinical trials using TGF-β inhibitors have failed indicating that the specific actions carried out by TGF-β in iCCA are yet not well delineated. Here, we show that TGF-β signalling is highly active in iCCA and exerts a prominent suppressor effect on tumour cells, that relies on a functional canonical SMAD2/3/4 signalling. Thus, TGF-β inhibitors promote, instead of inhibit, tumour cell growth. NADPH oxidase 4 (NOX4), a downstream mediator of the TGF-β signalling pathway, is strictly expressed in cancer-associated fibroblasts (CAF) of iCCA and acts in concert with NOX1 to regulate CAF functions. Using a dual NOX4/NOX1 inhibitor impaired CAF actions and reduced tumour growth in vitro and in vivo. Collectively, our findings reveal an actionable way to specifically target TGF-β protumorigenic actions in CAF from iCCA without undesirable side effects on tumour cells.

overall_design:
To investigate the role of the TGF-β signalling pathway in cholangiocarcinoma (CCA) tumour cells we exposed two CCA cell lines (HuCCT1 and RBE) to TGF-beta 1 (2 ng/ml) or a TGF-β receptor I inhibitor, galunisertib (10 µM) for 16 hours and then we performed gene expression profiling analysis using RNAseq data.
To investigate the effects of inhibiting the TGF-β signalling pathway at different levels on liver myofibroblasts we exposed three cell lines of hepatic stellate cells (HSC) with different degree of activation (LX2-HSC  <hTERT-HSC < HSC-GFP) to  a TGF-β receptor I inhibitor, galunisertib (10 µM) or to the dual NOX4/NOX1 inhibitor setanaxib (40 µM) for 48 h and then we performed gene expression profiling analysis using RNAseq data.

first: Isabel

last: Fabregat


title: Pre-rRNA spatial distribution and functional organisation of the nucleolus

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: The multi-layered nucleolus serves as the primary site of ribosome biogenesis, where successive maturation of small (SSU) and large (LSU) ribosomal subunit precursors occur. However, the spatio-functional relationship between pre-rRNA processing and nucleolar substructures and how this adapts to changing cellular physiological demands have remained incompletely understood. Here, our spatiotemporal analyses revealed a compartment-specific ribosomal subunit processing in human nucleoli, with SSU processomes maintained in fibrillar center/dense fibrillar component/periphery dense fibrillar component (FC/DFC/PDFC) domains while LSU pre-rRNAs largely transited to PDFC/granular component (GC) regions. Slow proliferating cells exhibited unexpected 5' external transcribed space (5' ETS)-centered SSU processing impairment, accompanied by FC/DFC structural remodeling and retarded SSU outflux. Direct 5' ETS processing perturbation at least partially recapitulated these FC/DFC alterations, supporting the functional interdependence between SSU processing and nucleolar architecture. Notably, anamniote bipartite nucleoli with merged FC/DFC compartments, exhibited distinct 5' ETS distribution and slower pre-rRNA flux compared to multi-layered nucleoli in amniotes. Introducing a FC/DFC interface to bipartite nucleoli enhanced processing efficiency, indicating that evolutionary emergence of nested FC/DFC may have optimized pre-rRNA processing. Collectively, depicting the spatiotemporal distribution of pre-rRNAs revealed an essential role of 5' ETS-centered SSU processing in maintaining nucleolar substructures and suggested a possible evolutionary advantage of the multi-layered structure in amniotes.

overall_design: RNA-seq profiling of H9-derived arcuate neurons on differentiation day 0 (D0) and day 30 (D30) to analyze pre-rRNA processing factor expression dynamics.

first: Yu-Hang

last: Pan

first: Lin

last: Shan

first: Yu-Yao

last: Zhang

first: Zheng-Hu

first: Yuan

first: Shi-Meng

last: Cao

first: Xiao-Qi

last: Liu

first: Jun

first: Ling-Ling

last: Chen


title: Transcriptome profiling of colorectal cancer and paired normal tissues using Affymetrix HGU133-X3P arrays

city: ankara

first: nevin

last: belder

address: gumusdere

country: Turkey

institute: ankara university

summary:
Background:
Colorectal cancer (CRC) is a major global health concern, responsible for a significant number of cancer-related deaths. In this context, the development of accurate gene signatures is of paramount importance for predicting prognosis and guiding therapeutic decisions. This study was undertaken with the specific aim of creating an expression-based risk assessment model to predict overall survival (OS) in CRC patients.
Methods:
We analysed 49 paired FFPE tumours and normal tissue samples from sporadic CRC cases using Affymetrix HGU133-X3P arrays. We identified candidate prognostic genes by combining transcriptome profiling with public mRNA and miRNA microarray datasets. Univariate Cox regression analysis determined essential genes predicting OS. A prognostic risk score was developed using the expression of selected genes and patient stage, validated with two independent GEO datasets (GSE17536 and GSE40967).
Results:
We found 845 differentially expressed genes (FDR≤0.001, fold change ≥2) mainly enriched in the ECM-receptor interaction pathway. Four overexpressed genes in this pathway were identified as critical regulators of CRC. The high expression of these genes correlated with poor prognosis. Our four-gene prognostic signature, validated with independent datasets, stratified CRC patients into low- and high-risk groups with significant OS differences.
Conclusion:
Our risk-score model, developed and validated in this study, holds significant potential as a prognostic tool for predicting survival and clinicopathological features in CRC patients. Its successful application could enhance the precision of therapeutic decisions in clinical practice.

overall_design: We conducted gene expression profiling using Affymetrix HGU133-X3P arrays on RNA extracted from 49 paired normal and tumour tissue FFPE specimens of colorectal cancer patients. The aim was to identify dysregulated genes and pathways associated with colorectal cancer and construct a gene signature model to stratify CRC patients into low—and high-risk groups for predicting survival.

