title: Mapping of Rpo21 RNA-binding sites in Saccharomyces cerevisiae with abrogated binding of Nab3 to PIC2

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: Using CRAC, we compared the transcriptomic occupancy of Rpo21 in a Saccharomyces cerevisiae BY4741 parental strain (PIC2-GFP) and two derived mutants lacking Nab3 RNA-binding sites in PIC2. The purpose of the experiment was to determine that changes in the abundance of differentially expressed transcripts, which had been previously identified by RNA-sequencing, were not caused by alterations in Rpo21 occupancy and transcription. Sequencing outputs were processed using the pyCRAC pipeline and peak calling was performed with DBPeaks, our newly developed package for identification and comparison of binding sites defined by RNA-binding footprinting techniques (e.g., CRAC, iCLIP, PAR-CLIP, etc.).

overall_design: Two biological replicates of CRAC experiments performed in a parental Saccharomyces cerevisiae strain (PIC2-GFP) and two derived mutants: mut-Nab3-BS and mut-NNS-BS. While mut-Nab3-BS lacks Nab3 RNA-binding sites in PIC2, the other strain has no Nab3 or Nrd1 RNA-binding sites in PIC2 (mut-NNS-BS). All strains encoded RPO21-HTF (HIS6-TEV-3xFLAG). When SC-Ura cultures containing 1% (w/v) raffinose reached an OD600 of 1, cells were UV cross-linked (254 nm; 500 mJ/cm2) in the Vari-X-linker (UVO3) and rapidly filtered on 0.8 μm membranes (Merck) using a filtration device connected to a vacuum pump. Membranes were collected in 50 mL tubes, flash frozen by submersion into liquid nitrogen and stored at -80ºC until the day of the experiment.  On the day of the experiment, pellets were resuspended in a volume of lysis buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40, 1U/mL of RQ1 RNase-free DNAse (Promega) and 1 EDTA-free protease inhibitor cocktail (Roche)/ 50 mL and 5 mM β-mercaptoethanol) corresponding to twice their mass. Lysates were then transferred to a fresh 50 mL tubes, where they were mixed with 2 volumes of 0.5 mm zirconia beads (Thistle Scientific), and vortexed at maximum speed for five 1-minute intervals alternated with 1-minute incubations on ice. An additional volume of lysis buffer was pipetted into each sample before partitioning the cell debris by centrifugation at 4ºC (4000 rpm, 15 minutes) and spinning down lighter impurities in an additional centrifugation step (10000 rpm, 20 minutes) at 4ºC. Immunoprecipitation of the labelled protein from the supernatant was achieved during a two-hour incubation of the sample with 75 µL of anti-FLAG® M2 magnetic beads (Sigma-Aldrich, M8823-5ML) which had been previously washed three times with 1 mL TN150 buffer. Immobilised beads underwent three 5-minute washes with TN1000 buffer (50 mM Tris pH 7.8, 1 M NaCl, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and three additional 5-minute washes in 2 mL TN150 buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol). Afterwards, beads were resuspended in 550 µL of TN150 and incubated with 1 µL of a 1:100 dilution of RNace-It™ for exactly 5 minutes at 37 °C. To prevent overdigestion of co-immunoprecipitated transcripts and elute the bait proteins from the anti-FLAG beads, the solution was mixed with 0.4 g of guanidium hydrochloride (Gu-HCl) and the necessary volume of NaCl and imidazole (pH 8.0) to reach a final concentration of 300 mM and 10 mM respectively. After removing the beads, samples were pipetted onto 50 µL of Ni-NTA agarose resin (Qiagen) equilibrated with wash buffer I (6 M Gu-HCl, 10 mM imidazole, 300 mM NaCl, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and incubated at 4 °C overnight while rotating at 12 rpm.  Upon Ni-NTA binding, beads were transferred to Pierce columns (Thermo Fisher Scientific) and washed twice with 500 µL of wash buffer I before undergoing three additional washes of 500 µL with NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40, 5 mM β-mercaptoethanol). Alkaline phosphatase treatment was performed by resuspending immunoprecipitated RNA-protein conjugates in 80 µL of NP-PNK buffer containing 4 units of FastAP thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and 80 units of RNasin® ribonuclease inhibitor (Promega) and incubating the samples at 37 °C for 1 hour. Dephosphorylation was stopped upon addition of 500 µL of wash buffer. Having equilibrated the Ni-NTA agarose with three washes of 500 µL with NP-PNK, we performed adapter ligation by resuspending the beads 80 µL of reaction mix containing 0.6 µM of the applicable App-PE 3′ adapter (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’), 30 units of T4 RNA ligase 2 truncated K227Q (New England Biolabs), 60 units RNasin® (Promega) and 10% (w/v) polyethylene glycol 8000 (PEG 8000). The reaction took place at 25 °C for six hours.  After washing once with 500 µL of wash buffer I and three times with 500 µL of NP-PNK buffer, we 5’end radiolabelled co-immunoprecipitated RNAs by incubating the Ni-NTA resin with 60 µL of NP-PNK buffer containing 30 µCi 32P-γATP (PerkinElmer) and 30 units of T4 polynucleotide kinase (New England Biolabs). After a 40-minute incubation of the reaction at 37ºC, ATP (Roche) was supplemented to a final concentration of 1 mM and the reaction continued for another 20 minutes. The reaction was stopped by washing three times with 500 µL of wash buffer I and three 500 µL washes of NP-PNK buffer followed before the addition of the 5′ linker ligation mix. The reaction took place in a volume of 80 µL of NP-PNK buffer supplemented with 1.25 µM of the fitting adapter, 40 units of T4 RNA ligase 1 (New England Biolabs), 80 units of RNasin® and 10 mM ATP (Roche).  5’ adapter ligation was left to proceed overnight at 16 °C for all bait proteins. The adapter sequences were 5’-ACACGACGCTCTTCCGATCTNNNTAAGCN-3’  and 5’-ACACGACGCTCTTCCGATCTNNNCGCTTAGCN-3’ for PIC2-GFP repeats 1 and 2 respectively; 5’-ACACGACGCTCTTCCGATCTNNNGTGAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNTAGTGCN-3’ for mut-Nab3-BS replicates 1 and 2 respectively;  and 5’-ACACGACGCTCTTCCGATCTNNNACTCAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNGTGACAN-3’ for mut-NNS-BS libraries 1 and 2 respectively. After pooling suitable libraries together, the samples and its corresponding traces were submitted to Novogene, where paired-end sequencing of 150 bp-reads was performed in a NovaSeq 6000 system (Illumina).

first: Sofia

last: Esteban Serna


title: Mapping of Nab3 RNA-binding sites in Saccharomyces cerevisiae with suboptimal expression of PIC2.

status: Public on Nov 15 2025

country: United Kingdom

summary: Using CRAC, we compared the transcriptomic occupancy of Nab3 in a Saccharomyces cerevisiae BY4741 parental strain (PIC2-GFP, i.e., WT) and two derived mutants overexpressing (pTEF1-PIC2) or lacking (KO) PIC2. The purpose of the experiment was to check whether overexpressing or preventing the expression of PIC2 (an established Nab3 mRNA target which, when overexpressed or deleted, causes severe cellular defects) would cause a re-distribution of Nab3 binding among its other target transcripts. Sequencing outputs were processed using the pyCRAC pipeline and peak calling was performed with DBPeaks, our newly developed package for identification and comparison of binding sites defined by RNA-binding footprinting techniques (e.g., CRAC, iCLIP, PAR-CLIP, etc.).

overall_design: Two biological replicates of CRAC experiments performed in a parental Saccharomyces cerevisiae BY4741 strain (PIC2-GFP) and two derived mutants: pTEF1-PIC2 and KO. While pTEF1-PIC2 encodes a LEU2 plasmid coding for the coding and untranslated region of PIC2 under the pTEF1 promoter, the KO strain has a kanMX6 cassette replacing the entire PIC2 gene. All strains encoded NAB3-HTF (HIS6-TEV-3xFLAG). PIC2-GFP and KO were transformed with the pRS415 LEU2 vector to allow for B13medium uniformity. When SC-Leu cultures containing 1% (w/v) raffinose reached an OD600 of 1, cells were UV cross-linked (254 nm; 500 mJ/cm2) in the Vari-X-linker (UVO3) and rapidly filtered on 0.8 μm membranes (Merck) using a filtration device connected to a vacuum pump. Membranes were collected in 50 mL tubes, flash frozen by submersion into liquid nitrogen and stored at -80ºC until the day of the experiment.  On the day of the experiment, pellets were resuspended in a volume of lysis buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40, 1 EDTA-free protease inhibitor cocktail (Roche) per 50 mL and 5 mM β-mercaptoethanol) corresponding to twice their mass. Lysates were then transferred to a fresh 50 mL tubes, where they were mixed with 2 volumes of 0.5 mm zirconia beads (Thistle Scientific), and vortexed at maximum speed for five 1-minute intervals alternated with 1-minute incubations on ice. An additional volume of lysis buffer was pipetted into each sample before partitioning the cell debris by centrifugation at 4ºC (4000 rpm, 15 minutes) and spinning down lighter impurities in an additional centrifugation step (10000 rpm, 20 minutes) at 4ºC. Immunoprecipitation of the labelled protein from the supernatant was achieved during a two-hour incubation of the sample with 75 µL of anti-FLAG® M2 magnetic beads (Sigma-Aldrich, M8823-5ML) which had been previously washed three times with 1 mL TN150 buffer. Immobilised beads underwent three 5-minute washes with TN1000 buffer (50 mM Tris pH 7.8, 1 M NaCl, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and three additional 5-minute washes in 2 mL TN150 buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol). Afterwards, beads were resuspended in 550 µL of TN150 and incubated with 1 µL of a 1:100 dilution of RNace-It™ for exactly 5 minutes at 37 °C. To prevent overdigestion of co-immunoprecipitated transcripts and elute the bait proteins from the anti-FLAG beads, the solution was mixed with 0.4 g of guanidium hydrochloride (Gu-HCl) and the necessary volume of NaCl and imidazole (pH 8.0) to reach a final concentration of 300 mM and 10 mM respectively. After removing the beads, samples were pipetted onto 50 µL of Ni-NTA agarose resin (Qiagen) equilibrated with wash buffer I (6 M Gu-HCl, 10 mM imidazole, 300 mM NaCl, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and incubated at 4 °C overnight while rotating at 12 rpm.  Upon Ni-NTA binding, beads were transferred to Pierce columns (Thermo Fisher Scientific) and washed twice with 500 µL of wash buffer I before undergoing three additional washes of 500 µL with NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40, 5 mM β-mercaptoethanol). Alkaline phosphatase treatment was performed by resuspending immunoprecipitated RNA-protein conjugates in 80 µL of NP-PNK buffer containing 4 units of FastAP thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and 80 units of RNasin® ribonuclease inhibitor (Promega) and incubating the samples at 37 °C for 1 hour. Dephosphorylation was stopped upon addition of 500 µL of wash buffer. Having equilibrated the Ni-NTA agarose with three washes of 500 µL with NP-PNK, we performed adapter ligation by resuspending the beads 80 µL of reaction mix containing 0.6 µM of the applicable App-PE 3′ adapter (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’), 30 units of T4 RNA ligase 2 truncated K227Q (New England Biolabs), 60 units RNasin® (Promega) and 10% (w/v) polyethylene glycol 8000 (PEG 8000). The reaction took place at 25 °C for six hours.  After washing once with 500 µL of wash buffer I and three times with 500 µL of NP-PNK buffer, we 5’end radiolabelled co-immunoprecipitated RNAs by incubating the Ni-NTA resin with 60 µL of NP-PNK buffer containing 30 µCi 32P-γATP (PerkinElmer) and 30 units of T4 polynucleotide kinase (New England Biolabs). After a 40-minute incubation of the reaction at 37ºC, ATP (Roche) was supplemented to a final concentration of 1 mM and the reaction continued for another 20 minutes. The reaction was stopped by washing three times with 500 µL of wash buffer I and three 500 µL washes of NP-PNK buffer followed before the addition of the 5′ linker ligation mix. The reaction took place in a volume of 80 µL of NP-PNK buffer supplemented with 1.25 µM of the fitting adapter, 40 units of T4 RNA ligase 1 (New England Biolabs), 80 units of RNasin® and 10 mM ATP (Roche).  5’ adapter ligation was left to proceed overnight at 16 °C for all bait proteins. The adapter sequences were 5’-ACACGACGCTCTTCCGATCTNNNTAAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNATTAGCN-3’ for PIC2-GFP (WT) repeats 1 and 2 respectively; 5’-ACACGACGCTCTTCCGATCTNNNTGGAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNACTCAGCN-3’ for pTEF1-PIC2 replicates 1 and 2 respectively;  and 5’-ACACGACGCTCTTCCGATCTNNNTGTCACN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNGCACTAN-3’ for both mut-NNS-BS libraries. After pooling suitable libraries together, the samples and its corresponding traces were sequenced using a benchtop MiniSeq system (Illumina), which performed single-end sequencing of 150 bp-reads.

