title: Identification of novel mRNA splicing isoforms in human myogenesis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Myogenesis, the process of muscle formation and regeneration, requires significant changes in gene expression program. However, alternative splicing during human myogenesis has not been systematically studied. Here, we examined mRNA splicing changes during myogenesis in two human myoblast cell lines using hybrid transcriptomic approaches by combining short-read (Illumina) and long-read (Nanopore) RNA-seq analyses. We identified 13,853 new significant splicing isoforms  (60,582 in total), with RNAs increasing and decreasing in abundance between days 0 and 3 (3,771 and 3,649, respectively), and between days 3 and 5 (1,302 and 1,109, respectively). We identified 1,937 significant differential transcript usage events (DTU), which pathways were involved in muscle regulation. Findings were validated using RT-qPCR and across mouse and human models, including clinical samples from peripheral artery disease patients. Artificial Intelligence algorithms predicted 595 myogenesis-associated high-confidence novel protein-coding splicing isoforms. Our findings underscore the importance of mRNA splicing isoforms in muscle biology.

overall_design: 36 samples from 2 cell lines sequenced from 0-day to 5-day

first: Donega

last: Stefano

first: Banskota

last: Nirad

first: Yang

last: Jen-Hao

first: Rossi

last: Martina

first: Piao

last: Yulan

first: Tsitsipatis

last: Dimitris

first: Peterson

last: Charlotte A.

first: McDermott

last: Mary M.

first: Gorospe

last: Myriam

first: De

last: Supriyo

first: Ferrucci

last: Luigi


title: Expression data from mandible under 1G and 1/6G

status: Public on Nov 18 2025

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

summary: Bone formation, but not resorption, was promoted under lunar gravity, which was suggested to be related to mastication. Appropriate oral and dental management is necessary in lunar life.

overall_design: To determine the effects of different gravitational forces on mice during spaceflight, the mice were maintained on the International Space Station (ISS) for approximately one month. Gravity was set to 1/6G (0.167 g = lunar gravity = partial gravity) to mimic the gravity of the moon, as the most feasible future missions are to explore the moon. Habitat cage units (HCUs) were placed on the floor, each housing six mice, and a short radius centrifuge (MARS-S) was used to generate 1/6G. In contrast, the mice in the 1G group were housed on Earth and in the same MHU as those in the 1/6G group were.

first: Kotaro

last: Sato

last: Akatsuka


title: MFF marks a metabolic vulnerability of multiple myeloma

city: Catanzaro

first: Claudia

last: Veneziano

address: Viale Europa, Località Germaneto

department: Department of Experimental and Clinical Medicine

country: Italy

institute: "Magna Graecia" University of Catanzaro

type: Expression profiling by high throughput sequencing

summary: Increased mitochondrial fragmentation drives significant metabolic reprogramming that contributes to tumor progression. We explored the functional role of MFF (Mitochondrial Fission Factor), a key regulator of mitochondrial fragmentation, in the pathobiology of multiple myeloma (MM).  MFF was found overexpressed in MM primary samples and cell lines, driving altered mitochondrial dynamics and metabolic reprogramming. MFF silencing inhibited MM cell proliferation, survival, and colony formation in vitro and in vivo. MFF overexpression promoted oxidative phosphorylation (OXPHOS) and a shift towards mitochondrial metabolism, while MFF knockdown favored glycolysis. These metabolic alterations were associated with alterations in lactate intracellular levels. Interestingly, lactate transporter inhibitors, in combination with MFF-targeting strategies, synergistically reduced MM cell viability and overcame proteasome inhibitor (PI) resistance. These findings highlight MFF as a key regulator of mitochondrial dynamics and metabolic adaptation in MM.

overall_design: RNA samples extracted from H929 OE MFF and AMO-BZB shMFF myeloma cell lines were profiled for RNA seq analysis.

first: Amodio

last: Nicola

first: Gallo Cantafio

last: Maria Eugenia


title: Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [RNA-Seq]

city: Beijing

first: Feng

last: Kong

address: Qinghuayuan Street

country: China

institute: Tsinghua University

summary: Epigenetic memory undergoes drastic reprogramming in intergenerational gamete-to-embryo transition. H3K27me3, a histone mark catalyzed by PRC2 (Polycomb Repressive Complex 2), is an evolutionally conserved histone mark that plays essential roles in stably repressing developmental genes to maintain cell-type-specific programs.  In mice, H3K27me3-mediated epigenetic memory, however, undergoes both resetting at classic Polycomb targets and inheritance of broad H3K27me3 domains that mediate noncanonical imprinting (noncanonical H3K27me3 domains) during early embryogenesis. How such erasure and inheritance are achieved simultaneously remains elusive. Here, through temporal profiling of chromatin occupancy, we show that PRC2 associates with H3K27me3 at both Polycomb targets and noncanonical domains in growing oocytes. PRC2 then pre-disassembles and dissociates from chromatin in mature oocytes, before H3K27me3 erasure at Polycomb targets after fertilization. PRC2 reappears at Polycomb targets in blastocysts when H3K27me3 initiates restoration. By contrast, noncanonical H3K27me3 domains persist to blastocysts, where PRC2 rapidly rebinds by the end of 1-cell embryos until blastocysts. Mechanistically, we found that such noncanonical PRC2 action is regulated by EZHIP, a PRC2 inhibitory factor. By doing so, EZHIP plays a key role in both H3K27me3 erasure and intergenerational inheritance, as well as H3K27me3 re-establishment. Ezhip is highly translated around fertilization, which strongly restricts PRC2 activity, leading to gradual decrease of H3K27me3. Upon knockout of maternal Ezhip, PRC2 becomes hyperactive, binds promiscuously in the genome and deposits widespread H3K27me3. Consequently, H3K27me3 allelic bias and noncanonical imprinting, including imprinted X chromosome inactivation, are impaired. Unexpectedly, the widespread ectopic H3K27me3 paradoxically causes de-repression of H3K27me3 targets, possibly due to dilution of H3K27me3 effectors. Loss of Ezhip further attenuates H3K27me3 restoration at Polycomb targets during peri-implantation, and leads to gene dysregulation and sub-lethality after implantation. Taken together, we uncover PRC2 noncanonical chromatin association during the parental-to-embryonic transition and identify Ezhip as a crucial regulator for both erasure and inheritance of intergenerational epigenetic memories.