first: Nevin

last: Belder

first: Sulgun

last: Charyyeva

first: Edibe

last: Ece Abacı

first: Hakimu

last: Kawalya

first: Namood-e

last: Sahar

first: Nader

last: Omidvar

first: Berna

last: Savaş

first: Arzu

last: Ensari

first: Hilal

last: Ozdag


title: CD226 + B Cells in Primary Sjögren's Syndrome:A Key Player in Clinical:Manifestations and Disease Pathogenesis

city: Suzhou

first: Cuiping

state: Jiangsu

address: Ganjiang Road 178#

institute: Jiang Su institue of immunology

summary: The costimulatory molecule CD226 has emerged as a key regulator of immune responses, yet its role in B cell-mediated pathogenesis of primary Sjögren's syndrome (pSS) remains poorly understood. The purpose of this study was to explore the relevance between CD226 + B cells and clinical features in pSS patients and to clarify the potential role of CD226-mediated B cell biological functions in contributing to the pathogenesis of pSS.Here, we identified a distinct CD226 + CD19 + B cell subset that exhibited pathogenic features in pSS. CD226 was significantly upregulated on B cells in the peripheral blood and salivary glands of pSS. patients.CD226 + CD19 + B cell showed a stronger correlation with clinical features, disease activity, and prognosis in pSS patients.The ROC curve demonstrated that CD226+CD19+ B cell exhibited significant diagnostic capability to distinguish pSS patients from healthy controls and to differentiate disease activity.This subset also exhibited heightened activation and pro-inflammatory phenotypes.Thereby,CD226+B cell may potentially be a promising therapeutic target and biomarker for the treatment of pSS.

overall_design: To investigate the functional role of CD226+CD19+ B cells in pSS, CD226+CD19+ and CD226−CD19+ B cell subsets were isolated from splenic mononuclear cells of NOD mice via FACS, followed by transcriptome-wide microarray profiling to delineate their differential molecular signatures

first: Ping

last: Zhao

first: Saizhe

last: Song

first: Song

first: Cheng

last: Peng

first: Wei

last: Cheng

first: Xin

last: Chang

first: Changhao

last: Xie

first: Zhongli

last: Hu


title: Effect of SWI/SNF inhibition on gene expression in hormone-producing cells [RNA-seq]

city: Houston

first: H. Courtney

last: Hodges

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: To test the functional dependency of SF-1-dependent gene expression on SWI/SNF catalytic activity, we treated two human steroidogenic adrenocortical carcinoma (ACC) cell lines H295R and CU-ACC1 with 1 μM of SWI/SNF inhibitor BRM014 or equal volume of DMSO for 72 hours and performed RNA-seq. SWI/SNF inhibition strongly reduced the expression of steroidogenic genes targeted by the transcription factor SF-1, as well SF-1 (NR5A1) and β-catenin (CTNNB1) themselves.

overall_design: RNA-seq in cells treated with DMSO or 1 μM BRM014

first: Yuen

middle: S

last: Chan

first: H


title: Chromatin profiling following SWI/SNF inhibition in H295R or HEK 293T cells [ChIP-seq]

summary: To assess the genome-wide effect of acute SWI/SNF inhibition on SF-1/β-catenin chromatin binding, we treated H295R or HEK 293T cells with 1 µM of SWI/SNF inhibitor BRM014 or DMSO vehicle control for 1 hour and performed ChIP-seq. Pronounced loss of chromatin occupancy was observed for SF-1 and β-catenin at enhancer sites bound by ARID1A-containing cBAF complexes.

overall_design: Chromatin occupancy profiling in H295R or HEK 293T cells treated with SWI/SNF inhibitor or DMSO vehicle control.


title: DNA accessibility sites requiring SWI/SNF or β-catenin activity [ATAC-seq]

summary: To reveal the effects of β-catenin knockout or acute SWI/SNF (BAF) inhibition on chromatin accessibility, we performed knockout of β-catenin or treated cells with 1 µM of BAF inhibitor BRM014 or DMSO vehicle control and performed ATAC-seq. Analysis of altered DNA accessibility in H295R cells revealed that sites with Steroidogenic Factor-1 (SF-1) motifs had the strongest loss of DNA accessibility. In HEK 293T cells, sites with motifs belonging to β-catenin binding partners (specifically YAP binding-partner TEAD, SOX, or FOXO motifs) had loss of DNA accessibility upon either BAF inhibition or β-catenin knockout.

overall_design: ATAC-seq in H295R or HEK 293T cells


title: Elevated EGR1 Binding at Enhancers in Excitatory Neurons Correlates with Neuronal Subtype-Specific Epigenetic Regulation

city: Blacksburg

first: Hehuang

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

summary: In this study, we generated epigenetic maps profiles to perform comparative histone modification analysis between excitatory and inhibitory neurons. We found that neuronal cell-type specific histone modifications are enriched in super enhancer regions containing abundant EGR1 motifs. Further CUT&RUN data validated that more EGR1 binding sites can be detected in excitatory neurons and primarily located in enhancers. RNA-seq data generated from FACS-sorted excitatory and inhibitory nuclei provided additional evidence supporting the neuronal subtype-specific regulatory function of EGR1.

overall_design: RNA-seq was performed for the FACS-sorted excitatory and inhibitory nuclei from adult mouse brain.

first: Xiguang

last: Xu

first: Liduo

last: Yin


title: Differential Expression of Long Non-Coding RNA in Postmenopausal Fibroids

status: Public on Jul 18 2025

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

summary: This study aimed to characterize the differential expression profile of long non-coding RNA transcripts in postmenopausal leiomyomas compared to their paired myometrium

overall_design: Analysis of lncRNA expression profiles from RNA-seq data in six paired myometrium and leiomyoma specimens from postmenopausal women

first: Tsai-Der

last: Chuang

first: Shawn

last: Rysling

first: Nhu

last: Ton

first: Daniel

last: Baghdasarian


title: Z138-SNP_array_data

city: Barcelona

first: Renée

last: Beekman

address: Carrer Dr. Aiguader 88

institute: CRG

summary: The Z138 cell line is a mantle cell lymphoma cell line carrying the t(11;14) translocation. SNP array data analysis combined with chromosome sorting data allowed to identify heterozygous SNPs on the wildtype and translocated chromosome 11. Subsequent mapping of HiC reads to these alleles allowed to assess the interchromosomal interactions and thus indirectly nuclear chromosome positioning of these alleles, showing that that derivate 11 moves inwards.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from Z138 cell in culture.