last: Esteban-Serna


title: Effect of circ72039 overexpression on gene expression related to gemcitabine sensitivity in pancreatic cancer cell lines

city: Suita

first: Naoko

last: Sekiguchi

department: Gastroenterological surgery

country: Japan

institute: The university of Osaka

type: Expression profiling by high throughput sequencing

summary: Understanding the molecular characteristics of gemcitabine sensitivity in pancreatic cancer is essential for advancing individualized treatment strategies. This study identifies circ720309 as a potential contributor to improve gemcitabine sensitivity. circ72309 decreased cytidine deaminase, a nucleoside enzyme which transforms gemcitabine into an inactive form, via reactive oxygen species activity, and increased solute carrier family 29 member 1 (SLC29A1), a nucleoside transporter which imports gemcitabine into cells, by regulating targeted miRNAs.

overall_design: To identify circRNAs associated with gemcitabine sensitivity, a gemcitabine-resistant pancreatic cancer cell line (GR3) was established from MIAPaCa-2 and differences in circRNA expression between the two cell lines were examined.

first: Yoshito

last: Tomimaru

first: Hidenori

last: Takahashi

first: Hidetoshi

last: Eguchi


title: Systemic miR-26a deficiency attenuates pulmonary fibrosis via PTEN upregulation and downstream TIMP-1 suppression

city: Hiroshima

first: Arisa

last: Hamada

state: Hiroshima

address: Kasumi, Minami-ku,

department: Department of Molecular and Internal Medicine

institute: Graduate School of Biomedical and Health Sciences, Hiroshima University

summary: To identify factors that suppressed fibrosis in miR-26a KO mice, we performed a comprehensive comparison of total lung mRNA expression levels between the WT and miR-26a KO groups using RNA sequencing analysis.

overall_design: WT and KO mice were euthanized on day 0 (prior to BLM OA) and day 7 after BLM OA.  Both the day 0 and day 7 groups were subjected to identical procedures from sample collection through RNA sequencing.

first: Kiyofumi

last: Shimoji

first: Taku

last: Nakashima


title: Transcriptomic analysis of pathway activation after decitabine treatment in EBV+ vs EBV- gastric cancer [RNA-Seq]

status: Public on Nov 14 2025

city: Boston

first: Yin

last: Wang

address: 181 Longwood Ave

country: USA

institute: Brigham and Women's Hospital

summary: Epstein-Barr virus associated gastric cancer (EBVaGC) accounts for ∼9–10% of gastric cancers worldwide and is defined by a distinctive molecular profile, including extreme hypermethylation of the DNA. Targeting this aberrant methylation may be a potential therapeutic strategy. EBV ⁺ gastric cancer cell lines (YCCEL1, SNU719) and EBV ⁻ lines (AGS, SNU16, HGC27) were treated with a DNA methyl-transferase inhibitor (DNMT), decitabine (DCB), for three days followed by RNA sequencing to identify EBV-specific responses.

overall_design: EBV+ cell lines (YCCEL1 and SNU719) and EBV- cell lines (AGS, SNU16 and HGC27) were treated with DCB for 72 hours or DMSO as the control.

first: Benjamin

middle: E

last: Gewurz


title: Tramadol Triggers Paraptotic Cell Death through ATF4 in Breast Cancer Cells

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114201, Taiwan

country: Taiwan

institute: National defense medical center

summary: Breast cancer treatment has significantly improved, achieving a five-year survival rate of 90%. However, 30% to 50% of survivors continue to suffer from persistent pain, a common long-term side effect. Tramadol, an analgesic often prescribed for postsurgical pain, has recently been shown to have anticancer effects on breast cancer cells. The use of tramadol in postoperative care has been associated with reduced recurrence and improved survival rates, but the mechanisms involved in its anticancer activity are not fully understood. This study explored how tramadol induces paraptosis, a form of nonapoptotic cell death, by focusing on endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) pathways in breast cancer cells. The findings revealed that tramadol treatment increased ROS levels, triggering ER stress and activating the p-eIF2α/ATF4/CHOP signaling axis. This stress response led to cytoplasmic vacuolization and mitochondrial dysfunction, both of which are key features of paraptosis. Inhibiting ROS production or blocking the ATF4 pathway reduced tramadol-induced paraptosis, confirming the critical role of these mechanisms in breast cancer cells. In summary, tramadol induces paraptosis in breast cancer cells by activating ROS and ER stress, offering potential insight into its anticancer effects. These findings could have implications for improving both pain management and cancer treatment outcomes in breast cancer patients.

overall_design: MDA-MB-231 and MCF-7 cells were treated with 0 or 1 mg/ml of tramadol for 4 h. Total RNA was isolated and subjected to RNAseq analyses.

first: Yi-Hsuan

last: Huang

first: Shih-Ming


title: A comprehensive study on the co-culture interaction between endophytic Fusarium and host Sanghuangporus

city: Lanzhou City

first: Lan

middle: Lan

last: Yu

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

country: China

institute: Northwest Normal University

summary: Fungal-fungal interactions frequently result in alterations to the metabolomic profiles of the interacting fungi, with potential ramifications in both industrial and agricultural contexts. In this present study, an endophytic strain of Fusarium sp. MF20 was isolated from the fruiting bodies of Sanghuangporus vaninii. An optimized co-culture system was then established to explore the changes in metabolite profiles resulting from the fungal-fungal interaction, employing a comprehensive analysis integrating transcriptomics and metabolomics. This foundational work paves the way for the enhanced industrial exploitation of Sanghuangporus, a medicinally valuable and rare fungi

sample_organism:
Fusarium sp.
Sanghuangporus vaninii

platform_organism:
Fusarium sp.
Sanghuangporus vaninii

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq of twelve samples in two different treatment groups

first: Yanjun

last: Ma

first: Lanlan

first: Jingming

last: Zhang

first: Rong

last: Li


title: RNAseq of conventional dendritic cells generated from mouse bone marrow cultures under different conditions

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Type 1 conventional dendritic cells (cDC1s) are infrequent immune cells with an essential role in orchestrating immune responses to malignancies or infections. Despite their significance in regulating adaptive immunity, the absence of efficient manufacturing techniques to produce adequate yields of cDC1s has hindered their application in therapeutic settings. Here, we find that Interleukin-4 (IL-4) enhances the yield of cDC1 cells produced from Flt3 ligand (Flt3L) cultures of hematopoietic progenitors from either mice or humans, while inhibiting the generation of plasmacytoid DCs. IL-4 acted predominantly on DC progenitors and its activity relied on the cell intrinsic expression of IL4-RA or STAT6. Both in vitro and in vivo, cDC1s that had been stimulated by IL-4 were effective in activating and promoting the expansion of cytotoxic CD8 T cells. Gene expression analysis pointed to a critical role for IL-4 in promoting cDC1 proliferation in vitro. Overall, our research reveals an unanticipated role for IL-4 in fostering the development and manufacture of bona-fide cDC1s, making it easier to employ them for further mechanistic studies, and opening the door to leveraging their potential use in human diseases.

overall_design: RNA-seq profiling of sorted cDC1 and cDC2s generated from mouse bone marrow cultures with different conditions:  Flt3L, Flt3L + IL-4, Flt3L + IL-4+ OP9, Flt3L + OP9, Flt3L + IL-4 + OP9DL-1, and Flt3L + OP9DL-1. Three biological replicates per group except the cDC2 Flt3L + IL-4 + OP9DL-1 group, which has two replicates. Samples were sequenced with an Illumina NextSeq 500 sequencing system, producing between 18-93 million single end 86 bp reads per sample.

first: Hannah

middle: D

last: Coughlan

first: Stephen

middle: L

last: Nutt

first: Michael

last: Chopin


title: A dual role of EZH2 in regulating A-to-I RNA editing and mRNA stability through ADAR1

first: Yanqiang

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a widespread modification in mammals. Cumulative evidence has suggested the altered A-to-I editing profile in prostate cancer (PCa), but the underlying mechanism remains unclear. Here, we discover enhancer of zeste homologue 2 (EZH2) as a novel ADAR interactor and editing regulator in PCa. Through competing with Interleukin Enhancer Binding Factor 2 (ILF2) for ADAR1 binding, EZH2 reshapes the substrate selectivity of ADAR1 and thus exhibits a bidirectional role in editing regulation. Moreover, EZH2 depletion induces the translational repression of Transportin-1 (TRN1), which further results in the accumulation of cytoplasmic ADAR1 to protect many oncogenic transcripts from degradation. Consistently, depletion of ADAR1 dramatically enhances the sensitivity of PCa cells and tumors to EZH2 selective degraders. Collectively, our study highlights the significance of EZH2-ADAR1 cascade in governing RNA editing and mRNA stability, which may provide novel perspectives for the advancement of EZH2-targeting cancer therapies.

overall_design: RNA-seq (n=4 for siCTRL, n=4 for siEZH2, n=6 for siADAR1 and n=5 for siADAR2) was isolated from C4-2 cells were used to detect RNA editing(0h). To analyze the impact of EZH2 or ADAR1 suppression on mRNA decay rate, control, EZH2- or ADAR1-deficient C4-2 cells were incubated with 5 μg/ml ActD (Sigma). Cell samples were collected at 0, 3, 6, 12 and 24 h post-treatment. Human true PCR-free 30x coverage WGS of C4-2 cells was considered as cell line reference genome. eCLIP-seq of EZH2, ADAR and ILF2 were profomed to detect their RNA binding target in C4-2.