overall_design: To investigate the function of EZHIP in H3K27me3 intergenerational transition, we deleted Ezhip in mouse oocytes or embryos, and compared gene expression between wild-type and Ezhip KO oocytes or mKO embryos. At least two replicates were involved for each sample.

first: Yitian

last: Zeng

first: Wei

last: Xie


title: Modeling human bone marrow endosteal niches using induced pluripotent stem cells in xeno-free conditions

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Endosteal bone marrow (BM) niches are crucial to sustain non-steady-state hematopoiesis but are challenging to be modelled in their cellular and molecular complexity in standardized, human settings. We report a developmentally-guided approach to generate a macro-scale organotypic model of BM endosteal niches (engineered vascularized osteoblastic niche, eVON) based on human induced pluripotent stem cells (hiPSC) and porous hydroxyapatite scaffolds. Vascular and osteoblastic cells derived from the same hiPSC self-assembled into complex and long-lasting vascular networks integrated within osteogenic matrix. The system supported hematopoiesis in vitro and was stable upon implantation in vivo. Transcriptomic analysis revealed osteogenic, vascular and neural cells expressing key niche signals (e.g., CXCL12, KITLG and VEGFA) in human-specific patterns. The eVON could be perturbed at cellular (removing vascular cells) and molecular (deregulating VEGF signaling) levels to study contribution of the endosteal vasculature to myelopoiesis. The eVON offers unprecedented possibilities to dissect human pathophysiological hematopoiesis in endosteal BM.

overall_design: Three different hiPSC lines (409B2, Wibj and WTC) are differentiated into osteogenic and vascular cells in porous hydroxyapatite scaffolds to generate a standardized and physiological model of the human bone marrow endosteal niche, termed as engineered vascularized osteoblastic niche (eVON). eVONs generated from 409B2, Wibj and WTC cells were compared at transcriptomic level through scRNA-seq.

first: Qing

last: Li

first: Marina

middle: T

last: Nikolova

first: Gangyu

last: Zhang

first: Igor

last: Cervenka

first: Dominik

last: Bürri

first: Evelia

last: Plantier

first: Andrea

last: Mazzoleni

first: Anaïs

last: Lamouline

first: Barbara

last: Treutlein

first: Ivan

last: Martin

first: Andrés

last: García-García


title: FSTL3 overexpressed is key factor modulating the ovarian tumor microenvironment of syngenic mouse model

city: Boston

first: Maeva

middle: general

last: Chauvin

state: MA

address: 55 fruit st

country: USA

institute: general hosp corp d/b/a mass general hosp

summary: This study aims to investigate the role of FSTL3 in ovarian cancer progression and treatment resistance in HGSOC, and validate FSTL3 as a potential therapeutic target. We found that FSTL3 expression was associated with a fibrotic microenvironment, correlating with an increased abundance of cancer-associated fibroblasts (CAFs), cancer cells with a more mesenchymal phenotype. Tumors overexpressing FSTL3 revealed immune evasion, notably by reducing immunocytes infiltration.

overall_design: To investigate the role of FST and FSTL3 in modulating the tumor microenvironment, we engineered cancer cell models by knocking out FST (FSTKO) and overexpressing human FSTL3  in our KPCA syngeneic ovarian cancer cells. These modified cells were then intraperitoneally grafted into C57BL/6 mice. Tumors were harvested and  dissociated for single cell RNA library constuction and sequencing (N=4 pooled tumors per genotype, 5 000 cells)

first: David

last: Pepin


title: Analysis of GlycoRNAs in Glioma Cell Lines LN229 and U87

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

type: Non-coding RNA profiling by high throughput sequencing

summary: A number of studies have identified a novel class of biomolecules, namely glycosylated RNAs (glycoRNAs), which may play important roles in cellular physiology, pathology and immunity. However, whether glycoRNAs are present in glioma cells and what their functions are remain unanswered. In this study, through N-Azidoacetylmannosamine-tetraacylated (Ac4ManNAz) labeling method, glycoRNAs were enriched and purified from glioma cell lines LN229 and U87. Northern blot was performed to test the presence of glycoRNAs. It is noteworthy that we developed a sequencespecific RNA capture magnetic bead system to enrich for a specific glycoRNA such as U2, U4, and Y5. The components of glycoRNAs were analyzed and identified through RNA sequencing and chromatography-mass spectrometry.

overall_design: We sought to analyze the composition of glycoRNAs enriched in glioma cells. Through a series of processes including Ac4ManNAz labelling, small RNA extraction, DBCObiotin treatment, purification by streptavidin magnetic beads and Zymo column, glycoRNAs from U87, LN229 and Hela cells were purified and used for small RNA deep sequencing analysis. RNA samples from U87, LN229 and Hela cells treated with Ac4ManNAz were designated U87-24h, LN229-24h and Hela-24h, respectively. RNA samples from U87, LN229 and Hela cells without Ac4ManNAz treatment served as inputs and were designated U87-0h, LN229-0h and Hela-0h, respectively. The analysis of small RNA expression revealed significant differences in the expression profiles among the three cell types.


title: Nanostring analysis of tumor and lymph nodes from mice with either neoantigen (B16KVP) or wild-type (B16F10) tumors that were given naïve pmel-1 adoptive T cell therapy or No Treatment

city: Atlanta

first: Megen

middle: Claire

last: Wittling

state: GA

address: Winship Cancer Institute  Emory University 1365C Clifton Rd. NE Suite C5068, Bays 1-5

department: Surgery

institute: Emory University

summary: Two separate experiments were performed. Experiment 1: Mice were subcutaneously injected with either B16F10 or B16KVP tumors. 6 days later, they were given 5Gy total body irradiation as a lymphdepletion regimen. Then the next day, 500,000 naïve pmel-1 CD8 T cells were injected via the tail vein into these mice. 5 days after adoptive cellular therapy, these mice were sacrified and the tumors and tumor draining lymph nodes harvested for Nanostring analysis. Experiment 2: Mice were subcutaneously injected with either B16F10 or B16KVP tumors. 6 days later, they were given 5Gy total body irradiation as a lymphdepletion regimen. Then the next day, mice were given no treatment or 500,000 naïve pmel-1 CD8 T cells were injected via the tail vein into these mice. 5 days after adoptive cellular therapy, these mice were sacrified and the tumors harvested for Nanostring analysis.