first: Silvia

last: Bea

first: Cristina

last: Lopez


title: H3K27 and H3K9 Methylation Mask Potential CTCF Binding Sites to Maintain 3D Genome Integrity

status: Public on Jul 17 2025

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

summary: The three-dimensional (3D) genome structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing Topologically Associated Domains (TADs) and promoter-enhancer loops, contributing to proper cell differentiation and development. Although CTCF binds the genome with high sequence specificity, its binding sites are dynamically regulated during development, and aberrant CTCF binding is linked to diseases such as cancer and neurological disorders, and aging. However, the mechanisms controlling CTCF binding remain unclear. Here, we investigated the role of repressive chromatin modifications in CTCF binding using H3K9 methyltransferase-deficient immortalized mouse embryonic fibroblasts (iMEFs) and H3K27 methyltransferase EZH1/2 inhibitor. We found that H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding. These changes were associated with alterations in 3D genome architecture and gene expression, suggesting that repressive chromatin modifications preserve proper chromatin organization by preventing aberrant CTCF binding. Additionally, while CTCF binding sites repressed by H3K9 methylation were bound by CTCF in early mouse embryos, those repressed by both H3K9 and H3K27 methylation remained inaccessible, with early embryonic-specific H3K27 methylation forming at these sites. These findings implicate that H3K27 methylation prevents abnormal CTCF binding in early embryos, ensuring proper genome organization during development.

overall_design: ChIP-seq profiles of CTCF in immortalized mouse embryonic fibroblasts

first: Yoichi

last: Shinkai


title: SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [ChIP-seq]

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

summary: Despite the pleiotropic role of SUMOylation, this pathway mainly functions to repress innate immunity in myeloid cells. Inactivating SUMOylation triggers a potent basal type I interferon (IFN1) response, amplified and coupled with an inflammatory response upon stimulation. These findings transposed to pre-clinical models with the demonstration that SUMOylation inhibitors (SUMOi) activate antitumor immunity in an IFN1-dependent manner. Yet, how SUMOylation represses immune signaling remains largely unknown. We identified murine MORC3, a critical transcriptional repressor of the IFNB1 gene, as the top SUMO2/3 substrate in myeloid cells. We show that, in human monocytes, SUMO functions to repress basal IFNB1 in cis through an atypical/repeated MORC3-regulated element (MRE) concentrating/homing multiple PU.1 binding motifs. Inhibiting SUMOylation induces a 3D genome reorganization centered on the MRE, which, in turn, acquires both insulator and PU.1-driven enhancer activities, together with loss of H3.3 and H3K9me3 repressive marks and increased PU-1 binding. Paradoxically, MORC3, that binds PU.1, is massively recruited, yet unable to repress the MRE.  Finally, we show that both MORC3 ATPase cycle and SUMOylation are critical for full MORC3 repressive activity. Our study identifies an unconventional mechanism in which SUMO, in concert with MORC3, orchestrates a metastable H3.3/H3K9me3 heterochromatin state on a multi-PU.1 binding platform element to shutdown unscheduled myeloid-specific IFN1 response.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Serie 1 : ChIP-seq H3.3 in RAW 264.7 macrophages upon ML-792 treatment
Serie 2 : ChIP-seq Morc3 and in RAW 264.7 macrophages
Serie 3 : ChIP-seq SUMO2/3 and H3K9me3 in RAW 264.7 macrophages upon ML treatment
Serie 4 : ChIP-seq MORC3 in BlaER1 monocytes, WT, IFNAR-/-, IFNAR-/- MORC3-/-, upon TAK treatment and H3K9me3 in BlaER1 monocytes, WT upon TAK treatment
Serie 5 : ChIP-seq MORC3 and H3K9me3 in BlaER1 lymphocytes ctrl
Serie 6 : ChIP-seq MORC3 in BlaER1 lymphocytes, upon TAK treatment
Serie 7 : ChIP-seq H3.3 in BlaER1 cells, WT, upon TAK treatment
Serie 8 : ChIP-seq SUMO2/3 in BlaER1 cells IFNAR-/-
Serie 9 : ChIP-seq CTCF, H3K27me3 and H3K4me3 in BlaER1 cells WT, upon TAK treatment
Serie 10 : ChIP-seq H3K9me3 in IFNAR -/- and IFNAR -/- MORC3 -/- BlaER1 monocyte
Serie 11 : ChIP-seq MORC3 in THP1 macrophages (PMA treated) upon TAK treatment

first: Amandine

last: Goffeney

first: Victoria

last: Morel

first: Anne

last: Dejean


title: Dynamics of in vivo vitamin D signalling in Human immune cells

city: Olsztyn

first: Carsten

last: carlberg

address: Tuwima 10

country: Poland

institute: institute of animal reproduction and food sciences of polish academy of sciences

summary: In this study, we analyse the in-vivo modulation of the transcriptome of human PBMCs over a time course by a bolus of vitamin D3 (80000 IU).

overall_design: PBMCs of 1 healthy individual was collected directly before the uptake of vitamin D bolus and over a time course of 04h, 24h and 48h after in take of the vitamin D bolus. Analysis was performed to identify the response vitamin D target genes over time.

first: Tanya

last: Tripathi

last: Carlberg


title: SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [4C-seq]

overall_design: 4C-seq around the IFNB1 gene and its regulatory region in BlaER1 immune cell line in control condition and under SUMO inhibition

first: François

last: Charon

first: Daan

last: Noordermeer


title: Development and validation of multivariate predictors of primary endocrine resistance to tamoxifen and aromatase inhibitors in luminal breast cancer reveal drug-specific differences [HumanMethylationEPICv2]

city: Munich

first: Guokun

last: Zhang

address: Marchioninistr. 15

institute: IBE LMU

type: Methylation profiling by genome tiling array

summary: In the WSG-ADAPT trial (NCT01779206), HR+/HER2-EBC patients underwent pre-operative short-term endocrine therapy (pET). Treatment response was determined by immunohistochemical in-situ labeling of cycling cells (G1 to M-phase) with Ki67 before and after pET. We performed Infinium MethylationEPICv2-based DNA methylation analysis post-pET in a validation cohort2 (n=176, unmatched). Predictive indices of endocrine resistance under both treatments were calculated.