first: Yang

last: Yi

first: Qi

last: Cao

first: Kaifu

last: Chen


title: Species-specific phyllosphere responses to external pH change

city: Hickory Corners

first: Kadeem

last: Gilbert

state: MI

address: 3700 E Gull Lake Dr

department: Plant Biology

institute: Michigan State University

summary: The leaf surface, known as the phylloplane, represents the initial point of contact for plants in their interaction with the aboveground environment. Although prior research has assessed how leaves respond to external pH variations, particularly in the context of acid rain, there remains a limited understanding of the molecular mechanisms through which plants detect, respond to, and mitigate cellular damage.  To look at plant responses to external pH changes,  we measured the phylloplane pH for five species with variable phylloplane pH that ranged in the dry control. Moreover, we investigated the phylloplane pH in response to three pH treatments (pH 6.5, 4, and 2) and found that plants can modify their phylloplane pH, and this buffering ability is species-specific.   Among the species analyzed, only Gossypium displayed a strong buffering ability. For treatments where leaves were exposed to either pH 6.5 or pH 4, Gossypium alkalinized the phylloplane pH slightly higher than the dry control pH. Remarkably, when leaves were exposed to pH 2, Gossypium was able to buffer the pH to 6 within five minutes. Furthermore, our transcriptional analysis indicated that the responses to external pH changes varied among species, highlighting differentially expressed genes associated with calcium (Ca2+) signaling pathways, as well as Ca2+ and H+-ATPases pumps. These findings also suggest that pH stress negatively impacts photosynthesis, and that both wetness and moderate pH shifts may trigger additional abiotic and biotic stress signaling pathways.

sample_organism:
Gossypium hirsutum
Gossypium arboreum
Nepenthes rafflesiana
Beta vulgaris
Nepenthes bicalcarata

overall_design: We selected five different species with predicted pH levels ranging from alkaline to acidic to assess a broad initial phylloplane pH: Gossypium arboreum, Gossypium hirsutum, Beta vulgaris, Nepenthes bicalcarata, and Nepenthes rafflesiana.  For each species, we exposed one leaf of three biological replicates per species to one of three pH treatments (6.5, 4, 2) for 5 minutes and  we collected unsprayed leaves for each species as dry controls.

first: Cristal

last: Lopez-Gonzalez

first: Jean-Baptiste

last: Floch

first: Tanya

last: Renner


title: Genome-wide screening of FOXM1 expression  in multiple myeloma cells

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

institute: Jichi  Medical  University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analyzed expression of FOXM1 gene  in multiple myeloma using ChIP-seq.

overall_design: We isolated fixed chromatin from KMM1 cells and performed immunoprecipitation with anti-FOXM1 antibody, followed by deep sequencing.

first: Jiro

last: Kikuchi


title: Single-cell transcriptomic datasets of the amphibious plant Water wisteria

city: Wuhan

first: Gaojie

address: Donghu Southroad 7

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Global climate changes cause severe floods that hinder plant development and breeding. The phenomenon in which a single plant can significantly alter its leaf shape structure and physiology based on surrounding environments is known as heterophylly, a trait commonly observed in amphibious plants. Heterophylly is a special survival strategy that enables adaptation to both submerged and terrestrial conditions, aiding in response to environmental changes. Molecular mechanisms of heterophylly are not well understood due to a lack of models. Hygrophila difformis, also known as Water wisteria, shows typical heterophylly in terrestrial and submerged environments, and is an emerging model plant to explore heterophylly. In this study, we conducted single-cell RNA sequencing (scRNA-seq) analysis of isolated protoplasts from both terrestrial and submerged shoots of H. difformis to obtain data on the gene expression patterns of tissue-specific cells. These scRNA-seq data enabled the identification of gene expression patterns by cell types, providing a foundation to elucidate the molecular mechanisms of heterophylly and plant environmental adaptations at a single-cell level.

overall_design: ScRNAseq of  the amphibious plant Hygrophila difformis under terrestrial and submerged conditions from shoot protoplasts


title: RNA-seq profiling of mouse Sertoli cell line after siDhx37 knockdown

city: Luoyang

first: Yuqing

last: Jiang

state: China

address: No. 263, Kaiyuan Avenue, Luolong District

institute: The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology

summary: Sertoli cells play a crucial role in supporting spermatogenesis in the testes. In this study, we aimed to investigate the molecular changes in Sertoli cells after the knockdown of Dhx37, a gene involved in RNA splicing and gene regulation. siDhx37 was transfected into the mouse Sertoli cell line, followed by RNA-seq analysis at Day 0 and Day 3 post-transfection. The results reveal that Dhx37 depletion affects the expression of key genes involved in Sertoli cell function, spermatogenesis, and cell cycle regulation. Differentially expressed genes (DEGs) were identified, highlighting pathways related to cellular processes, including cell proliferation, apoptosis. Our findings suggest that Dhx37 may play an important regulatory role in Sertoli cells by modulating the expression of genes necessary for their function in male reproduction.

overall_design: RNA-seq profiling of wildtype mouse Sertoli cells and their knockdown derivatives (siDhx37) at Day0 and Day3 post-transfection.

first: Huifang

last: Peng

first: Hongwei


title: mRNA-seq profiles of gastrocnemius of 24-day-old Nnt-mut and Nnt-wt male mice

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: mRNA-seq profiles from gastrocnemius muscle of 24-day-old  Nnt-wt and Nnt-mut male mice were compared. Result showed that Oxidative phosphorylation (OXPHOS) was the most significantly regulated KEGG pathway. All regulated OXPHOS genes were downregulated in Nnt-mut group. Three genes for carnitine palmitoyltransferase (CPT) system were all downregulated. CPT1B were not changed in protein level but pACC/ACC was increased in Nnt-mut group.

overall_design: Gastrocnemiuse muscle mRNA-seq profiles were obtained from two strains of 24-day-old male mice. These mouse strains are: B6JRccHsd(B6J)-Nnt<+>/Wuhap (Nnt-wt) and B6JRccHsd.B6J-Nnt<C57BL/6J>/Wuhap (Nnt-mut) (n=12 per strain).

first: Jingyi

last: Song

first: Jaap

last: Keijer

first: Sander

last: Grefte


title: Upfront Menin-inhibitor resistance in multiply pretreated leukemias

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary: Inhibitors of the Menin-KMT2A interaction are promising agents for the treatment of KMT2A-rearranged (KMT2A-r) leukemias. We evaluated Menin inhibition in patient derived xenografts of KMT2A-r leukemias with high-risk features. Three AMLs with high-risk fusion partners (MLLT10, MLLT4) and two infant ALL samples were sensitive to Menin inhibition. We also evaluated serial samples from two patients with multiply relapsed ALL. We found that highly pretreated KMT2A::AFF1 ALL samples were much less sensitive compared to cells obtained earlier in the same patients’ disease course. Since none of the patients had been treated with a Menin inhibitor, resistance in these highly pretreated samples was acquired in the absence to Menin inhibitor exposure. Transcriptomic analysis documented sustained on-target efficacy towards the canonical targets in the Menin-inhibitor in resistant cells. Targeted genomic analysis documented the emergence of multiple co-mutations, including RAS pathway and TP53 mutations, although neither was sufficient to induce Menin-inhibitor resistance in vitro. Downregulation of KMT3D may account for resistance in one patients; inactivation of KMT2C/D has been reported to result in Menin inhibitor resistance, and KMT2C-edited cells from this patient were selected for in VTP containing growth conditions. Future studies will need to clarify more broadly which genomic/epigenomic alterations drive upfront resistance. Regardless of mechanism, our data supports using Menin-inhibitors upfront or in early lines of therapy before substantial genomic or epigenomic evolution has occurred.

overall_design: Samples from a pediatric leukemia patient from two different time points (5.1 and 5.2) were banked at the Children’s Hospital of Philadelphia (CHOP) Institutional Review Board (IRB) Protocol IRB# 10-007767. Samples were obtained with parental informed consent according to the Declaration of Helsinki and IRB approval. 6-8 week old NSG (NOD-scid IL2Rgnull) mice were obtained from Jackson laboratories® and maintained under specific pathogen free conditions. 24-48 hours prior to transplantation, mice were conditioned with 25 mg/kg busulfan i.p. Previously banked patient leukemia samples were thawed, resuspended in PBS and injected into the tail vein.  Mice underwent monitoring for leukemia development using weekly serial bleeds. Treatment with VTP-50469 0.1% chow was started once peripheral blood engraftment in the range of 1-5% was seen (day 14 for sample 5.1, and day 7 for sample 5.2). After three weeks of treatment, mice were sacrificed and leukemia cells were isolated by and sorted on live (FSC vs SSC and DAPI negative), human CD45+, mouse CD45-. RNA was extracted using the RNeasy mini kit from QIAGEN.

first: Hongbo

last: Xie

first: Leila

last: Mahdavi

first: Fatemeh

last: Alikarami


title: Profiling of immune cell subsets and functional characteristics of cervical cancer based on single cell RNA sequencing

city: Changchun

first: Xiaosong

last: Wang

state: Jilin

address: No.519 Dongminmin Street Changchun 130021, China

institute: Department of Translational Medicine, the First Hospital of Jilin University

summary: A comprehensive characterization of immune cells within the tumor microenvironment (TME) of cervical squamous cell carcinoma (CSCC) is essential to advance understanding of tumor biology and guide immunotherapy development. Using single-cell RNA sequencing, we analyzed 14,441 immune cells isolated from tumor tissues and paratumor tissues of three CSCC patients. This analysis identified nine major immune cell subsets, including CD8+ T cells, regulatory T cells (Tregs), natural killer/T cells (NK/T cells), B cells, plasmacytoid dendritic cells (pDCs), and macrophages. Notably, elevated CCR7 expression in exhausted CD8+ T cells was associated with improved prognosis, suggesting it as a preliminary candidate for an immunoregulatory target that warrants further investigation. Additionally, CCL5 levels were elevated in Tregs, indicating a possible involvement in their recruitment to the tumor site that requires further validation. By integrating data on tumor suppressors, oncogenic factors, cytokines, and chemokines, we performed differential gene expression analyses across immune populations, identifying candidate genes for further mechanistic investigation. This systematic comparison of the TME between tumor and paratumor tissues reveals dynamic changes in the immune landscape, providing insights and suggesting potential targets for further study to enhance understanding and treatment of CSCC.

overall_design: Fresh squamous cervical cancer specimens were collected from three patients undergoing primary surgery at the Department of Obstetrics and Gynecology, First Hospital of Jilin University, between June 2019 and August 2020. None received preoperative treatment.Samples of cervical squamous cell carcinoma (CSCC), both tumor and paratumor, were procured from the tumor mass and regions located 1 cm away from the tumor boundary, respectively. The tissue samples were washed with PBS (CORNING) before being stored in MACS Tissue Storage Solution (Miltenyi Biotec). Subsequently, they were processed into single-cell suspensions.


title: Spatial and single cell transcriptomics in the human Entorhinal Cortex across diverse risk of Alzheimer’s disease

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: We present the first spatially-resolved transcriptomics and single-nucleus RNA-sequencing integrated dataset from the entorhinal cortex (ERC) of postmortem human brain donors. ERC is implicated in early progression of Alzheimer’s Disease (AD) and we chose this brain region to study gene expression changes associated with AD risk by comparing APOE E2 and E4 allele carriers. Donors with no AD diagnosis or widespread neurodegeneration were exclusively selected. As AD risk is increased in African Ancestry in contrast to European Ancestry backgrounds, and AD risk is also increased in women compared to men, our dataset included donors from these different backgrounds. We identified a pre-myleinating oligodendrocyte sub-cluster with transcriptomic changes strongly associated with APOE E4 carriers. These changes were present in both ancestry backgrounds, although they were more pronounced in African Ancestry donors. To facilitate future studies based on this dataset, we provided the raw and processed data, and created interactive web applications.