overall_design: Experiment 1:3 mice with B16F10 tumors given naïve pmel-1 ACT and 3 mice with B16KVP tumors given naïve pmel-1 ACT were sacrificied 5 days post-transfer and the draining lymph nodes and tumors processed for Nanostring analysis. Experiment 2: 5 mice with B16F10 tumors given no ACT, 5 mice with B16F10 tumors given naïve pmel-1 ACT, 5 mice with B16KVP tumors and given no ACT, and 5 mice with B16KVP tumors given naïve pmel-1 ACT were sacrificied 5 days post-transfer and the tumors processed for Nanostring analysis.

first: Amalia

last: Rivera Reyes

first: Hannah

middle: M

last: Knochelmann


title: Diversity and Heterogeneity of Extracellular Vesicles and Brain-Penetrating Amembranous Non-Vesicular Nanoparticles in Glioblastoma

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Advances in understanding intercellular communication through extracellular vesicles (EVs) and non-vesicular extracellular nanoparticles (NVEPs) have been limited by their cellular heterogeneity and unclear origins. Using sequential ultracentrifugation, we identified high- and low-density EVs and performed multi-omics analyses on four EV/NVEP categories, including supermeres. Our findings reveal that extracellular RNA, RNA-binding proteins, and other cellular proteins are differentially expressed among EVs and NVEPs. Notably, supermeres can penetrate the blood-brain barrier, in a manner dependent on their intact RNA and protein structure, and distribute throughout the CNS. Supermeres preferentially interact with microglia at higher levels than other CNS cell types. These interactions lead to decreased TGFβ expression, suggesting an immunomodulatory role. This study highlights supermeres as a promising platform for CNS therapeutic delivery.

overall_design: Total RNA were collected from 1) cultured cells, and 2) large extracellular vesicles (LEV), 3) small extracellular vesicles (SEV), 4) large nanoparticles (exomeres), and 5) small nanoparticles (supermeres) secreted by the cells. The collection were done in 4 series (A, C, D, E). RNA-seq were performed in two batches (A series and others). In total there are 20 samples.

first: Al

last: Charest


title: Bulk mitotic ATACseq for Polo-like kinase 1 maintains transcription and chromosomal accessibility during mitosis

city: Madison

first: Zhouyuan

last: Shen

state: Wisconsin

address: 1111 Highland Ave

department: Medicine

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We found that Polo-like kinase 1 (Plk1) activity directly on chromatin sustains global transcription and chromosomal accessibility in mitosis. Inhibition of Plk1 leads to significant overall downregulation of accessibility on mitotic chromosomes, especially at promoter and transcription start site (TSS) regions. Therefore, Plk1 activity sustains global chromosomal accessibility in mitosis, facilitating transcription factor binding and ensuring proper transcriptional activity, which maintains mitotic fidelity.

overall_design: To study chromosomal accessibility in mitosis and the effect of Plk1 activity, RPE1 Plk1-/- EGFP-Plk1as (Burkard et al., 2007) were arrested in prometaphase before 2 hour DMSO or Plk1 inhibitor 10 µM 3MB-PP1 treatment. Before collection, mitotic index of each sample was measured (>95%). Bulk cell ATAC seq were performed in 4 biological repliactes.

first: Kristin

last: Adams

first: Ryan

last: Moreno

first: Jessica

last: Lang

first: Mark

last: Burkard


title: Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [RNA-seq]

city: Los Alamos

first: Eric

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

summary: Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells). Treatment induced substantial (13%) genomic rearrangement that rebounds despite persistent gene expression changes and spreading of acetylation. The chromatin functional landscape (accessibility, active transcription modification, and gene expression) is controlled and locus-specific, while chromatin contacts are globally altered resulting in a moderate weakening of topologically associating domains. Chromatin states are more dynamic at transcriptionally active loci while genes with reduced expression are epigenetically stable suggesting chromatin architectural turnover and nucleosome remodeling is locus-specific and underlies the bidirectional expression changes. Thus, local 3D chromatin and genome structural dynamics is integral for loci regulation in response to epigenomic perturbation. The partial persistence of these altered features may have larger implications for efficacy of epigenetic drugs in amelioration of disease states.

overall_design: We performed multi-omic assessments of human lung carcinoma (A549) cells with and without HDACi drug treatment to identify genome-wide transcriptional, epigenomic, and chromatin structural responses. A concentration of 10 µM SAHA was chosen for subsequent experiments as this treatment considerably altered acetylation on lysine 27 of histone 3 (H3K27ac) while still retaining viable cells at 48 hours post treatment for chromatin structure-function characterization. Time course experiments were conducted in triplicate; control (mock-treated) and treated (10 µM SAHA) A549 cells were collected at 24 and 48 hpt. Genome-wide assays for control and treated paired cells included ChIP-seq (H3ac, H3K27ac, H3K4me3) and RNA-seq, each with three biological replicates, and Hi-C with two biological replicates. ATAC-seq samples from three biological replicates per condition were generated from a separate repeated experiment.

first: Vrinda

last: Venu

first: Cullen

last: Roth

first: Samantha

middle: H

last: Adikari

first: Anna

last: Vlot

first: Kyle

middle: A

last: Sullivan

first: Chanaka

last: Abeyratne

first: Daniel

last: Jacobson

first: Shawn

middle: R

last: Starkenburg

first: Karissa

middle: Y

last: Sanbonmatsu

first: Christina

last: Steadman


title: Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [ChIP-seq]


title: BLU-222, a Potent CDK2 Inhibitor, Synergizes with CDK4/6 Inhibitors to Overcome Drug Resistance in HR–Positive and Triple-Negative Breast Cancer by Inducing p21 and p27