overall_design: DNA was submitted for DNA methylation analysis using HumanMethylationEPICv2 (EPICv2) BeadChips (Illumina, CA, USA), including an additional restore step for FFPE material.

first: Clarissa

last: Gerhäuser

first: Hans

last: Kreipe

first: Nadia

last: Harbeck


title: Effect of Arginine Supplementation on Liver and Pectoral Muscle: Tissue-Specific Lipid Metabolism in Broilers

city: Haidian

first: Awais

last: Ali

state: Beijing

address: Room No. 106, International Student Dormitory, Chinese Academy of Agricultural Sciences

institute: Majorbio

summary: Abdominal fat (AF) and intramuscular fat (IMF) are key carcass traits in broilers but managing both is challenging due to their contrasting effects. Arginine (Arg) supplementation has potential effect in lipid metabolism, however its tissue specific effect remains poorly understood. The objective of this study was to investigate the tissue specific effect of Arg supplementation on growth performance and fat metabolism in both liver and pectoral muscle in broilers. A total of 480 Arbor Acre chicks were randomly assigned to four groups: Control (0 g/kg), Arg (1.8 g/kg), 5X Arg (9 g/kg) and 10X Arg (18g/kg), with 12 replicates of 10 birds each. Overall, high Arg supplementation (5X, 10X) significantly impaired growth performance, reducing average daily gain and feed intake, accompanied by elevated serum AST and IFN-γ levels (p<0.05). Liver transcriptomics analysis revealed that 10X Arg significantly enriched PPAR signaling pathway, promoting fatty acid oxidation while suppressing lipogenic genes. Conversely, in pectoral muscle, high Arg (10X) promoted intramuscular fat deposition which was associated with downregulation of PPAR-α (p<0.05) and increased expression of key lipogenic genes involved in de novo lipogenesis (SREBP-1c, FAS, ACC and SCD). Moreover, Arg supplementation modulated drug metabolism genes in liver, including EPX and RRM2, suggesting potential impacts on detoxification pathways. These findings underscore the importance of precise Arg dosing to optimize broiler growth, immune function, and carcass quality by targeting its tissue specific metabolic effect.

overall_design: 48 Liver samples, subjected to RNA Sequencing including one control and three treatments i.e. Arg, 5X Arg, 10X Arg in Arbor Acres broilers

first: Xuan

last: Liu

first: Mebratu

last: Melaku

first: Waqar

last: Iqbal

first: Bao

last: Yi

first: Ruqing

last: Zhong

first: Liang

last: Chen

first: Teng

last: Ma

first: Hongfu


title: Direct, bisulfite-free 5mC and 5hmC sequencing at single-cell resolution

city: Oxford

first: Jingfei

last: Cheng

state: Oxfordshire

address: Roosevelt Drive

institute: University of Oxford

summary: We report the first direct sequencing methodologies, termed scTAPS and scCAPS+ (exclusive to 5hmC), which enable quantitative detection of 5mC and 5hmC at single-base resolution and single-cell level. With ~90% mapping efficacy, our methods accurately benchmark 5mC and 5hmC profiles in CD8+ T and mES cells, respectively. Notably, scCAPS+ revealed a global increase in 5hmC within the hippocampus of aging mice, particularly evident in non-neurons.

overall_design: scTAPS and scCAPS+ were benchmarked in human CD8+ T cells and mouse embryonic stem cells (mESCs) respectively to validate their performance. Furthermore, we utilized scCAPS+ to elucidate the dynamics of aging-related 5hmC in the hippocampal region, examining both neurons and non-neuronal cells derived from young (3 months) or aged (18 months) mice.

first: Xiufei

first: Linzhen

last: Kong

first: Xiao

last: Shu

first: Haiqi

last: Xu

first: Masato

last: Inoue

first: Marion

last: Fernández Berrocal

first: Dagny

last: Døskeland

first: Shivan

last: Sivakumar

first: Yibin

first: Jing

last: Ye

first: Chun-Xiao

last: Song


title: SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [RNA-seq]

city: Paris

first: Yann

last: Loe-Mie

institute: Institut Pasteur

overall_design: RNA-seq in BlaER1 monocytes, WT, IFNAR-/-, IFNAR-/- MORC3-/-, upon TAK treatment

first: Amandine

last: Goffeney

first: Anne

last: Dejean


title: Development and validation of multivariate predictors of primary endocrine resistance to tamoxifen and aromatase inhibitors in luminal breast cancer reveal drug-specific differences

first: Guokun

last: Zhang

summary: In the WSG-ADAPT trial (NCT01779206), HR+/HER2-EBC patients underwent pre-operative short-term endocrine therapy (pET). Treatment response was determined by immunohistochemical in-situ labeling of cycling cells (G1 to M-phase) with Ki67 before and after pET. We performed targeted next generation sequencing and Infinium MethylationEPIC-based DNA methylation analysis post-pET in a discovery cohort (n=364, responder (R) and non-responder (NR) pairs matched for clinicopathologic features) and a validation cohort (n=270, unmatched). Predictive indices of endocrine resistance under both treatments were constructed using lasso penalized logistic regression.

overall_design: DNA was submitted for DNA methylation analysis using HumanMethylationEPIC (EPIC) BeadChips (Illumina, CA, USA), including an additional restore step for FFPE material.

first: Clarissa

last: Gerhäuser

first: Hans

last: Kreipe

first: Nadia

last: Harbeck


title: NanoTag - an IgG-free method for mapping DNA-protein interactions

status: Public on Jul 16 2025

city: Zurich

first: Maria

last: Dimitriu

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH Zurich

summary: Background: Genome-wide profiling of DNA-protein interactions in cells can provide important information about mechanisms of gene regulation. Most current methods for genome-wide profiling of DNA-bound proteins such as ChIP-seq and CUT&Tag use conventional IgG antibodies to bind the target protein(s). This limits their applicability to targets with available high affinity and specificity antibodies and prevents their use for other targets. Here we describe NanoTag, an IgG-free method derived from CUT&Tag to profile DNA-protein interactions. NanoTag is based on a fusion between an anti-GFP nanobody and Tn5 transposase that can map GFP-tagged proteins associated with chromatin in a fast, cost-effective and animal-free manner. Results: We used NanoTag to indirectly profile the histone mark H3K4me3 genome-wide via its binding partner TATA box-binding protein-associated factor 3 (TAF3) and the transcription factors Nanog and CTCF in mouse embryonic stem cells (mESCs). NanoTag results show high inter-replicate reproducibility, high signal-to-noise ratio and strong correlation with CUT&Tag datasets, validating its accuracy and reliability. Conclusions: NanoTag provides a novel, flexible and cost-effective IgG-free method to generate high resolution DNA-binding profiles in cells and tissues.