overall_design: We obtained tissue blocks of postmortem human brain entorhinal cortex (ERC) from 31 neurotypical adult brain donors carrying either E2 or E4 APOE alleles from both African and European ancestry. For each donor, a sample was generated for both spatially resolved transcriptomics with 10x Visium, and single nucleus RNA-seq with 10x Chromium. Visium data showed 9 transcriptional distinct spatial domains. snRNA-seq data was clustered into 38 fine subtypes across 8 broad cell types. Differential expression between APOE carrier status (E2+ vs. E4+) was performed at the cluster level in both data types.

first: Louise

middle: A

last: Huuki-Myers

first: Heena

middle: R

last: Divecha

first: Svitlana

middle: V

last: Bach

first: Madeline

last: Valentine

first: Nicholas

middle: J

last: Eagles

first: Bernard

last: Mulvey

first: Rahul

last: Bharadwaj

first: Ruth

last: Zhang

first: James

last: Evans

first: Melissa

last: Grant-Peters

first: Ryan

last: Miller

first: Joel

last: Kleinman

first: Shizhong

last: Han

first: Thomas

middle: M

last: Hyde

first: Stephanie

middle: C

last: Page

first: Danie

last: Weinberger

first: Mina

last: Ryten

first: Kristen

last: Maynard

first: Leonardo

last: Collado-Torres


title: Spatial and single cell transcriptomics in the human Entorhinal Cortex across diverse risk of Alzheimer’s disease [Visium]

first: Keri

last: Martinowich

first: Louise

last: Huuki-Myers

first: Heena

last: Divecha

first: Svitlana

last: Bach

first: Daniel


title: Phospholipid Scramblase 1 (PLSCR1) Regulates Interferon-Lambda Receptor 1 (IFN-λR1) and IFN-λ Signaling in Influenza A Virus (IAV) Infection

city: PROVIDENCE

first: Alina

middle: Xiaoyu

last: Yang

state: RI

address: 171 Meeting Street, Room 624

department: Molecular Microbiology and Immunology

institute: Brown University

summary: Phospholipid scramblase 1 (PLSCR1) is an antiviral interferon-stimulated gene (ISG) that has several known anti-influenza functions. However, the mechanisms in relation to its expression compartment and enzymatic activity have not been completely explored. Moreover, only limited animal models have been studied to delineate its role at the tissue level in influenza infections. Our results showed that Plscr1 expression was highly induced by influenza A virus (IAV) infection in vivo and in airway epithelial cells treated with IFN-λ. We found that infected Plscr1-/- mice exhibited exacerbated body weight loss, decreased survival rates, heightened viral replication, and increased lung damage. Interestingly, transcriptomic analyses demonstrated that Plscr1 was required for the expression of type 3 interferon receptor (Ifn-λr1) and a large subset of ISGs upon IAV infection. The impaired expression of Ifn-λr1 and downstream ISGs may be responsible for delayed viral clearance and worse lung inflammation in Plscr1-/- mice. PLSCR1 acts as a transcriptional activator of IFN-λR1 by directly binding to its promotor after IAV infection. In addition, PLSCR1 interacted with IFN-λR1 on the cell surface of pulmonary epithelial cells following IAV infection, suggesting it also modulated IFN-λ signaling via protein-protein interactions. The lipid scramblase activity of PLSCR1 was found to be dispensable for its anti-flu activity. Finally, single-cell RNA sequencing data indicated that Plscr1 expression was significantly upregulated in ciliated airway epithelial cells in mice following IAV infection. Consistently, Plscr1floxStopFoxj1-Cre+ mice with ciliated epithelial cell-specific Plscr1 overexpression showed reduced susceptibility to IAV infection, less inflammation and enhanced Ifn-λr1 expression, suggesting that Plscr1 primarily regulates type 3 IFN signaling as a cell intrinsic defense factor against IAV in ciliated airway epithelial cells. Our research will elucidate virus-host interactions and pave the way for the development of novel anti-influenza drugs that target human elements like PLSCR1, thereby mitigating the emergence of drug-resistant IAV strains.

overall_design: To determine if IFN signaling pathways are regulated by Plscr1 during IAV infection, RNA sequencing of a total of 20,700 genes was performed using pooled samples from Wt and Plscr1-/- mouse lungs infected with 300 pfu of IAV. A comprehensive examination of interferons and their receptors revealed that Ifn-λr1 expression was significantly lower in Plscr1-/- mice, despite high expression of Ifn-λ at both 3 and 7 dpi

middle: X

first: Lisa

last: Ramos-Rodriguez

first: Parand

last: Sorkhdini

first: Dongqin

first: Carmelissa

last: Norbrun

first: Sonoor

last: Majid

first: Sanghyun

last: Lee

first: Yong

first: Michael

last: Holtzman

first: David

middle: F

last: Boyd

first: Yang

last: Zhou


title: Netrin-1 disrupt high-fat-diet-induced adipogenesis via the PPARγ and Wnt/β-catenin signaling pathways

status: Public on Nov 17 2025

city: guangzhou

first: shi

last: hang

address: 58 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Metabolically healthy fat remodeling is able to maintain a certain degree of systemic metabolic homeostasis, although factors involved in this process have not been fully clarified. Here we demonstrate that adipose Netrin-1, originally known as an axon guidance molecule, is associated with development of obesity and type 2 diabetes. We have observed improved systemic metabolic parameters that are attributable to increased inguinal white adipose tissue (iWAT) mass in male high-fat-fed transgenic mice lacking adipose-specific Netrin-1 expression (Ntn1AKO).  Preadipocytes extracted from the Ntn1AKO mice also exhibited increased cell proliferation, accompanied by decreased collagen deposition. Effects of Ntn1 in both adipocytes and preadipocytes were observed to be directly regulated by HIF-1α . Moreover, WAT-specific overexpression of Ntn1 disrupted metabolic equilibrium regardless of fat intake. Further investigation revealed that overexpressing Ntn1 attenuated adipogenesis by inhibiting the PPARγ while activating the Wnt/β-catenin pathways. In summary, our current study suggests that adipose Ntn1 regulate adipogenesis and function and may therefore be considered as a potential therapeutic target for obesity and diabetes.

overall_design: The transcriptomic profiles of  WAT were collected from Ntn1 ako and WT mice

first: Hang

last: Shi

first: Jiang

middle: H

last: Tang


title: BRG1 loss is frequent in lung cancer and transforms lung epi-thelial cells via transcriptional and epigenetic reprograming

city: Albuquerque

first: Steven

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

type: Methylation profiling by genome tiling array

summary: Background/Objectives: BRG1 loss-of-function (LOF) mutation is found in ~10% non-small cell lung cancer (NSCLC) but its role in lung tumorigenesis is unclear and investigated in this study. Methods: BRG1-knockout (KO) lines were generated from various non-malignant, pre-malignant, and malignant human lung epithelia-derived cell lines using CRISPR. Effects of BRG1-KO on cell growth, transcriptome, methylome, and epigenetic therapy were compared with wild-type (BRG1-WT) isogenic controls using standard in vitro and in vivo assays. Results: BRG1 protein was expressed in all non/pre-malignant lung epithelial cells but lost in 47% (14/30) of NSCLC cell lines. BRG1-KO and cigarette smoke (CS) exposure individually transformed human bronchial epithelial cell lines (HBECs) as evident by anchorage-independent growth. BRG1-KO and CS produced additive to synergistic effects on sensitivity to transformation that differed across HBECs. RNA-seq analysis revealed BRG1-KO significantly changed expression of over 8,500 genes on average impacting lung development, function, damage repair and cancer pathways including axonal guidance, pulmonary wound healing, and epithelial-to-mesenchymal transition (EMT). BRG1-KO also led to hypermethylation of >47,000 promoter CpGs within ~9,500 genes on average in different HBECs that included silencing of epithelial genes involved in EMT and tumor suppressor genes. BRG1-KO also moderately increased the in vitro and in vivo sensitivity of NSCLC cells to some epigenetic drugs. Conclusion: BRG1-LOF is frequent in NSCLC, can drive transformation of lung epithelial cells to acquire properties of premalignant cells indicating a potential role in lung cancer initiation, and sensitizes lung tumors to epigenetic therapy.

overall_design: DNA methylation profiling was done between HBECs with or without BRG1-KO, cigarette smoke airosol exposure, or both.

first: Mathewos

last: Tessema

first: Christin

last: Yingling

first: Loryn

last: Phillips

first: Kieu

last: Do

first: Maria

last: Picchi

first: Randy

last: Willink


title: Transcriptomics reveals orchestration of larval and juvenile development and metamorphosis in Southern Flounder Paralichthys lethostigma

city: Austin

first: Hans

last: Hofmann

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: The University of Texas

summary: Developmental transitions involve changes in the genetic programs governing molecular processes. Characterizing these genetic programs gives us insight into how genes work to orchestrate developmental transitions in morphology, physiology, or even behavior. One fascinating developmental transition, metamorphosis, bridges larval and juvenile periods. Southern Flounder, a flatfish, is an ideal model system to investigate these developmental states due to dramatic phenotypic changes during metamorphosis. Here, we use transcriptomics to investigate how genetic programs orchestrate larval development, metamorphosis, and juvenile development in Southern Flounder. Our analysis of Southern Flounder transcriptomes comprehensively describes distinct larval and juvenile genetic programs that overlap during metamorphosis. We also describe a third genetic program that peaks during metamorphosis. These results provide insight into molecular orchestration of flatfish and teleost metamorphosis and more generally into how the timing of genetic programs orchestrates metamorphosis. We also propose that these program trajectories can be used to pinpoint timing of metamorphosis in animals with less phenotypically distinct larval and juvenile forms.

overall_design: Bulk RNA-seq profiling of the Southern Flounder (Paralichthys legostigma) at 8 post-hatch developmental time timepoints.

first: Laura

last: Sisk-Hackworth

first: Matthew

last: Petershack

first: Cindy

last: Faulk

first: Rebecca

last: Young

first: Lee

last: Fuiman


title: Transcriptomic analysis and experimental verification reveal the involvement of PI3K/AKT signaling pathway in high-altitude cognitive dysfunction [6_OHG]

city: xi'an

first: linlin

last: jing

state: Shaanxi

address: NO.277 Yanta West Road, Yanta District

institute: The first affiliated hospital of xi'an jiaotong university

summary: Our Prior research has shown that 6-hydroxygenistein (6-OHG) alleviates hypobaric hypoxia induced brain injury (HHBI) achieved by its powerful antioxidant, anti-inflammatory, and anti-apoptotic capabilities, but its mechanism still requires additional investigation. The objective of this study was to uncover the protective mechanism of 6-OHG against HHBI based on transcriptomics analysis and experimental validation.The RNA-Seq analysis revealed 1585 differentially expressed genes (DEGs) between the Con and Mod groups, with 460 upregulated and 1125 downregulated. Between the 6-OHG and Mod groups, there were 679 DEGs, including 348 upregulated and 331 downregulated genes. Go and KEGG function analyses highlighted the PI3K/AKT signaling pathway as a crucial regulatory mechanism. Western blot analysis showed that HH exposure caused a decrease in the ratios of p-PI3K/PI3K and p-AKT/AKT in the mouse brain, but this effect was reversed by 6-OHG treatment, indicating that 6-OHG activates the PI3K/AKT signaling pathway. Furthermore, LY294002, a selective PI3K inhibitor, effectively blocked this activation and also abolished the protective effects of 6-OHG on histopathological damage, as well as its antioxidant, anti-inflammatory, and anti-apoptotic activities in HHBI mice. In summary, 6-OHG mitigates HHBI by activating the PI3K/AKT signaling pathway, suggesting its potential therapeutic application for HHBI treatment.