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

summary: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) combined with endocrine therapy are the standard first-line treatment for hormone receptor-positive, HER2−negative (HR+/HER2−) metastatic breast cancer, but resistance develops over time. In triple-negative breast cancer (TNBC), the efficacy of CDK4/6i is unclear. Our study shows that the selective CDK2 inhibitor BLU-222, while effective alone, enhances synergistic activity when combined with CDK4/6i in resistant HR+/HER2− and TNBC models, leading to increased apoptosis and cell cycle arrest. In vivo, combining BLU-222 with palbociclib or ribociclib showed significant antitumor effects across 8 models, resulting in durable tumor regression and extended survival. Mechanistically, BLU-222, alone or with palbociclib, upregulated p21 and p27 expression and enhanced p21 binding to CDK2 as well as p21 and p27 binding to CDK4 complexes. CRISPR knockout of p21 or p27 in palbociclib-resistant cells eliminated this synergy. Further, RNA sequencing showed that the combination treatment upregulated senescence and interferon pathways, offering insights into the observed therapeutic synergy.

overall_design: Once the transplanted tumors reached an average volume of 200 mm³, mice were randomized to the indicated treatment arms and treated with vehicle, palbociclib (50 mg/kg once daily, oral gavage), BLU-222 (60 mg/kg twice daily, oral; 50 mg/kg or 100mg/kg twice daily, oral ), or a combination of palbociclib (50 mg/kg) and BLU-222 (50 or 60 mg/kg) plus fulvestrant (2.5 mg/kg, once weekly, subcutaneous). At the end point, tumors were collected for RNA-seq analysis.

first: Linjie

last: Luo

first: Xiayu

last: Rao

first: Jing

last: Wang


title: Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [Hi-C]


title: Identification of lncRNA PRNCR1/miR-642a-5p/SSTR3 ceRNA network as novel biomarkers in detection of type 2 diabetes mellitus

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Microarray analysis and RNA sequencing were performed in strictly grouped sample of peripheral blood mononuclear cells (PBMCs) from T2DM cases and healthy controls. In total, 328 upregulated and 203 downregulated lncRNAs companied with 173 upregulated and 155 downregulated mRNAs, and 24 upregulated and 18 downregulated miRNAs were identified in T2DM under a fold change filter of > 1.5 and P value < 0.05. Functional enrichment (KEGG and GO) analysis showed that differentially expressed mRNAs were mainly related to biological processes, such as cell response to endogenous stimulus, intracellular signal transduction, cGMP-PKG signaling pathway, and pancreatic secretion. Signiﬁcant downregulation of lncRNA PRNCR1, IRAIN, together with miR-1268b and SSTR3, and upregulation of   lncRNA AC021491.4, miR-30c-2-3p, miR-642a-5p and TNFRSF10B were validated by quantitative real-time PCR (qRT-PCR) in T2DM compared with matched controls.
PRNCR1 was localized in the cytoplasm, and AGO2 RIP and dual luciferase reporter assays indicated that PRNCR1 directly sponges miR-642a-5p to downregulate the expression of SSTR3. The receiver operating characteristic (ROC) curves showed that PRNCR1 had a high diagnostic accuracy for differentiating T2DM from healthy controls.

overall_design: The experiment is divided into two groups: the healthy control group and T2DM cases. Then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

first: Shushu

last: Long


title: Mitochondrial translation drives activated CD8+ T cell dysfunction

city: Shanghai

first: Yunzhu

address: 280 South Chong Qing Rd

institute: Shanghai Jiao Tong University School of Medicine

summary: Enhancing CD8+ T cell function is crucial for improving cancer immunotherapy. Through CRISPR screening and validation, we identified that mitochondrial translation is upregulated in activated and exhausted CD8+ T cells, leading to the accumulation of misfolded proteins that induce mitochondrial stress and contribute to T cell dysfunction. Inhibition of this over-translation using low doses of chloramphenicol (CAP) significantly enhanced the antitumor activity of activated CD8+ T cells by promoting their expansion and reducing apoptosis and exhaustion. Low-dose CAP treatment preserved oxidative phosphorylation (OXPHOS) and cytokine production while restoring mitochondrial membrane potential. Furthermore, CAP facilitated the import of mitochondrial protein precursors, shifted HSP70 pools binding toward NFATc1, and limited its nuclear translocation, thereby reducing exhaustion markers of TIM-3 and PD1. Notably, a short course of low-dose Linezolid, a commonly used antibiotic and mitochondrial translation inhibitor, improved the CD8+ T cell ratio in the peripheral blood of patients with diffuse large B cell lymphoma. These findings highlight mitochondrial translation inhibition as a promising strategy to enhance CD8+ T cell function and potentially improve the effectiveness of cancer immunotherapy.

overall_design: For the pooled CRISPR screen, we used CRISPR-FOCUS (http://cistrome.org/crispr-focus/) to design two libraries: a mini-library targeting 171 mitochondrial tRNA-binding proteins, and a broader library targeting 1,331 translation-related proteins, with 10 sgRNAs per gene. Naïve OT1 CD8+ T cells expressing Cas9 were first activated with anti-CD3/CD28 antibodies, followed by retroviral transduction with the sgRNA library, achieving a transduction efficiency of approximately 30%. After a two-day culture to allow for sgRNA editing and mCherry expression, 3 × 10⁶ mCherry-positive cells were sorted as the Input sample using a FACSAria Fusion Cell Sorter (BD). Subsequently, 2 × 10⁷ cells were co-cultured with 1 × 10⁶ purified CD11c+ cells in the presence of 10 ng/ml IL-2 and 5 μg/ml OVA peptide for three days. After expansion, 3 × 10⁶ mCherry-positive cells were sorted as the expanded sample. Genomic DNA was then extracted using the Blood and Cell Culture DNA Maxi Kit (Qiagen), and two rounds of PCR amplification were performed to amplify the sgRNAs and add Illumina adaptors, using NEBNext High-Fidelity 2× PCR Master Mix (New England BioLabs).

first: Hua-bing

last: Li

first: Baiwen


title: Discovery of a small-size imidazole-benzoindolium ligand for binding to KRAS promoter G-quadruplex that inhibits cancer growth with enhanced immunomodulation

city: Shenzhen

first: Xiaodong

address: Xueyuan Avenue

institute: Shenzhen University

summary: KRAS overactivation is commonly present in a diversity of solid tumors. Recently, small-molecule inhibitors of KRAS G12C mutation are approved for clinical use, ending the long era of KRAS as an ‘undruggable’ target. However, new approaches to suppress a wide spectrum of KRAS abnormalities are still needed to be developed. G-quadruplex (G4) locates in the nuclease hypersensitive element (NHE) region of the promoter, and controls KRAS expression. Only a few KRAS G4 ligands have been discovered to date, which possess coplanar aromatic scaffolds, falling outside “drug-like” chemical space, and have no satisfactory selectivity between KRAS G4 and other DNAs. In this study, a series of drug-like, indolium-based analogs specifically targeting KRAS G4 were engineered, and BN1 was decided as the most potent ligand. BN1 effectively suppressed KRAS expression, thereby downregulating MEK-ERK pathway and PD-L1 expression in tumor cells. In vivo experiments displayed that BN1 was an effective agent to reduce tumor burden with immunostimulatory effects, including the increase of CD8+ IFNγ+ cells, the decrease of CD4+ Foxp3+ cells and the regulation of cytokines. Collectively, it is the first time, to our knowledge, to report a KRAS G4-directed small-molecule ligand with antitumor efficacy related to enhanced immunomodulation.