overall_design: NanoTag and CUT&Tag data of TAF3 (H3K4me3-binding), Nanog and CTCF from mouse embryonic stem cells expressing GFP-tagged TAF3, Nanog and CTCF, respectively. For CUT&Tag, anti-GFP antibody was used. For NanoTag, anti-GFP nanobody was used.

first: Rodrigo

last: Arzate-Mejía

first: Leonard

last: Steg

first: Pierre-Luc

last: Germain

first: Isabelle

last: Mansuy


title: RNA sequencing analysis of prostate cancer cell line C4-2B with PCP4 overexpression.

city: Jinan

first: wenqiao

last: jia

state: Shandong

address: 107 Wenhua Xilu

department: Department of Health Management Center

institute: Qilu Hospital of Shandong University

summary: Transcriptome analysis was performed to determine the effect of overexpression of PCP4 in prostate cancer cell line C4-2B.

overall_design: Prostate cancer cells C4-2B transfected with expression vector containing PCP4 were used for RNA-seq analysis.

first: Wenqiao

last: Jia


title: Screening and identification of muscle pericyte-selective markers

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

summary: Pericytes, which share markers with smooth muscle cells (SMCs), are heterogenous cells. Pericytes in the brain and skeletal muscle have different embryonic origins, representing distinct subpopulations. One challenge in the field is that there are no subpopulation-specific pericyte markers. Here, we compared the transcriptomes of muscle pericytes and SMCs, and identified 741 muscle pericyte-enriched genes and 564 muscle SMC-enriched genes. Gene ontology analysis uncovered distinct biological processes and molecular functions in muscle pericytes and SMCs. Interestingly, the Venn diagram revealed only one gene shared by brain and muscle pericytes, suggesting that they are indeed distinct subpopulations with different transcriptional profiles. We further validated that GSN co-localized with PDGFRβ+SMA- cells in small and large blood vessels but not PDGFRβ+SMA+ cells, indicating that GSN predominantly marks pericytes and fibroblasts rather than SMCs in skeletal muscle. Negligible levels of GSN were detected in the brain. These findings indicate that GSN may serve as a selective marker for muscle pericytes.

overall_design: RNA-seq  profiling SMCs and pericytes in mouse skeletal muscle tissue

first: Yao

last: Yao


title: Exosomal miR-2137 from cadmium-treated hepatocytes drives renal ferroptosis via GPX4 suppression and is alleviated by selenium

first: Qian

last: Wen

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

summary: Cadmium (Cd) is a toxic heavy metal that has a significant impact on the liver and kidneys, rendering them highly susceptible to its toxic effects. However, the precise mechanism remains uncertain. Mice were exposed to Cd resulting severe ferroptosis and liver tissue damage via regulating hepatic GPX4 levels. It is noteworthy that despite the considerably lower concentration of Cd in the kidney compared to the liver, the oxidative damage observed in the exposed mice was significantly more severe in the kidney. It was therefore postulated that hepatic disorders may engage in such hepatorenal communication, thereby leading to the pathological phenotypes of distant organs under conditions of Cd exposure. The results of the mechanistic studies indicated that Cd-induced hepatocyte exosomes, which contain a variety of miRNAs produced by hepatocytes, such as miR-2137, etc., are capable of targeting renal GPX4 and reducing the level of GPX4 in renal cells. This resulted in the occurrence of ferroptosis in the kidneys. Injection of the appropriate dosage of Cd-induced exosomes, derived from hepatocytes, is sufficient to induce kidney damage in vivo. Our data support the hypothesis that treatment with an antagomir targeting miR-2137 is capable of inhibiting this process. Moreover, our findings revealed that selenium (Se) supplementation was sufficient to protect against Cd-induced hepatic and renal toxicity by elevating the expression level of selenoprotein GPX4 in vivo. In conclusion, we have identified liver-derived exosomes and their implications for hepatorenal communication under Cd exposure. This provides a new target for understanding the mechanism of Cd-induced hepatorenal communication. Our findings indicate that exosomes may serve as biomarkers and potential therapeutic agents for the exposure of Cd toxicity.

overall_design: C57BL/6J mice were maintained on a diet supplemented with 2 ppm SeMet for three months. During the final seven days, mice received daily intraperitoneal injections of CdCl₂ (1.25 mg/kg). After the treatment, liver tissue samples from the mice were collected for RNA-seq sequencing analysis.

first: Lixing

last: Zhan


title: STEMIN transcription factor drives selective chromatin remodelling for gene activation within a relaxed chromatin during reprogramming in the moss Physcomitrium patens

city: Okazaki

first: Ruan

middle: Morné

last: De Villiers

state: Aichi

address: 38 Nishigonaka, Myodaiji

department: Basic Biology

institute: National Institutes of Natural Sciences

summary: Land plants exhibit remarkable cellular plasticity, readily reprogramming differentiated cells into stem cells in response to internal and external stimuli. While chromatin remodelling is crucial for cellular reprogramming, its interplay with gene expression during reprogramming into stem cells remains elusive. In the moss Physcomitrium patens, wounding induces reprogramming of leaf cells facing wounded cells to change into chloronema apical stem cells through the activation of the AP2/ERF transcription factor STEMIN. In this study, we employed combined single-nuclei RNA and ATAC-sequencing to explore the interplay between gene expression and chromatin dynamics during STEMIN-mediated reprogramming. Profiling 20,883 single-nuclei from gametophores, protonemata, and cut leaves, we identified eleven distinct cell types including reprogramming leaf cells. Our analysis revealed that reprogramming leaf cells exhibit a partly relaxed chromatin landscape and STEMIN transcription factors selectively enhance accessibility at specific genomic loci essential for stem cell formation. Thus, our results indicate that wounding initiates a broad chromatin relaxation, creating a permissive environment and specific transcription factors act to refine this permissive state by specifically relaxing chromatin regions critical for reprogramming.