overall_design: RNA-Seq analysis of Con, Mod, and 6-OHG groups

first: Linlin

last: Jing

first: Yu

last: Xin

first: Gege

last: Wang

first: Chenyu

last: Yang

first: Huiping

last: Ma


title: Tissue-type plasminogen activator expression is required for proper CNS myelination

city: Paris

first: Barbara

last: Delaunay-Piednoir

address: 11 Place Marcelin Berthelot

department: CIRB

country: France

institute: INSERM

summary: Oligodendrocytes form myelin sheaths, a process regulated by intrinsic and extrinsic signals. Endothelial derived-tissue-type plasminogen activator (tPA) has been previously recognized for its role in aiding oligodendrocyte migration during (re)myelination. Moreover, it is well established that oligodendrocytes express de novo tPA following myelin damage, possibly reflecting the initiation of a regenerative program. However, its role in differentiation and myelination has remained unclear. This study aims to uncover the role of endothelial- and oligodendrocytes-derived tPA in developmental myelination. It appears that tPA is transiently expressed in myelinating oligodendrocytes in mice and humans. tPA deficiency delays oligodendrocyte maturation and causes persistent myelin defects, leading to motor impairments. Endothelial-derived tPA promotes myelin compaction, while oligodendrocyte-derived tPA supports myelin growth. These findings, along with previous research, highlight shared molecular mechanisms between developmental myelination and remyelination. Moreover, we highlight tPA’s dual roles in myelination and as a therapeutic target for dysmyelinating diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data throughout developmental stages and between conditional knock-out mice versus control mice.

first: Isabelle

last: Bardou


title: A human multi-organoid platform to model immune dynamics in cardiac injury and disease

city: Oxford

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: We devised a microphysiological system (MPS) coupling comBOs (combined bone and bone marrow organoids) and VCOs (vascularised cardiac organoids), enabling the recruitment of immune cells to VCOs follwing ischemic injury. Ischemia was modelled by exposing VCOs to hypoxic culture conditions (1% O2 for 24 hrs) before co-culture in our MPS. single nuclear RNA-sequencing was used to assess fibrosis and immune cell infiltration after cardiac injury.

overall_design: Control and injured vascularised cardiac organoid samples after 2 days and 5 days of injury (1% O2 for 24 hours to mimic hypoxia) and co-culture with combined bone and bone marrow organoids

first: Jasmeet

middle: S

last: Reyat

first: Gowishan

last: Poologasundarampillai

first: Amirpasha

last: Moetazedian

first: Julie

last: Rayes

first: Abdullah

middle: O

last: Khan


title: Effect of adenoviral E1A on oxaliplatin response in oxaliplatin-sensitive and resistant human colorectal cancer HCT116 cells

city: Saint-Petersburg

first: Alisa

last: Morshneva

state: Saint-Petersburg

address: Tihoretsky prospect, 4

department: Department of molecular and cellular interactions

country: Russia

institute: Institute of Cytology, RAS

summary: Resistance to chemotherapy drugs, including oxaliplatin, remains a major challenge in the treatment of colorectal cancer, often leading to treatment failure and poor patient outcomes. Overcoming chemoresistance by sensitizing tumor cells represents a critical therapeutic goal. Adenoviral early region 1A (E1A) has been proposed as a promising gene therapy agent capable of modulating cellular pathways to enhance sensitivity to chemotherapeutic agents. This dataset contains RNA-seq profiling of human colorectal cancer cell lines that are either oxaliplatin-sensitive (HCT116) or oxaliplatin-resistant (HCT116 oxpl-R), treated with oxaliplatin, in the context of doxycycline-induced adenoviral E1A expression. The experiment includes eight conditions: untreated controls, E1A expression alone, oxaliplatin treatment alone, and combined E1A expression with oxaliplatin treatment, each in both sensitive and resistant cell lines. The comprehensive experimental design enables the dataset to be divided into three independent analyses: A) Comparison of baseline transcriptomic profiles between oxaliplatin-sensitive and resistant cells (conditions 1 and 5); B) Investigation of the transcriptional response to oxaliplatin in sensitive and resistant cells (conditions 1, 3, 5, and 7); C) Evaluation of the impact of adenoviral E1A expression on the transcriptomes of sensitive and resistant cells alone (conditions 1, 2, 5, and 6) and in combination with oxaliplatin treatment (all eight conditions); This dataset provides valuable insights into the molecular mechanisms underlying oxaliplatin resistance and the potential role of E1A gene therapy in sensitizing colorectal cancer cells to chemotherapy.

overall_design: RNA-seq profiling of oxaliplatin-sensitive (HCT116) and oxaliplatin-resistant (HCT116 oxpl-R) human colorectal cancer cells after 24 hours of treatment with 25 µM oxaliplatin, following doxycycline-induced expression of adenoviral E1A. The study includes eight experimental conditions: (1) HCT116 control, (2) HCT116 E1A, (3) HCT116 oxaliplatin, (4) HCT116 E1A + oxaliplatin, (5) HCT116 oxpl-R control, (6) HCT116 oxpl-R E1A, (7) HCT116 oxpl-R oxaliplatin, and (8) HCT116 oxpl-R E1A + oxaliplatin.

first: Morshneva

last: Alisa

first: Igotti

last: Maria


title: SOX2 phosphorylation during mitosis limits genomic damage [ChIP-Seq 2]

city: Edinburgh

first: Charles

middle: A C

last: Williams

state: Midlothian

address: 5 Little France Dr, Bioquarter, Scottish Ctr For Regenerative Medicine, Scottish Ctr For Regenerative Medicine

department: Institute for Regeneration and Repair

institute: University of Edinburgh

summary: Pioneer transcription factors (TFs) such as SOX2 play critical roles in control of stem cell identity and are dysregulated in many human cancers. For example, SOX2 regulates the self-renewal of neural stem cells (NSCs), and is typically highly expressed in glioblastoma stem cells, where it is known to induce an immature NSC-like state. Here, we explored the regulation of SOX2 by phosphorylation during cell division and identify an unexpected role for mitotic SOX2 as an inducer of genomic damage. We find that SOX2 adopts a distinct phosphorylated state in NSCs during mitosis, regulated by the mitotic kinase CDK1. Mapping of SOX2 genome occupancy and chromatin accessibility shows that a subset of SOX2 remains bound to the interphase targets, consistent with mitotic bookmarking, but phosphorylated SOX2 is redistributed to constitutive heterochromatin, including telomeres. Ablation of SOX2 phosphorylation leads to promiscuous chromatin binding across the genome and triggers prolonged mitotic transit times and increased susceptibility to DNA damage. These findings show that excessive levels of SOX2 protein in mitosis trigger inappropriate opening of chromatin and downstream chromosomal damage. Elevated levels of SOX2 in cancers may therefore have dual oncogenic roles: imposing stemness during interphase via their well-known transcriptional roles, but simultaneously inducing genomic damage during mitosis due to their unconstrained pioneer factor activity.

overall_design: Genome binding/occupancy profiling and transcriptional profiling were performed using ChIP-seq, RNA-seq and ATACseq). This dataset refers to the ChIPseq analysis of SOX2 phsophsorylated at S253 and total SOX2 during mitosis and interphase. Experimental groups include control mNSCs or those arrested in mitosis .

first: Dounia

last: Djeghloul

first: Nicolas

last: Veland

first: Alhafidz

last: Hamdan

first: Maria

last: Kalantzaki

first: Erika

last: Lo

first: Robert

last: Illingworth

first: Alex

last: Von Kriegsheim

first: Amanda

middle: G

last: Fisher

first: Abdenour

last: Soufi

first: Steven

last: Pollard


title: Effects of stable SpCas9 expression in affecting gene expression in DU145 cells

city: Chapel Hill

first: Pengda

last: Liu

state: NC

address: 21-246 Lineberger Building, 450 West Drive, CB7295 450 West Drive, CB7295

department: Biochemistry and Biophysics

institute: The University of North Carolina at Chapel Hill

summary: SpCas9 has been broadly used in gene editing, while as a bacterial protein, its effects on mammalian cell behavior remains unclear. We established stable SpCas9 expression in a panel of mammalian cell lines and found stable SpCas9 expression could affect cell growth in vitro. For example, we observed that SpCas9 expression promoted DU145 cell proliferation. To understand underlying mechansims, we performed this RNA-Seq analysis in DU145-NC (negative control) and SpCas9 expressing cells, aiming to find how SpCas9 modulates gene expression that may contribute to its cell proliferation control.

overall_design: DU145-NC and DU145-Cas9 cells in biological triplicates were used for bulk-RNA-Seq analysis.

first: Yu

last: Le

first: Yi

last: Jin


title: Maternal vitamin and mineral supplementation effects on fetal liver at birth

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

summary: We investigated gene regulatory relationships in the neonatal liver to identify potential mechanisms by which maternal vitamin and mineral supplementation during gestation influences developmental programming in heifer calves. Accordingly, the hepatic transcriptome was measured using RNA-Seq in 12 calves collected 30 h after calving from dams fed a diet initiated 60 days pre-breeding and con-tinuing throughout gestation (VTM or CON, n = 6/group). We identified 630 differentially expressed genes (DEGs) between treatment groups. We also identified 58 transcription factors (TFs) and 435 differentially connected genes (p < 0.05), suggesting maternal diet induced a regulatory rewiring of TFs and histone deacetylating genes. Further research should explore whether these transcriptional changes are linked to epigenetic modifications established at birth, persist throughout postnatal development, and potentially contribute to multigenerational inheritance.

overall_design: Liver transcriptomes were profiled by RNA-Seq in calves collected 30 h after birth from dams fed either a basal diet (CON; n = 6) or the basal diet plus a vitamin and mineral premix (VTM; n = 6; 113 g•  heifer−1•d−1), starting 60 days pre-breeding and continuing through gestation.

first: Carl R

last: Dahlen


title: Derivation of Genetically-Defined Murine Hepatoblastoma Cell Lines with Angiogenic Potential

city: pittsburgh

first: Huabo

last: Wang

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

summary: Most hepatoblastomas (HB) are associated with aberrant expression of β-catenin (B), YAP (Y) and/or NRF2 (N) transcription factors and can be modeled in mice by over-expressing pairwise of triple combination of these. Virtually no human or murine HB cell lines exist that bear these mutations. We describe here an efficient way to generate cell lines from primary BN and YN tumors. Moreover, one of the BN lines shows a remarkable ability to trans-differentiate into endothelial cells under hypoxic conditions that may facilitate angiogenesis. These cell lines along with previousl-derived BN and BYN lines showed similar sensitivities to drugs commonly used to treat HB. Because the approach for cell line derivation we describe is quite general, it should allow for the generation of additional lines driven by less common factors. A collection of such permanent and well-characterized cell lines will facilitate studies that are difficult or impractical to perform in vivo

overall_design: Total RNAs were isolated as previously described using RNeasy columns (Qiagen). Only samples with RIN values >8.0 were processed further. Library preparation and sequencing were performed at the Pittsburgh Liver Research Center’s Core Sequencing laboratory (https://livercenter.pitt.edu/gsbc/#Sequencing) using an AVITI/Illumina instrument. Analyses were performed using nf-core/rnaseq version 3.12.0 as previously described. Genes with low expression (average counts among all groups < 1) were filtered out. Normalized counts were generated by DESeq2 and then used for statistical quantification and heat map generation.