overall_design: To investigate the antitumor mechanisms of a small molecule G-quadruplex compound (BN1) against breast cancer cells, we treated MDA-MB-231 cells with BN1 for 24 h, and then performed gene expression profiling analysis obtained from RNA-seq of 3 duplicate cell samples.

first: Qianwen

last: Nie

first: Minghao

last: Hu


title: EZHIP-mediated PRC2 inhibition is required to maintain H3K27me3-dependent imprinting post fertilization [ChIP-Seq]

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

country: France

institute: Institut Curie

summary: Zygote inherits parental genomes with distinct chromatin structure. In eutherian mammals, this asymmetry is seen as crucial for embryonic development notably through its involvement in gene imprinting. Besides the well-established role of DNA methylation for gene imprinting, H3K27me3 has also been shown to mediate a transient form of imprinting in mice. Here, we show that maternal deletion of Ezhip, a negative regulator of PRC2, while increasing the asymmetric distribution of H3K27me3 among the parental genomes at the zygotic stage, in fine, impairs H3K27me3-dependent imprinting and mitigates X Chromosome Inactivation in pre-implantation embryos. We show that EZHIP protein, translated from the maternal pool of RNAs, is present during the first cell divisions post-fertilization. It limits PRC2 enzymatic, avoiding the flattening of H3K27me3 deposition throughout the genome and the equalization of H3K27me3 deposition on the two parental genomes. Our study reveals the necessary inhibition of PRC2 activity post-fertilization for proper development in mice.

overall_design: Cut&Run-Seq for H3K27me3 was conducted on wt and Ezhip matKO oocytes, 2C embryos, and blastocysts to assess the impact of maternal depletion of Ezhip on Polycomb function during the early stages of embryonic development.

first: Raphael

last: Margueron

first: Seynabou

last: Diop

first: Katia

last: Ancelin

first: Ambre

last: Petitalot

first: Patricia

last: Legoix


title: Circular RNA PTPN4 Contributes to Blood-Brain Barrier Disruption During Early Epileptogenesis

city: nanjing

first: jiurong

last: yang

institute: 东南大学

summary: Circular RNAs (circRNAs) are crucial regulators of gene expression, exhibiting dynamic expression patterns during both normal brain development and diverse pathological states. In this study, we report the elevated expression of CircPTPN4 in the brain tissue and plasma during early epileptogenesis in a murine temporal lobe epilepsy model. Overexpression of CircPTPN4 disrupts the tight junctions of brain microvascular endothelial cells (BMECs), compromising blood-brain barrier (BBB) integrity. Mechanistically, CircPTPN4 functions as a competitive endogenous RNA by sequestering miR-145a-5p, thereby upregulating endothelin-converting enzyme-1 (ECE-1). Subsequent ECE-1-mediated endothelin-1 (ET-1) production activates the p38/MAPK pathway, downregulating tight junction protein expression. Knockdown of CircPTPN4 attenuated tight junction disruption and BBB impairment during acute epileptogenesis while reducing spontaneous seizure frequency in chronic epilepsy. These findings establish the CircPTPN4/miR-145a-5p/ECE-1 axis as both a diagnostic biomarker and therapeutic target for BBB preservation in early-stage epilepsy.

overall_design: This study employed a mice model of temporal lobe epilepsy (TLE) and an in vitro epileptic discharged neuron model to investigate the integrity of the BBB and the tight junctions of brain microvascular endothelial cells (BMECs) under epileptic conditions.To identify dysregulated circRNAs in the brains of epileptic mice, we performed circRNA sequencing analysis on cortical tissue 24 hours after status epilepticus. Furthermore, circRNA-miRNA interactions and miRNA-target gene associations were examined through biotinylated RNA pull-down assays, fluorescence in situ hybridization (FISH), and luciferase assays. In vivo viral interventions were utilized to modulate gene expression, including the knockdown and overexpression of circPTPN4 and endothelin-converting enzyme-1 (ECE-1), while miR-145a-5p mimics and inhibitors were applied in vitro to evaluate their functional effects.

first: Jiurong

last: Yang


title: LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2 [RNA-Seq]

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

summary: Organisms regulate cell size and shape to function efficiently. Aberrant cell morphogenesis is commonly associated with disease, yet gene-regulatory mechanisms remain unknown. CISTR-ACT was the first lncRNA involved in inter-chromosomal contacts and Mendelian disease, and is associated with mean corpuscular volume (red blood cell size). Here, functional dissection of CISTR-ACT’s DNA- and RNA-encoded mechanisms by in vitro and in vivo perturbations reveal that CISTR-ACT regulates cell size across cell types and species. CISTR-ACT’s locus is embedded in a stable inter-chromosomal environment which contains cell size genes that are regulated by CISTR-ACT in trans. CISTR-ACT’s RNA also has function and directly interacts with transcription factor FOSL2 to guide its regulation of cell morphogenesis and cell-cell adhesion genes. In the absence of CISTR-ACT, the FOSL2-chromatin binding is perturbed. Our study exemplifies how a functionally conserved lncRNA regulates cell size with multiple modes of action and ultimately contributes to clinically relevant phenotypes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq from CRISPR techniques (Cas9, CasRx, CRISPR-Display) to modulate CISTR-ACT in C-28/I2, RPMI 2650, K562, and iPSC-derived neural progenitor cells. RNAseq from Cistr knockout mouse tissue (blood, bone marrow, cerebellum, cerebral cortex, hippocampus, hypothalamus).

first: Katerina

last: Kiriakopulos

first: Katty

last: Soleimanpour

first: Brandon

middle: J

last: McMurray

first: Benjamin-Israel

last: Moke

first: Jordan

last: Chalmers

first: Jeremy

middle: D

last: Newton

first: Milad

last: Mokhtaridoost

first: Kate

last: Delfosse

first: Mai

last: Ahmed

first: Taylor

last: De Young

first: Cassandra

last: Wong

first: Sigmar

last: Stricker

first: Yun

first: Brian

last: Nieman

first: Anne-Claude

last: Gingras

first: Monica

last: Justice

first: Julie

middle: L

last: Lefebvre

middle: G


title: First in class small molecule inhibitor of oncogene AVIL in glioblastoma

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 1574 Broad Crossing Rd, , Charlottesville

institute: university of virginia

summary: Compound A  or DMSO treatment with GBM U87 cell samples

overall_design:
Gene expression of U87 cells treated with DMSO or Compound A.