overall_design: Wild type (Wt) Physcomitrium patens (Hedw.) Mitt. and the derived triple deletion mutant ∆stemin1∆stemin2∆stemin3#6-48-1 (ste)(Gu et al., 2020) were grown from disrupted gametophyte tissue on solid BCDAT medium (Nishiyama et al., 2000) at 25°C under continuous white light for 1 week to propagate protonemata or 22 days to generate gametophore enriched samples. Nuclei for the gametophore samples (T00) were isolated directly from tissue harvested from BCDAT medium-grown plates after 22 days of cultivation. For time-course experiments, 22-day-old tissue was collected in liquid BCDAT medium, subjected to mechanical disruption using a Polytron 1200E homogenizer and then allowed to recover in liquid BCDAT medium on an illuminated shaker. Nuclei were isolated and pooled as follows: nulcei isolated 3, 4.5, and 6 hours after disuption were pooled for the 3-6 h timepoint (T03); nuclei isolated 10, 12, and 14 hours after disruption were pooled for the 10-14 h timepoint; nuclei isolated 24 and 36 hours after disruption and nuclei isolated from 1-week-old protonemata were pooled for the 24-36 h +protonemata time point (T24).

last: de Villiers

first: Gergo

last: Palfalvi

first: Akinori

last: Kanai

first: Yutaka

last: Suzuki

first: Mitsuyasu

last: Hasebe

first: Masaki

last: Ishikawa


title: Effect of Jab1 knockdown on gene expression during disease progression in acute myeloid leukemia

city: Wuhan

last: Zhang

state: Hubei

address: Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuchang District

department: Department of Hematology

institute: Wuhan University

summary: The progression of acute myeloid leukemia (AML) is a complex process involving various cellular activities. In this context, our research focuses on the role of Jab1 as a key regulatory factor. Specifically, Jab1 plays a crucial role in regulating apoptosis and proliferation, providing support for the proliferation and survival of AML cells. As a c-JUN transcription co-activator, Jab1 participates in multiple transcriptional regulatory networks, influencing the gene expression of cells. Through RNA-seq data analysis, we present a detailed molecular framework, elucidating the impact of Jab1 downregulation on gene expression. This provides important insights for a comprehensive understanding of the molecular mechanisms underlying this disease, offering robust support for future research and therapeutic strategies.

overall_design: To investigate the regulatory role of Jab1 in the proliferation and survival of acute myeloid leukemia cells, we established a cell line using shRNA to knock down the target gene in MOLM13 cells.


title: RNA-seq and Ribo-seq of RPS29 knockdown in SH-SY5Y

city: Shanghai

first: wei

last: xu

state: China

address: dongan road,131

institute: Fudan University

overall_design: 1) RNA-seq analysis of RPS29 knockdown in SH-SY5Y. 2) Ribo-seq analysis of RPS29 knockdown in SH-SY5Y.

first: Wei

last: Xu

first: Zhixin

last: Qiu


title: NanoString BC360 gene signatures in luminal breast cancer

first: Guokun

summary: We analyzed a cohort of 220 early breast cancer patients with ER-positive and/or progesterone receptor (PR)-positive, HER2-negative tumors.

overall_design: RNA was submitted for NanoString BC360 analysing. Nanostring profiling was accomplished following the protocol provided along with the kits including hybridization, purification and immobilization, counting and analysis. It included 728 specific genes.

first: Clarissa

last: Gerhäuser

first: Hans

middle: H

last: Kreipe

first: Nadia

last: Harbeck


title: SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance

first: Yann

last: Loe-Mie

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

overall_design: Refer to individual Series


title: Age-dependent Inflammatory Signaling in the Pulmonary Endothelium

city: New York

first: Rebecca

last: Hough

state: New York

address: 3959 Broadway, CHN 10-24

institute: Columbia University Irving Medical Center

summary: Acute Lung Injury (ALI) causes the highly lethal Acute Respiratory Distress Syndrome (ARDS) in children and adults, for which therapy is lacking. Children with Pediatric ARDS (PARDS) have a mortality rate that is about half of adults with ARDS. Improved ALI measures can be reproduced in rodent models with juvenile animals, suggesting that physiologic differences may underlie these different outcomes. Here, we show that pneumonia-induced ALI caused inflammatory signaling in the endothelium of adult mice which depended on Yes-associated protein (YAP). This signaling was not present in 21-day-old weanling mice. Transcriptomic analysis of lung endothelial responses revealed nuclear factor kappa-B (NF-kB) as significantly increased with ALI in adult versus weanling mice. Blockade of YAP signaling protected against ALI and NF-kB nuclear translocation in adult mice. Our results demonstrate an important signaling cascade in the lung endothelium of adult mice that is not present in weanlings. We suggest other pathways may also exhibit age-dependent inflammatory signaling, which would have important implications for therapeutics in the adult and pediatric age groups.

overall_design: Bulk RNA-seq of freshly isolated endothelial cells from weanling (P21) and adult (10 week old) C57BL/6J mice 24h after induction of pneumonia by intranasal instillation of Pseudomonas aeruginosa and saline (controls).