first: Keyao

last: Chen

first: Edward

last: Prochownik


title: Pathogenetic mechanisms of muscle-specific ribosomes in dilated cardiomyopathy (AC16 RNA-seq)

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street, P&S 10-401

institute: Columbia University

summary: The heart employs a specialized ribosome in its muscle cells to translate genetic information into proteins, a fundamental adaptation with an elusive physiological role. Its significance is underscored by the discovery of neonatal patients suffering from often fatal heart failure caused by rare biallelic variants in RPL3L, a muscle-specific ribosomal protein that replaces the ubiquitous RPL3 in cardiac ribosomes. RPL3L-linked heart failure represents the only known human disease arising from mutations in tissue-specific ribosomes, yet the underlying pathogenetic mechanisms remain poorly understood despite an increasing number of reported cases. While the autosomal recessive inheritance pattern suggests a loss-of-function mechanism, Rpl3l-knockout mice display only mild phenotypes, attributed to up-regulation of the ubiquitous Rpl3. Interestingly, living human knockouts of RPL3L have been identified. Here, we report two new cases of RPL3L-linked severe neonatal heart failure and uncover an unusual pathogenetic mechanism through integrated analyses of population genetic data, patient cardiac tissue, and isogenic cells expressing RPL3L variants. Our findings demonstrate that patient hearts lack sufficient RPL3 compensation. Moreover, contrary to a simple loss-of-function mechanism often associated with autosomal recessive diseases, RPL3L-linked disease is driven by a combination of gain-of-toxicity and loss-of-function. Most patients harbor a recurrent toxic missense variant alongside a non-recurrent variant. The non-recurrent variant is often loss-of-function and enables partial compensation through RPL3, similar to Rpl3l-knockout mice. However, the recurrent missense variant exhibits increased affinity for the RPL3/RPL3L chaperone GRWD1 and 60S biogenesis factors, retains 28S rRNA in the nucleus, disrupts ribosome biogenesis, and induces severe cellular toxicity that extends beyond the loss of ribosomes. These findings elucidate the pathogenetic mechanisms underlying muscle-specific ribosome dysfunction in neonatal heart failure, providing critical insights for genetic screening and therapeutic development. Our findings also suggest that gain-of-toxicity mechanisms may be more widespread in autosomal recessive diseases, especially for those involving genes with paralogs.

overall_design: whole cell polyA RNA-seq and nuclear RNA-seq of human AC16 cells expressing RPL3L variants

first: Michael

last: Murphy


title: The extracellular matrix influences the miRNA landscape of human mesenchymal stromal/stem cells

city: Saint Petersburg

first: Roman

middle: E.

last: Ushakov

address: Tikhoretsky av., 4

institute: Institute of Cytology of the Russian Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Mesenchymal stromal/stem cells (MSCs) are promising therapeutic tools secreting a broad repertoire of pleiotropic molecules that promote tissue repair and regeneration. Recent advances in cell sheet technique demonstrate powerful improvement of MSCs regenerative capacity within the sheet retaining appropriate microenvironmental cues and suggest the instructing role of extracellular matrix (ECM). We found previously that the secretome of MSCs cultured on decellularized MSCs-derived ECM (dECM) is significantly enriched with dozen of cytokines, chemokines and growth factors in comparison to the secretome of MSCs cultured on routine plastic dishes. Enriched secretome was shown to have improved chemotactic and angiogenic properties, to stimulate C2C12 myoblast proliferation and promote skeletal muscle regeneration in murine in vivo model (Ushakov et al., 2024; Ushakov, Burova, 2024). Here we report novel findings about dECM-induced changes in miRNAs profile, another regulatory component of MSCs secretome. We performed miRNA-seq and found 17 differentially expressed miRNAs in endometrial MSCs (MESCs) with miR-146a-5p most upregulated. We also checked it’s expression in MSCs of various origin exposed to dECM and found miR-146a-5p upregulation to be correlated with general dECM-induced paracrine response. Besides, we found that miR-146a-5p mimic transfected to C2C12 myoblasts promote their proliferation suggesting miR-146a-5p contribution to myotropic effects of enriched secretome. These results provide new insights into how ECM as the component of MSCs niche influences secretory phenotype and modulate MSCs therapeutic properties.

overall_design: miRNA-seq profiling of mesenchymal stromal/stem cells derived from desquamated endometrium of menstrual blood of three healthy donors cultured for 72 hours on control plastic (polystyrene) dishes and cell-derived decellularized extracellular matrix (dECM)-coated dishes.

middle: E

first: Elena

middle: B

last: Burova


title: Molecular and spatial profiling of multiple sclerosis lesions identifies dysfunctional lipid efflux as a driver of chronic active inflammation

city: Bonn

first: Qian

address: Venusberg Campus 1/Gebäude 99

country: Germany

institute: DZNE

summary: Compartmentalized inflammation is considered a critical factor in driving the progression of multiple sclerosis (MS). Yet, the mechanisms sustaining its persistence remain poorly understood. A hallmark of this persistent and slowly evolving inflammatory process are chronic active MS lesions. In this study, we created a high-resolution, single-cell molecular and spatial atlas of chronic inflammation in MS. To accomplish this, we combined single-nucleus RNA sequencing (snRNA-seq) with single-cell spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH) to examine MS lesions, specifically focusing on those exhibiting chronic active immune pathology characterized by lymphocyte presence. Our integrative profiling uncovered the molecular landscape of glial and immune cells, their disease-associated states, and the surrounding microenvironments. Within the lesion rim, we identified CD8+ T cell niches with lipid-associated microglia. To demonstrate the utility of this spatially resolved atlas of chronic active MS lesions as a resource for future discovery, we investigated the role of lipid-associated microglia in experimental autoimmune encephalomyelitis (EAE). Our findings showed that inhibiting cholesterol efflux increased the formation of lipid-storing phagocytes, "foamy microglia," which actively drive inflammatory processes in EAE and represent tractable therapeutic targets for pharmacological modulators of sterol metabolism. These results provide a framework for system-level insights into cell-type diversity and represent a valuable resource for advancing the study of neuroinflammation in MS.

overall_design: 8-week-old male Cx3cr1CreERT2/+; Abca1flox/flox; Abcg1flox/flox experimental animals (KO) and Cx3cr1CreERT2/+ controls (Ctrl) were used for EAE experiments. Myelin oligodendrocyte glycoprotein (MOG)-EAE was induced in mice purchased from Charles River Laboratories by subcutaneous immunization with 200 mg of MOG peptide 35–55 (MOG35–55) in complete Freund’s adjuvant (Mycobacterium tuberculosis at 3.75 mg ml−1; BD) and intraperitoneal injection twice with 500 ng of pertussis toxin (Sigma). Animals were examined daily and scored for clinical signs of disease. If disease did not start within 15 d of induction or the clinical score rose above 4, animals were excluded from the analysis. Clinical scores were defined as: 0, normal; 0.5, loss of tail tip tone; 1, loss of tail tone; 1.5, ataxia and mild walking deficits (slip off the grid); 2, mild hind limb weakness, severe gait ataxia and twist of the tail causing rotation of the whole body; 2.5, moderate hind limb weakness and inability to grip the grid with the hind paw but ability to stay on an upright tilted grid; 3, mild paraparesis and falls from an upright tilted grid; 3.5, paraparesis of the hind limbs (legs strongly affected but move clearly); 4, paralysis of the hind limbs and weakness in the forelimbs; 4.5, forelimbs paralyzed; 5, moribund or dead. Tamoxifen administration commenced 4 weeks before immunization. Mice were deeply anesthetized and perfused with cold PBS. The spinal cord was removed from vertebrae and cervical and thoracal parts (C1-Th10) of the spinal cord were used for scRNA-seq experiments. Cells were isolated with a previously established isolation protocol using gentleMACS with the Papain Neural Tissue Dissociation Kit (Miltenyi Biotec) and actinomycin D (catalogue no. A1410, Sigma-Aldrich) at a final concentration of 45 mM. After dissociation, myelin debris was removed from the cell suspension using Myelin Removal Beads II (Miltenyi Biotec). Cells were resuspended in 0.04% BSA + PBS and counted using an automated cell counter (TC20, Bio-Rad).


title: Disordered DNA methylation leads to targetable transcriptional plasticity in ATRT [WGBS]

last: Koldobskiy

state: MD

address: 1800 Orleans St., Bloomberg 11379

department: Oncology

institute: Johns Hopkins University

type: Methylation profiling by high throughput sequencing

summary: Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive but genetically simple pediatric central nervous system tumor, defined by biallelic inactivation of the chromatin regulator SMARCB1 with remarkably few other cooperating mutations. Despite its genetic homogeneity, ATRT exhibits profound clinical and epigenetic heterogeneity, with three major subgroups (ATRT-TYR, ATRT-MYC, and ATRT-SHH) defined by DNA methylation and transcriptional signatures. Beyond these subgroup-defining features, we aimed to investigate epigenetic variability within tumors by applying whole-genome bisulfite sequencing and probabilistic modeling to quantify stochastic DNA methylation in primary ATRT samples encompassing all three subgroups. We show that ATRT exhibits a destabilized and increasingly stochastic methylome. While ATRT global methylation patterns diverge according to subgroup, some methylation perturbations, such as hypermethylation and increased methylation entropy over bivalent promoters, are consistent across subgroups. We find that methylation stochasticity alterations map onto potential drivers of ATRT, such as LIN28a, the HOXD cluster for ATRT-MYC, and OTX2 for ATRT-TYR, and identify actionable targets, such as hypermethylation of the tumor suppressor CDKN2a across all subgroups. We investigate the sensitivity of the aberrant DNA methylation landscape of ATRT to pharmacologic DNA methyltransferase inhibition and histone deacetylase inhibition (HDACi). We show that decitabine leads to profound demethylation of patient-derived ATRT cell lines, including reversal of hypermethylation at bivalent promoters and the CDKN2a locus. The addition of HDACi leads to dramatic gene expression changes, including upregulation of innate immune signaling pathways, such as STING/interferon signaling, genes under the regulation of bivalent promoters, and reactivation of the tumor suppressor CDKN2A. The combination of DNMTi and HDACi synergistically reduces cell viability. Taken together, we show that ATRT has a highly stochastic methylome sensitive to epigenetic manipulation.

overall_design:
WGBS on 22 primary patient samples of ATRT and 4 normal fetal brain controls. Additional files include WGBS output from 4 ATRT cell lines, CHLA02, CHLA05, CHLA06, and CHLA266, treated with 5 days of 100 nM decitabine +/- RG2833.