>>>Submitter states that IDAT files are not available for this study because it was performed a long time ago and the files were not kept <<<

first: Hui

last: Li


title: Rerouting phosphoenolpyruvate in sugar-rich tissues enables increased fatty acid biosynthesis

city: Urbana

first: Gabriel

last: Beuchat

email: beuchat2@illinois.edu, beuchag@uw.edu

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois at Urbana Champaign

summary: Metabolic engineering in the vegetative tissues of highly productive C4 crop, such as sugarcane, to produce oil is a promising strategy to convert solar energy into biofuel. However, biofuel production needs to be increased to meet the commercial requirements. To address this challenge, we deployed a novel approach to redirect phosphoenolpyruvate flux into plastids via overexpressing a plastidial phosphoenolpyruvate/phosphate translocator (PPT1). The concept was first tested in Arabidopsis. Excitingly, the results showed overexpressing AtPPT1 boosted fatty acid levels in leaves of sugar-rich sweet11;12;13 mutant rather than in the wild type. Increased fatty acid and oil accumulation were observed in older leaves of the triple mutant rather than in young leaves. Metabolomic analysis revealed that overexpressing AtPPT1 enabled the transition of the glycolytic intermediate metabolites from accumulating in sweet11;12;13 mutant back to a similar level as wild type. Under sugar-rich physiological conditions, overexpressing AtPPT1 triggers systematic transcriptomic changes involving class II trehalose-6P synthase (TPS) mediated signaling pathway, which regulates fatty acid synthesis. The strategy was further confirmed in sugarcane, where overexpressing sorghum SbPPT1 driven by a cane stem-specific promoter boosted fatty acid levels (>20% increase) in mature internodes of transgenic sugarcane plants without leading to obvious growth penalty. Positive correlations were observed between fatty acid level and SbPPT1 expression level. In summary, our work reported that directing phosphoenolpyruvate into plastids of sugar-rich tissues can stimulate fatty acid biosynthesis in vegetative tissues. Our strategy promises to achieve commercial-scale lipid production in engineered sugarcane.

overall_design: Wild Type and Sugar Rich Triple mutant arabidopsis were grown under normal conditions, one set as control and the other overexpressing AtPPT1

first: Jiang

last: Wang

first: Xueyi

last: Xue

first: Michael

last: Tang

first: Viet Dang

last: Cao

first: Timothy

last: Changa

first: Yaxin

first: Stephen

middle: P

last: Long

first: Fredy

last: Altpeter

first: Li-Qing

last: Chen


title: EZHIP-mediated PRC2 inhibition is required to maintain H3K27me3-dependent imprinting post fertilization

first: Laia

last: Richart

overall_design: Single cell/embryo RNA samples were prepared from wt and Ezhip matKO oocytes, 2C embryos, blastocysts, and E6.5 extraembryonic ectoderm to assess the impact of maternal depletion of Ezhip on the early stages of embryonic development.

first: Raphael

last: Margueron

first: Seynabou

last: Diop

first: Katia

last: Ancelin

first: Ambre

last: Petitalot

first: Patricia

last: Legoix


title: ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development [seRNA-Seq]

city: Bethesda

first: Guanghui

last: Yang

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Upon fertilization, the mouse zygotic genome is activated and maternal RNAs as well as proteins are degraded. Early developmental programs are built on proteins encoded by zygotic mouse genes that are needed to guide early cell fate commitment. The box C/D snoRNA ribonucleoprotein (snoRNP) complex is required for rRNA biogenesis, ribosome assembly and pre-mRNA splicing essential for protein translation. Zinc finger, HIT type 3 (encoded by Znhit3) is previously identified as a component in the assembly of the box C/D snoRNP complex. Using gene-edited mice, it identifies Znhit3 as an early embryonic gene whose ablation reduces protein translation and prevents mouse embryos development beyond the morula stage. The absence of ZNHIT3 leads to decreased snoRNA and rRNA abundance which causes defects of ribosomes and mRNA splicing. Microinjection of Znhit3 cRNA partially rescues the phenotype and confirms that ZNHIT3 is required for mRNA translation during preimplantation development.

overall_design: To explore RNA profile changes in early mouse embryos caused by Znhit3 ablation, single Znhit3-/- or control embryos were collected at different developmental stages for RNA-seq analysis.

first: Qiliang

last: Xin

first: Jurrien

last: Dean


title: RNA buffering upon transcriptional distorsion

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

summary: use existing TT-seq data on mESC upon auxin-based removal of transcriptional activators (Zzz3-AID and Yeats2-AID, Fisher...Tora 2021) and newly obtained total RNA-seq data from the same cell lines treated with auxin to infer changes in synthesis and degradation rates of mRNAs controlled by these proteins.

overall_design: Total RNA from wildtype (WT) and mutant mouse ES E14 cell lines treated with auxin for 24 h. RNA from two independent clones per murtant cell line were sequenced.