first: Memet

middle: T

last: Emin

first: Alexandra

last: Dubuisson

first: Prisha

last: Sujin Kumar

first: Carsten

last: Knutsen

first: Cristina

last: Alvira


title: Single-cell transcriptomics reveal synergistic and antagonistic effects of GATA1s and T21 on hematopoiesis

city: Philadelphia

first: Eric

last: Wafula

state: PA

address: 2714-2720 South Street

department: DBHi

institute: Children's Hospital of Philadelphia

summary: Trisomy 21 (T21), or Down syndrome (DS), is associated with baseline macrocytic erythrocytosis, thrombocytopenia, and neutrophilia, as well as transient abnormal myelopoiesis (TAM) and myeloid leukemia of DS (ML-DS). TAM and ML-DS blasts both arise from an aberrant megakaryocyte-erythroid progenitor and exclusively express GATA1s, the truncated isoform ofGATA1, while germlineGATA1smutations in a non-T21 contextleadto congenital cytopenia(s) without a leukemic predisposition. This suggests that T21 and GATA1s perturb hematopoiesis independently and synergistically in hematopoietic progenitors (HPCs), but this is challenging to study due to limited access to relevant human progenitorpopulations. To dissect individual developmental impacts, we used single-cell RNA-sequencing to interrogate HPCs from isogenic human induced pluripotent stem cells differing only by chromosome 21 and/orGATA1status. These HPCs were surprisingly heterogeneous and displayed lineage skew dictated by T21 and/or GATA1s. T21 and GATA1s each disrupted temporal regulation of lineage-specific transcriptional programs and specifically perturbed cell cycle genes. Trajectory inference revealed that GATA1s nearly eliminated erythropoiesis, slowed MK maturation, and promoted myelopoiesis in the euploid context, while in T21 cells, GATA1s competed with the enhanced erythropoiesis and impaired megakaryopoiesis driven by T21 and give rise to immature erythrocytes, MKs, and myeloid cells. The use of isogenic cells revealed distinct transcriptional programs that can be attributed specifically to T21 and GATA1s, and how together they result in HPC proliferation at the expense of maturation, consistent with a pro-leukemic phenotype.

overall_design: To investigate the role of GATA1s in the pathogenesis of congenital cytopenias and transient abnormal myelopoiesis, we used isogenic euploid and Trisomy 21 induced pluripotent stem cell (iPSC) lines with wild-type GATA1 or GATA1s. We performed gene expression profiling analysis and trajectory inference on data obtained from single-cell RNA sequencing of flow-purified hematopoietic progenitor cells differentiated from these iPSC lines.

first: Kaoru

last: Takasaki

middle: K

first: Sara

last: Kumar

first: David

last: Smith

first: Ying

last: Sit

first: Alyssa

middle: L

last: Gagne

first: Deborah

last: French

first: Christopher

last: Thom

first: Stella

last: Chou


title: The small molecule Pifithrin–α deactivates ETR1 to repress shade avoidance in Arabidopsis

first: Lin

last: Li

address: 220 Handan Road

institute: Fudan university

summary: Shade avoidance syndrome (SAS) commonly occurs in plants sensing shading and the proximity of neighbors, leading to morphological and physiological changes that are detrimental to plant health and consequently crop yield. Controlling SAS could prove beneficial for sustainable agriculture.Here, we performed a phenotype-based chemical screen in Arabidopsis and identified pfifithrin (PFT-α) as a compound that suppresses shade-induced hypocotyl elongation and gene expression.  Through genetic, biochemical, and molecular approaches, we demonstrated that PFT-α mimics ethylene by deactivating the ethylene receptor ETR1. This action influences the expression of Phytochrome-Interacting Factors (PIF4 and PIF7) and subsequently inhibits shade-induced hypocotyl elongation. Our findings suggest that PFT-α, acting as a potent ethylene mimic, plays a crucial role in hormone-regulated plant development and holds promise for modulating SAS in agricultural contexts.

overall_design: 4-day-old dark-grown Col-0 seedlings were transferred to 1/2 MS liquid medium complemented with 30 μM PFT-α, 10 μM ACC or 1‰ DMSO (v/v) for 4 h, and whole seedlings were collected.Set three biological replicates for each treatment.

first: Wenjing

last: Liang


title: Treatment-Induced Gene Expression Changes in Metastatic Renal Cell Carcinoma: Insights from a Syngeneic Mouse Model

status: Public on Jul 15 2025

city: Sapporo

first: KO

last: OKABE

state: Hokkaido

address: South-1, West-16, Chuo-ku

institute: Sapporo Medical University School of Medicine

summary: This study aimed to clarify the alterations in gene expression in metastatic renal cell carcinoma (mRCC) during disease progression and in response to treatment with immune checkpoint inhibitors using a syngeneic mouse mRCC model. RENCA cells were orthotopically implanted in BALB/c mice. Mice received first-line treatment with cabozantinib, anti-PD-1 antibody, or a combination. Tumor progression was monitored using serial micro- computed tomography. Lung metastasis samples were collected, and RNA sequencing was performed. Mice with apparent disease progression received second-line treatment with axitinib, everolimus, or lenvatinib after combination therapy. The median overall survival was 28, 34, 34, and 49 days in untreated mice and those treated with cabozantinib, anti-PD-1, or their combination, respectively (p < 0.05). RNA sequencing revealed upregulation of the fibroblast growth factor pathway in lung metastases after monotherapy, whereas mTOR pathway activation was observed only after combination therapy. Treatment-specific gene expression changes occur in mRCC, suggesting that the optimal target for sequential therapy in mRCC varies depending on prior treatment.

overall_design: This submission includes RNA sequencing data from lung metastases of a syngeneic mouse metastatic renal cell carcinoma model. RENCA cells were orthotopically implanted into BALB/c mice. Experimental groups include untreated controls and treatment groups receiving cabozantinib, anti-PD-1 antibody, or their combination as first-line therapy. Second-line treatment groups include axitinib, everolimus, or lenvatinib administered after combination therapy. The study investigates treatment-induced gene expression changes to evaluate molecular alterations and potential targets for sequential therapy. Each treatment group included biological replicates. Control samples (untreated) are included for comparison.

first: Ko

last: Okabe

first: Toshiaki

last: Tanaka

first: Tetsuya

last: Shindo

first: Yuki

last: Kyoda

first: Sachiyo

last: Nishida

first: Kohei

last: Hashimoto

last: Kobayashi

first: Naoya

last: Masumori


title: SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands

city: Cambridge

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

institute: University of Cambridge

summary: In mammalian genomes, cytosine modifications form a layer of regulatory information alongside the genetic code. Decoding this information is crucial to our understanding of biology and disease. Established sequencing methods cannot simultaneously resolve cytosine’s three most common forms—cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC)—across both strands of the DNA double helix. Thus, how epigenetic information is distributed in DNA remains unclear. We present an accurate and quantitative, base-resolution approach to sequence genomes, together with mC and hmC, in both strands of the same DNA fragment. We show that different forms of cytosine combine across the double helix at CpG sites to form discrete information states in the mouse epigenome. These CpG states have distinct genomic distributions—including at promoters, enhancers, and gene bodies—and have different relationships with transcription. We show that while all possible forms of hydroxymethylation occur, hmC is predominantly asymmetric and that different forms of asymmetric hmC are not equivalent. Our findings demonstrate that 5-hydroxymethylcytosine combines with different cytosine variants across the DNA double helix to form distinct states of regulatory information.