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

first: Michael A.

first: Ashley R.

last: Tetens


title: Investigating milk-derived extracellular vesicles as mediators of maternal stress and environmental intervention [miRNA-seqMilk]

first: Jordan

last: Marrocco

address: 3 Times Sq, Office 752

department: Biology

institute: Touro University

summary: It was our goal to identify changes in milk-derived extracellular vesicle miRNA cargos after maternal immune activation in lactating Sprague-Dawley rat mothers.

overall_design: Sprague-Dawley rats mothers were housed in either standard laboratory cages or in environmental enrichment. Rat dams were injected with either lipolysaccharide (LPS) to induce an immune response or a saline vehicle on postnatal day (P)10. Maternal milk samples were collected 2 hours later on P10 and again 24-hours post-injection on P11. Milk-derived extracellular vesicles were isolated from the milk samples and miRNA cargo evaluated.

first: Julia

last: Martz

first: Baila

last: Hammer

first: Tristen

last: Langen

first: Benjamin

last: Berkowitz

first: Benzion

first: Jasmyn

middle: A

last: Storm

first: Jueqin

last: Lu

first: Deepali

last: Lehri

first: Sanoji

last: Wijenayake

first: Amanda

last: Kentner


title: Liver-specific LXR inverse agonist restores lipid homeostasis in animal models and humans

city: Lausanne

first: Xiaoxu

last: Li

address: Station 15 - CH

country: Switzerland

institute: EPFL

summary: Despite advances in lipid-lowering treatment, atherosclerotic cardiovascular disease (ASCVD) remains the leading cause of mortality, underscoring the need for treatments that address residual risk. Targeting both the synthesis and clearance of triglyceride (TG)-rich lipoproteins is a promising approach. Liver X receptor (LXR) inhibition suppresses de novo lipogenesis and enhances clearance of TG-rich lipoproteins, but its clinical utility remains unexplored. Here, we demonstrate the pivotal role of LXR in lipid metabolism and metabolic diseases. In dysmetabolic animal models, LXR inverse agonists reduced plasma TG and cholesterol and improved insulin sensitivity by suppressing LXR activity and intestinal lipid absorption. Given concerns that systemic LXR inhibition may impair reverse cholesterol transport, we developed TLC-2716—an orally-administered, gut- and liver-restricted LXR inverse agonist. In human liver organoids modeling steatohepatitis, TLC-2716 reduced lipid accumulation and downregulated inflammation and fibrotic gene expression. In a Phase 1 clinical trial (NCT05483998), 14-day treatment with TLC-2716 was safe and resulted in placebo-adjusted reductions up to 38.5% in plasma TG and 60.8% in postprandial remnant cholesterol. These results highlight the safety and therapeutic potential of TLC-2716 as a novel treatment for managing dyslipidemia and reducing residual ASCVD risk.

overall_design: The effect of TLC-2716 on lipid accumulation was also evaluated in an induced pluripotent stem cell (iPSC)-derived human liver organoid (HLO) model established from human donors with different genetic backgrounds, including those with a known risk variant for MASH (the glucokinase regulatory protein [GCKR] rs1260326:C>T variant). Mutations in GCKR (GCKRTT) have been associated with increased hepatic DNL and plasma lipids, as well as metabolic diseases including diabetes and MASH. Briefly, the wildtype and GCKR mutation carried HLOs were exposed to high concentrations of oleate for three days to induce a steatotic MASH phenotype (sHLOs) and then treated with TLC-2716 or vehicle.

first: Masaki

last: Kimura

first: Archana

last: Vijayakumar

first: Robert

last: Myers

first: Takanori

last: Takebe

first: G. Mani

last: Subramanian

first: Johan

last: Auwerx


title: Disordered DNA methylation leads to targetable transcriptional plasticity in ATRT [RNA-seq]

city: Baltimore

first: Michael

last: Koldobskiy

overall_design: RNA-Seq was performed on 4 ATRT cell lines, CHLA02, CHLA05, CHLA06, and CHLA266, after 5 day treatment with low dose decitabine (100 nM) plus one day of 2.5 uM RG2833 on the 5th day. Cells were harvested 72 hours after the final treatment dose.

first: Michael A.

first: Ashley R.

last: Tetens


title: RNA sequencing of HSCs from ctrl mice or long-term ferulic acid treated mice

city: Chongqing

first: Shuzhen

last: Zhang

address: Gaotanyan zhengjie

institute: Army Medical University

summary: Analysis of differentially expressed genes in HSCs from ctrl mice or long-term ferulic acid treated mice

overall_design: Normal wild type mice without irradiation were treated with solvent ctrl or ferulic acid. Then, hematopoietic stem cells (HSCs, Lineage-, Sca-1+, c-Kit+, Flk2-, CD34-) from bone marrow of these mice were isolated, followed by RNA sequencing analysis.

first: Yimin

first: Jiacheng

last: Le

first: Changhong

last: Du


title: Disordered DNA methylation leads to targetable transcriptional plasticity in ATRT [WGBS cell line]

overall_design: WGBS on 22 primary patient samples of ATRT and 4 normal fetal brain controls. Additional files include WGBS output from 4 ATRT cell lines, CHLA02, CHLA05, CHLA06, and CHLA266, treated with 5 days of 100 nM decitabine +/- RG2833.


title: Investigating milk-derived extracellular vesicles as mediators of maternal stress and environmental intervention [miRNA-seqHippo]

first: Jordan

last: Marrocco

summary: It was our goal to identify changes in miRNA expression in the neonatal offspring hippocampus (on postnatal [P]10), after maternal immune activation in lactating Sprague-Dawley rat mothers.

overall_design: Sprague-Dawley rats mothers were housed in either standard laboratory cages or in environmental enrichment. Rat dams were injected with either lipolysaccharide (LPS) to induce an immune response or a saline vehicle on postnatal day (P)10. Offspring hippocampus was collected on postnatal day (P)12 and miRNA cargo evaluated.

first: Julia

last: Martz

first: Baila

last: Hammer

first: Tristen

last: Langen

first: Benjamin

last: Berkowitz

first: Benzion

first: Jasmyn

last: Storm

first: Jueqin

first: Deepali


title: A serum exosomal microRNA-based artificial intelligence diagnostic model for highly accurate detection of hepatocellular carcinoma [RNA-seq]

city: Daejeon

first: Tae-Su

last: Han

address: 125 Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: RNA sequencing was performed on mouse liver tissue samples from four groups: ND+oil (normal), WD+oil (NASH), ND+CCl₄ (cirrhosis), and WD+CCl₄ (HCC).

overall_design: RNA sequencing was conducted on liver tisues from C57BL/6N mice subjected to ND+oil, WD+oil, ND+CCl and WD+CCl treatments.

first: Dae-Soo

last: Kim

first: Sugi

last: Lee


title: CircSPINT2 Confers Sensitivity to Osimertinib via hsa-miR-1296-3p/RBP1 Axis and Inhibits NSCLC Progression

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

institute: Taipei Veterans General Hospital

summary: Lung adenocarcinoma (LUAD) is the most common type of lung cancer. Resistance to osimertinib, a 3rd generation EGFR-TKI, develops within 12 months in patients with EGFR T790M mutation. This study used RNA-seq to identify circular RNAs (circRNAs) regulating osimertinib resistance in LUAD. We identified circSPINT2 as downregulated in osimertinib-resistant cell lines (OR3, OR4, OR6, HOsR) compared to parental H1975 cells. circSPINT2 enhances osimertinib sensitivity by inducing apoptosis via the hsa-miR-1296-3p/RBP1 axis. circSPINT2 is proposed as a non-invasive biomarker for monitoring osimertinib resistance in LUAD.

overall_design: RNA-seq was performed on three osimertinib-resistant clones (OR3, OR4, OR6) derived from the H1975 NSCLC cell line and the parental H1975 cell line to profile circRNA expression. An independent osimertinib-resistant cell line (HOsR) was used for validation. Differential expression was validated by RT-qPCR for selected circRNAs.

first: Mong-Lien

last: Wang

first: Nalini Devi

last: Verusingam

first: Ping-Hsing

first: Alan Han-Kiat

last: Ong


title: Atg5 knockout down-regulates the KEGG pathway ‘Oxidative Phosphorylation’ in erastin2-treated primary PTECs

city: Suita

first: Sho

last: Matsui

address: Box D11, 2-2 Yamada-oka

department: Nephrology

institute: Osaka University Graduate School of Medicine

summary: To explore the mechanisms by which Atg5 deficiency sensitizes PTECs to ferroptosis

overall_design: mRNA profiles of control and Atg5KO primary PTECs during erastin2 treatment for 24 hours

first: Takeshi

last: Yamamoto


title: Hcn1-dependent engram neurons in the PVN encode gastric inflammatory memory [saline]

city: Jinan

first: E

last: Liu

state: Shandong Province

address: No. 44, West Wenhua Road, Lixia District, Jinan City, Shandong Province, China

institute: Shandong University School of Basic Medicine

summary: The brain encodes peripheral inflammatory signals, yet the mechanisms underlying the storage and retrieval of stomach-specific immune information remain unclear. This study reveals a novel pathway through which Fos-positive neurons in the paraventricular nucleus of the hypothalamus (PVN) regulate gastritis via a PVN–dorsal motor nucleus of the vagus–stomach neural circuit and the hypothalamic-pituitary-adrenal (HPA) axis. Using activity-dependent genetic labeling, chemogenetics, and optogenetics, we demonstrate that FosPVN neurons are essential for gastritis progression and can be activated by stress to drive chronic inflammation. Single-nucleus RNA sequencing (snRNA-seq) revealed significant upregulation of hyperpolarization-activated cyclic nucleotide-gated channel 1 (Hcn1) in FosPVN neurons during gastritis. Inhibiting Hcn1 reduced neuronal excitability and ameliorated gastric pathology. Crucially, repeated activation of FosPVN neurons forms a specific "inflammatory memory" leading to the persistence of disease, while stress can exacerbate gastric inflammation through these FosPVN neurons. Our findings elucidate the central neural mechanisms encoding gastric inflammation and identify Hcn1 as a potential therapeutic target for neuromodulatory treatment of chronic inflammatory diseases.

overall_design: Single-nucleus RNA-sequencing of male mice with oral gavage of  saline (saline group)

first: Xijia

last: Xin

first: Weikai

first: Qingyu

last: Ren

first: Yaqi

last: Tang

first: Qingwei

last: Yue

first: Jinhao

last: Sun


title: Gaq-stimulated gene expression is insensitive to Bromo extra terminal domain inhibitors in HEK 293 cells

city: Montreal

first: Jason

last: Tanny

address: 3655 Prom Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: Bromodomain and extraterminal domain (BET) family proteins are ubiquitous transcriptional co-activators that function broadly in gene expression programs associated with cellular differentiation, proliferation, and stress responses. Pharmacological inhibition of BET proteins with small molecules that disrupt bromodomain engagement with acetyllysine residues (such as JQ1), or that drive their degradation through the ubiquitin-proteasome system (such as dBET6), ameliorates pathological gene expression in a range of systems and shows promise as a potential therapeutic strategy. BET involvement in gene expression responses is not universal, and understanding of the cell-type and signaling pathway requirements that dictate BET dependence remains incomplete. We previously demonstrated that, in neonatal rat cardiomyocytes, GPCR-induced hypertrophy response depended strongly on the BET protein Brd4 when signaling was coupled to Gs, but not Gq. Here we tested whether Brd4 was differentially responsive to G protein isoforms in another cell type by expressing Gs or Gq-coupled Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) in HEK 293 cells. Gq induced expression of a group of early response genes and inflammatory genes in a manner largely insensitive to pharmacological BET inhibition, consistent with our previous data in cardiomyocytes. Gs activated a small subset of the Gq-induced genes, but this effect was largely reversed by the BET degrader molecule dBET6. Our data further suggest that there may be general signaling requirements to activate Brd4 across cell types.