first: DAVID

last: MORENO

first: AUDREY

last: FURST


title: Speedy A governs non-homologous XY desynapsis as a unique prerequisite for XY loop-axis organization

first: Dongteng

last: Liu

state: Guangdong

address: No. 1, Haiyuan First Road, Futian District

institute: The University of Hong Kong-Shenzhen Hospital

summary: In mouse early pachytene spermatocytes, the X and Y chromosomes undergo rapid non-homologous (NH) synapsis and desynapsis, but the functional significance remains unknown. Here, we report that pachynema-specific knockout of Speedy A (SpdyA) from telomeres caused persistent Y-X NH synapsis, with the entire Y axis synapsed onto the X axis. This persistent Y-X NH synapsis did not interrupt meiotic sex chromosome inactivation, recombination, or sex body formation, but it disrupted X-Y loop-axis organization and homologous X-Y desynapsis, leading to spermatocyte death. Similarly, persistent Y-X NH synapsis was also observed in pachytene spermatocytes lacking TRF1, where SpdyA was frequently lost from X-Y non-pseudoautosomal region (non-PAR) telomeres. Mechanistic studies revealed that the Serine 48 of SUN1 is a key SpdyA/CDK2 phosphorylation site needed for Y-X NH desynapsis. We propose that SpdyA governs Y-X NH desynapsis by stabilizing the linkage between the X-Y non-PAR telomeres and their LINC complexes, and that this process is regulated independently from other aspects of pachynema progression. Our findings suggest a key role for Y-X NH desynapsis in establishing proper X-Y loop-axis organization.

overall_design: To investigate whether meiotic sex chromosome inactivation (MSCI) is disrupted by persistent full Y-X non-homologous (NH) synapsis following Spdya deletion, synchronized Spdyafl/fl (control) and SpdyacKO testes were collected on RA11.5 (i.e., 11.5 days post RA restoration, equivalent to mid-late pachytene stage) and subjected to RNA-Seq analysis. Four mice were used for each group.

first: Dongliang

last: Li

first: Kui


title: lncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2  [ChIP-seq]

first: Philipp

last: Maass

summary: Organisms regulate cell size and shape to function efficiently. Aberrant cell morphogenesis is commonly associated with disease, yet gene-regulatory mechanisms remain unknown. CISTR-ACT was the first lncRNA involved in inter-chromosomal contacts and Mendelian disease, and is associated with mean corpuscular volume (red blood cell size). Here, functional dissection of CISTR-ACT’s DNA- and RNA-encoded mechanisms by in vitro and in vivo perturbations reveal that CISTR-ACT regulates cell size across cell types and species. CISTR-ACT’s locus is embedded in a stable inter-chromosomal environment which contains cell size genes that are regulated by CISTR-ACT in trans. CISTR-ACT’s RNA also has function and directly interacts with transcription factor FOSL2 to guide its regulation of cell morphogenesis and cell-cell adhesion genes. In the absence of CISTR-ACT, the FOSL2-chromatin binding is perturbed. Our study exemplifies how a functionally conserved lncRNA regulates cell size with multiple modes of action and ultimately   contributes to clinically relevant phenotypes.

overall_design: FOSL2 ChIPseq in RPMI 2650 cells.

first: Katerina

last: Kiriakopulos

first: Katty

last: Soleimanpour

first: Brandon

last: McMurray

first: Benjamin-Israel

last: Moke

first: Jordan

last: Chalmers

first: Jeremy

last: Newton

first: Milad

last: Mokhtaridoost

first: Taylor

last: De Young

first: Kate

last: Delfosse

first: Mai

last: Ahmed

first: Cassandra

last: Wong

first: Sigmar

last: Stricker

first: Yun

first: Brian

last: Nieman

first: Anne-Claude

last: Gingras

first: Monica

last: Justice

first: Julie

last: Lefebvre


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [wt RNA-seq]

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

summary: We provide a novel functional genomics atlas of non-coding regulatory elements derived from human neural stem cells (NSCs), using the massively parallel reporter assay ChIP-STARR-seq. ChIP-STARR-seq was performed in NSCs using chromatin immunoprecipitation for H3K27ac, H3K4me1, YY1 and SOX2, and the generated STARR-seq plasmid reporter libraries were profiled for their enhancer activity in H9 derived NSCs and human embryonic stem cells. Subsequently a multi-omics data integration was performed, including the development of a convolutional neural network called BRAIN-MAGNET that allows to predict the effect of single nucleotide variants in non-coding regulatory elements on the enhancer activity. The various data sets generated in this study include ChIP-seq experiments in NSCs, DNA sequencing of the generated plasmid libraries, RNA-seq of transfected cells from the ChIP-STARR-seq experiments, generated ATAC-seq data sets used for data integration and the contribution scores from BRAIN-MAGNET for each nucleotide assessed in this ChIP-STARR-seq study.

overall_design: RNA-seq datasets for wildtype NSCs = 2 datasets total

first: Stefan

first: Ruizhi

last: Deng


title: Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency [GRO-seq]

city: Boston

first: Roberto

last: Chiarle

state: Ma

address: Longwood 333

institute: Boston Childrens Hospital

summary: The EZH2 histone methyltransferase inhibitors tazemetostat and valemetostat have recently received approval for clinical use in follicular lymphoma and adult T-cell leukemia/lymphoma, respectively. In follicular lymphoma, the expression of AID is responsible for increased mutational signatures and genomic instability. Because EZH2 inhibitors induce epigenetic and transcriptional changes in normal and lymphoma B cells, we studied whether these inhibitors could alter the pattern of AID-mediated chromosomal translocations. Here we show that treatment with EZH2 inhibitors did not significantly change AID expression or AID-dependent chromosomal translocation frequency when used as monotherapy in either CH12F3 mouse B cells or MEC-1 human B cells. In contrast, when combined with PI3Kδ inhibition, which enhances AID expression, EZH2 inhibition significantly increased the frequency of chromosomal translocations compared to either EZH2 or PI3Kδ inhibition alone both in mouse CH12F3 cells and human MEC-1 cells. EZH2 inhibition also further enhanced translocation formation in mouse B cells that were Ligase4 deficient. Mechanistically, EZH2 inhibition in B cells depletes the repressive histone modification H3K27me3 while concurrently enhancing the active histone modification H3K27ac, thereby selectively increasing transcriptional activity and facilitating chromosomal translocation formation in the presence of high AID activity or Ligase4 deficiency. These findings highlight the impact of drugs that induce epigenetic changes to influence chromosomal translocations and demonstrate the genetic safety of EZH2 inhibitors as monotherapy while highlighting the increased risk of genomic instability when used in cells prone to translocations, such as B cells with high AID levels or DNA-repair deficiency.