overall_design: Simultaneous hydroxymethylation and methylation profiling on double-stranded DNA extracted from mouse embryonic stem cells (E14) by high throughput sequencing (custom library prep). Data were obtained from two independent replicates and samples included spike-in controls (Lambda, pUC19 and custom synthetic oligonucleotide duplexes) to assess the accuracy of methylation and hydroxymethylation calls.

first: Jack

last: Hardwick

first: Walraj

last: Gosal

first: Shankar

last: Balasubramanian


title: Piezo1-mediated Mechanotransduction Shapes ILC2 Translational Activity, Functions, and Lung Pathogenicity [II]

city: Seoul

first: MinYeong

last: Lim

address: 103, Daehak-ro, Jongno-gu

department: Department of biomedical scicence

institute: Seoul National University, College of Medicine

summary: Group-2 innate-lymphoid cells (ILC2s) are critical mediators of the type-2 immune responses in multiple lung pathologies. We show that Piezo1, a mechanosensitive ion channel, plays a key role in regulating ILC2 functions by linking mechanical cues to biochemical signaling pathways. Both murine and human ILC2s strongly express Piezo1, and its activation by Yoda1 selectively enhances IL-13 production through calcium influx, which activates the mTOR-S6K pathway. This pathway leads to translational reprogramming, favoring IL-13 translation. Piezo1-deficient in ILC2s impairs this process, reducing IL-13 levels and resulting in attenuated lung inflammation and fibrosis in mouse models of IL-33- or Alternaria alternata-induced airway inflammation and bleomycin-induced fibrosis. These findings position Piezo1 as a critical mediator of ILC2-driven type-2 immune responses and highlight its potential as a therapeutic target for lung diseases characterized by excessive inflammation. This streamlined understanding of Piezo1 function improves focus on its mechanistic role in lung pathology.

overall_design: Mouse lung ILCs sample from tamoxifen inducible Piezo1fl/fl x Id2-CreERT2 (cKO) or llittermate control Piezo1fl/fl mice (WT). We injected tamoxifen for Cre recombinase induction and intratracheal injection of rmIL-33 (250ng/ml) for 3 days interval for ILC2s enrichment. After last days of rmIL-33 injection, we sorted CD45+ Lin- CD127+ ILCs by Aria FACS sorter (BD bioscience).

first: Hye young

last: Kim

first: Seonjun

last: Park

first: Sungho


title: Revisiting oxygen toxicity: evolution and adaptation to superoxide in a SOD-deficient bacterial pathogen

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

summary: Defenses against oxidants are crucial for the virulence of pathogens, with superoxide scavenging enzymes (SOSEs) playing a vital role for most aerobes. However, our knowledge of superoxide adaptation primarily stems from the study of SOSE-encoding bacteria. Here, we investigated the evolution of a naturally SOSE-deficient pathogen (Leptospira spp.), along with the alternative mechanisms it recruits to combat superoxide stress. We demonstrate that emergence of pathogenic Leptospira correlated with SOD loss, but that a long-lasting adaptation to superoxide remains possible. We reveal that cysteine and leucine biosynthesis are the most induced pathways in response to superoxide and demonstrate the importance of sulfur metabolism in superoxide adaptation  in this SOSE-deficient model. We also propose cysteine oxidation as a key mediator of superoxide toxicity in the absence of SOSEs. This study challenges our conventional understanding of the oxygen toxicity theory and proposes a new model of superoxide adaptation through metabolic rewiring in bacteria.

overall_design: RNAs will be prepared from 3 replicates of the resistant L. interrogans strain and 3 replicates of the original clone before adaptation and RNAseq will be performed.

first: Marc

last: Monot

first: Samuel

last: Huete

first: Rania

last: Ouazahrou

first: Nadia

last: Benaroudj


title: Revisiting oxygen toxicity: evolution and adaptation to superoxide in a SOD-deficient bacterial pathogen [paraquat]

overall_design: To identify superoxide-induced mechanisms in pathogenic Leptospira, RNA-seq analyses were performed on L. interrogans exposed to 10 and 50 M of paraquat.


title: Identification of differentially methylated sites in COPD by exposure to biomass smoke

city: TLALPAN

first: SALVADOR

middle: GARCIA

last: CARMONA

state: CIUDAD DE MÉXICO

address: Calz. de Tlalpan 4502

department: INVESTIGACION

country: Mexico

institute: INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS

summary: Chronic obstructive pulmonary disease (COPD) is a complex and multifactorial pathology. It is characterized by persistent respiratory symptoms and is due, among other causes, to airway and/or alveolar abnormalities, generally caused by exposure to particulate matter or noxious gases. Biomass smoke exposure is an environmental risk factor that can modify methylation patterns in genes that participate or contribute to the development of  COPD.  The best known epigenetic mechanism in humans is cytosine methylation, which occurs by covalent modification of carbon 5 of cytosine (5-methyl cytosine, 5mC), mostly present in CG dinucleotides within the genome. CG dinucleotides tend to be in sequences called cytosine CpGon 5 (5-methyl cytosine, 5mC) islands, they are mostly present in CG dinucleotides within the genome. CG dinucleotides tend to be in sequences called CpG islands.

overall_design: An epigenome-wide association study was performed using the Illumina EPIC Infinium Methylation microarray in induced sputum samples from 45 women with COPD from biomass smoke exposure (EP-HL) and 46 women without COPD but with biomass smoke exposure (EXP-HL). The bioinformatic and statistical analysis was performed in the Rstudio environment.

last: GARCIA CARMONA

first: GLORIA

last: PEREZ RUBIO