overall_design: We performed RNA-seq comparing gene expression patterns in HEK 293 cells expressing either Gs- or Gq-coupled DREADD, in the presence or absence of BET inhibitors.

first: Ashika

last: Jain

first: Viviane

last: Page

first: Dominic

last: Devost

first: Darlaine

last: Petrin

first: Terence

last: Hebert


title: A serum exosomal microRNA-based artificial intelligence diagnostic model for highly accurate detection of hepatocellular carcinoma

first: Tae-Su

last: Han

summary: Exosomal miRNA expression profiling of annotated miRNAs was performed on mouse serum samples from four groups: ND+oil (normal), WD+oil (NASH), ND+CCl₄ (cirrhosis), and WD+CCl₄ (HCC).

overall_design: Exosomal RNA was extracted from serum samples of mice fed a normal diet (ND+oil), western diet (WD+oil), ND+CCl₄, or WD+CCl₄, and profiled for annotated miRNA expression using the NanoString nCounter Mouse v1 miRNA Panel.


title: REIIBP associated with RNA in Hela cells

city: 杭州市

first: 倩倩

last: 杨

state: 浙江省

address: 墩余路

institute: Westlake university

summary: We here report REIIBP associated with RNAs by PAR-CLIP.

overall_design: To investigate which kind of RNAs are associated with REIIBP, we established REIIBP stable Hela cell line. We then performed PAR-CLIP and analysed REIIBP associated RNAs.

first: Xiaochun

last: Yu

first: Qianqian

last: Yang


title: Suppressing Ephrin Receptor Signaling in the Paraventricular Nucleus Attenuates Psoriasis by Modulating Synaptic Plasticity and Immunity Homeostasis

first: Yaxiao

state: Shandong

address: Wenhuaxi Road 107

institute: Qilu hospital of Shandong University

summary: Psoriasis pathophysiology involves dysregulated neuroimmune crosstalk, yet the central mechanisms remain incompletely understood. Here, we demonstrate that the hypothalamic paraventricular nucleus (PVN) orchestrates cutaneous inflammation via a transsynaptic brain-skin circuit. Using neural tracing and chemogenetic approaches, we revealed functional connectivity between the PVN and both sympathetic neurons and psoriatic skin. Reactivation of Imiquimod (IMQ)-induced PVN-TRAPed neurons (forms a specific "inflammatory memory") are essential for psoriasis progression and can be activated to drive chronic inflammation. Single-nucleus RNA sequencing (snRNA-seq) identified Ephrin receptor A7 (Epha7) as a critical mediator of synaptic plasticity in PVN inflammatory engram neurons. Inhibition of PVN Ephrin receptor and ligand binding normalized dendritic spine remodeling, suppressed sympathetic nerve hyperactivity, and restored the balance of Th17/Treg cells in psoriatic-like mice. Mechanistically, blockade of Ephrin receptor attenuated sympathetic norepinephrine overflow, thereby rescuing Treg depletion and mitigating Th17-driven inflammation. This study identifies a PVN-sympathetic-skin axis, wherein the inhibition of PVN Epha7 restores skin immune homeostasis. Furthermore, this study elucidated the central neural mechanisms encoding skin inflammation, and promotes the transition of psoriasis treatment from single-target approaches to a neuroimmune synergistic strategy encompassing "brain-skin" interactions.

overall_design: Single-cell RNA-sequencing  of male mice smeared IMQ on the back (IMQ group).

first: Mengdong

last: Shi

first: Yanan


title: Influence of Ilimaquinone on gene expression in C. elegans

city: Gwangju

first: Yunju

last: Jo

address: 123, Cheomdangwagi-ro

institute: Gwangju Institute of Science and Technology

summary: To investigate the mechanism underlying Ilimaquinone’s lifespan-prolonging effects.

overall_design: C. elegans treated with 100 μM of IQ for 11 days was used to identify differential gene expression.

first: Ki-Tae

last: Ha

first: Taekyung

last: Kim

first: Eun-Sun

first: Se-Yun

last: Cheon


title: Analysis of Muscle and Blood RNA Samples from Patients with Myotonic Dystrophy Type 1 Reveals the Presence of New Mis-Splicing Biomarkers of Disease Severity

city: San José

first: Fernando

last: Morales

address: San Pedro de Montes de Oca

country: Costa Rica

institute: Universidad de Costa Rica

summary: To investigate biomarkers of disease severity in patients with myotonic dystrophy type 1 (DM1), we conducted RNA sequencing in blood, skin, and skeletal muscle (tibialis anterior, TA) from the same DM1 patients. This analysis revealed 937, 384, and 1216 mis-splicing events in muscle, blood, and skin, respectively. We determined the percent splice-in (ψ) values for 52 exons in muscle and 10 exons in blood, which correlated with repeat expansion sizes using the ePAL method; no such correlations were observed in skin. Notably, ψ values for nine exons in blood correlated with total splicing dysregulation in muscle (FDR < 0.05), suggesting their potential as biomarkers for DM1 disease severity. This study marks the first identification of: 1) splicing dysregulation in blood and skin, confirming tissue-specific splicing dysregulation, and 2) blood-based DM1 mis-splicing biomarkers of disease severity. For the first time, we present blood mis-splicing biomarkers that serve as a proxy for muscle splicing dysregulation, meeting the criteria for an ideal severity biomarker by being minimally invasive and capable of monitoring disease progression.

overall_design: The samples used in this study were derived from 35 DM1 patients, with RNA purified from three different tissues: blood, skeletal muscle (tibialis anterior-TA), and skin. The patient cohort was categorized into four clinical subtypes: two late-onset, twenty-four classical, four pediatric, and two congenital cases, along with three apparently asymptomatic individuals.

first: Melissa

last: Palma-Jiménez

first: Hailey

last: Olafson

first: Lizbeth

last: Ramírez

first: Eyleen

last: Corrales

first: Eric

middle: T

last: Wang


title: Effect of knockdown of CCDC137 on gene expression in bladder carcinoma cell T24.

city: Shenzhen

first: Haiyu

last: Zhang

institute: Shenzhen Second People’s Hospital

summary: To explore the function of CCDC137 in the regulation of gene expression in bladder cancer, we established CCDC137-knockdown T24 cells.  We then conduct gene expression profiling analysis using data obtained from RNA-seq of CCDC137-knockdown cells and control cells.

overall_design: Gene expression profiling analysis of RNA-seq data from T24 CCDC137-knockdown cells and control cells.

first: Weisheng

last: Huang

first: Mutong

last: Chen

first: Shuanzhu

last: Mou

first: Yuhan

last: Liu

first: Wendong

last: Jiang

first: Yue

first: Qiaolin

last: Mei

first: Bing

last: Yan

first: Hongbing


title: Transcriptional differences between freshly isolated and long-lived naïve P14 CD8 T cells prior to infection

city: Cincinnati

first: Yamato

last: Sajiki

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: The heterogeneity of antigen-specific naïve CD8 T cells has not yet been fully elucidated. We found that long-lived naïve CD8 T cells, incubated in naïve B6 mice for more than 30 days, generate significantly higher numbers of effector and memory CD8 T cells after lymphocytic choriomeningitis virus (LCMV)-Armstrong infection compared to freshly isolated naive CD8 T cells. To examine differences between long-lived and freshly isolated naive CD8 T cells prior to infection, a bulk RNA-seq analysis was performed.

overall_design: RNA-seq profiles of P14 T cell receptor transgenic CD8 T cells incubated in naive B6 mice for 1.5 days (fresh) and 35 days (long-lived).

first: Koichi

last: Araki


title: Transcriptional differences between effector cells derived from freshly isolated and long-lived naïve P14 CD8 T cells on day 5 post-infection.

summary: The heterogeneity of antigen-specific naïve CD8 T cells has not yet been fully elucidated. We found that long-lived naïve CD8 T cells, incubated in naïve B6 mice for more than 30 days, generate significantly higher numbers of effector and memory CD8 T cells after lymphocytic choriomeningitis virus (LCMV)-Armstrong infection compared to freshly isolated naive CD8 T cells. To examine the mechanism of why long-lived naive CD8 T cells exhibit superior responses to infection, we compared transcriptional profiles between effector CD8 T cells derived from long-lived and freshly isolated naive CD8 T cells.

overall_design: RNA-seq profiles of effector P14 T cell receptor transgenic CD8 T cells derived from freshly isolated and long-lived P14 CD8 T cells on Day 5 post-LCMV-Armstrong infection.


title: Environmentally Relevant Lead Exposure Impacts Gene Expression in SH-SY5Y Cells Throughout Neuronal Differentiation

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

summary: We performed high throughput transcriptomic analysis of SH-SY5Y cells during neural differentiation following continuous exposure to lead (Pb).

overall_design: We treated neuroblastoma cells, SH-SY5Y, with lead(Pb), at four doses (0µM, 0.16µM, 1.26µM, 10µM) beginning on Day 5 of neural differentiation, and continued exposure for the duration of the 18 day protocol. We conducted RNA-sequencing every three days beginning on Day 6, adapting the PlexWell plate-based RNA-sequencing method to analyze changes in gene expression resulting from Pb exposure.

first: Rachel

last: Morgan

first: Anagha

last: Tapaswi


title: Transcriptional analysis of Wt and CXCR5-KO cDC subsets

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: We used RNA-seq analyses and in vivo Heligmosomoides polygyrus (Hp) infection mouse models to identify roles for the CXCR5-expressing DCs in Th2 development.

overall_design: Triplicate samples of WT and CXCR5-deficient cDC1 and cDC2 dendritic cell populations were isolated for RNA-seq.

first: Christopher

middle: D

first: Frances

last: Lund

first: Miranda

middle: L

last: Curtiss


title: Role of MAIT cells in Glioblastoma

city: Bethesda

first: Seketoulie

last: Keretsu

address: Building 37,

department: Neuro-Oncology Branch

institute: National Institute of Health

summary: Glioblastoma (GBM) is the most aggressive primary brain cancer in adults and remains incurable. We used multi-omics and flow cytometry methods to investigate the role of mucosal-associated invariant T (MAIT) cells in GBM. In bulk RNA sequencing data analysis of GBM tissues, MAIT cell gene signature significantly correlated with poor patient survival. A scRNA-seq of CD45+ cells from 23 GBM tissue samples showed a diverse immune population in the GBM tumor microenvironment. Of the 23 GBM tissue samples analyzed, 15 (65.2%) were positive for MAIT cells. MAIT cells clustered with cell populations expressing a high level of transcription factor gene RORC, suggesting the enrichment of MAIT17 subset. The MAIT cell signature significantly correlated with the activity of tumor-associated neutrophils (TANs) and myeloid-derived suppressor cells (MDSCs). Multiple immune suppressive genes known to be used by TANs/MDSCs were upregulated in MAIT-positive tumors. Spatial imaging analysis of GBM tissues showed that all specimens were positive for both MAIT cells and TANs and localized enrichment of TANs. These findings highlight the MAIT-TAN/MDSC axis as a novel therapeutic target to modulate GBM’s immunosuppressive tumor microenvironment.

overall_design: The GBM patient cohort comprised nine patients newly diagnosed with GBM, seven patients with recurrent GBM who have not been treated with any immunotherapy, and seven recurrent GBM patients who were treated with neoadjuvant anti-PD1 therapy. CD45+ cells isolated from the GBM patients' tumor were used to perform scRNA-seq and scTCR-seq exeriments.

first: Masaki

last: Terabe

first: Alexander

last: Lee

first: Robert

last: Prins