overall_design: We performed GRO-seq to assess transcriptional alterations following treatment with Tazemetostat or Valemetostat in CH12F3 cells.

first: Jianli

last: Tao

first: Alessandri

last: Luca


title: ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development [SMARMseq]

first: Guanghui

last: Yang

overall_design: To explore changes of rRNA 2'-O-methylation in mouse embryos caused by Znhit3 ablation, embryos were collected after intercross of Znhit3+/- breeders and examined with a modified Ribo-meth sequencing method.

first: Qiliang

last: Xin

first: Jurrien

last: Dean


title: Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency [Cut&Tag for H3K27ac]

overall_design: We performed Cut&Tag on H3K27ac to assess histone modification (H3K27ac) alterations following treatment with tazemetostat or valemetostat in CH12F3 cells.


title: ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development [scRNA-Seq]

overall_design: To explore RNA profile changes in mouse 8-cell blastomeres caused by Znhit3 ablation, single blastomeres were collected from 8-cell embryos after intercross of Znhit3+/- breeders for RNA-seq analysis.


title: Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency

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

overall_design: Refer to individual Series


title: Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency [RNA-Seq]

overall_design: We performed RNA-seq to assess transcriptional alterations following treatment with tazemetostat or valemetostat in CH12F3 cells.


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [ATAC-seq]

overall_design: ATAC-seq for human neural stem cells (NSC_ATAC_rep1 and NSC_ATAC_rep2) and human embryonic stem cells  (ESC_ATAC_rep1 and ESC_ATAC_rep2)= 4 datasets


title: Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency [Cut&Tag for H3K27me3]

overall_design: We performed Cut&Tag on H3K27me3 to assess histone modification (H3K27me3) alterations following treatment with tazemetostat or valemetostat in CH12F3 cells.


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [ChIP-seq]

overall_design: ChIP-seq for H3K27ac, H3K4me1, SOX2 and YY1 + Input control in human neural stem cells; ChIP-seq for YY1 + Input control, and SOX2 + Input control in human embryonic stem cells = 16 datasets total


title: Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency [LAM-HTGTS for CH12F3 cell]

overall_design: We performed LAM-HTGTS to assess chromosomal translocation alterations following treatment with tazemetostat or valemetostat in CH12F3 cells.


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [plasmid DNA-seq]

overall_design: DNA-seq of ChIP-STARR-seq plasmid library (HIST: H3K27ac and H3K4me1, TF: SOX2 and YY1) in human neural stem cells = 4 datasets


title: A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [STARR-RNA-seq]

overall_design: STARR-RNA-seq datasets after transfection into NSCs or ESC = 16 datasets total


title: Bacterial RNA promotes proteostasis through inter-tissue communication in C. elegans

city: Basel

first: Geoffrey

last: Fucile

address: Spitalstrasse 41

department: sciCORE

institute: University of Basel

summary: Life expectancy has been increasing over the last decades, which is not matched by an increase in healthspan. Besides genetic composition, environmental and nutritional factors influence both health- and lifespan. Diet is thought to be a major factor for healthy ageing. Here, we show that dietary RNA species extend healthspan inC. elegans. Inherent bacterial-derived double stranded RNA reduces protein aggregation in aC. elegansmuscle proteostasis model. This beneficial effect depends on low levels of systemic selective autophagy, the RNAi machinery in the germline, even when the RNA is delivered through ingestion in the intestine and the integrity of muscle cells. Our data suggest a requirement of inter-organ communication between the intestine, the germline and muscles. Our results demonstrate that bacterial-derived RNAs elicit a systemic response inC. elegans, which protects the animal from protein aggregation during ageing. We provide evidence that low stress levels are beneficial for healthspan.

overall_design: To investigate whether any or a specific bacterial-derived RNA would protectC. elegansfrom protein aggregate accumulation and promote proteostasis, we performed total RNA seq and smRNA seq on the three bacterial strains (OP50, OP50(xu363) and HT115)using both total RNA and a library enriched for small RNA molecules.

first: Emmanouil

last: Kyriakakis

first: Anne

last: Spang


title: The effect of a cottonseed oil-enriched diet on lipid profiles

city: Athens

first: Chad

middle: M.

last: Paton

address: 100 Cedar St #211

institute: University of Georgia

summary: This study was designed to validate cottonseed oil as a bioactive lipid in a mouse model

overall_design:
Comparative gene expression profiling analysis of RNA-seq data to determine which pathways and targets were differentially regulated in response to a cottonseed oil-enriched diet compared to other high-fat diets

Please note that according to the workflow report, PCA analysis showed SFO_4 was an extreme outlier from its sample group and FastQC results indicated possible contamination, so it was omitted from the expression analysis.

first: Yura

last: Son

first: Leah

middle: S

last: Halls


title: The effects of IDH1 R132H autopalmitoylation on gene expressions in U87 cells

city: Charlestown

first: Lu

last: Hu

state: Massachusetts

address: Building 149, 13th St

department: Dermatology

institute: Massachusetts General Hospital

summary: Gain-of-function mutations of isocitrate dehydrogenase 1 (IDH1) lead to neomorphic enzymatic activities and the production of oncometabolite R-2-hydroxyglutarate (2-HG), contributing to the tumorigenesis of several human cancers. It has been shown that fatty acid biosynthesis is required for the growth of IDH1 mutant tumors, but the underlining mechanisms are unclear.  We developed new activity-based chemical probes to study protein autopalmitoylation, and identified that the oncogenic IDH1 (R132H) mutant is uniquely autopalmitoylated at cysteine 269 (C269), which is not observed in the wild type IDH1. Molecular dynamic simulations suggest that palmitoylation of the R132H mutant could occur in a hydrophobic pocket, and enhance its dimerization, consistent with our experimental results. In addition, in vitro autopalmitoylated recombinant IDH1 mutant protein showed enhanced enzymatic activities. In cells expressing IDH1 (R132H) mutant, exogenous fatty acids enhance mutant IDH1 activities through promoting C269 autopalmitoylation, and loss of C269 palmitoylation reverses mutant-induced metabolic reprograming and hypermethylation phenotypes, and impairs cell transformation. Interestingly, a clinical IDH1 mutant inhibitor (LY3410738) strongly inhibits autopalmitoylation by binding to the lipid-binding pocket and covalently modifying C269. Our study reveals that autopalmitoylation conferred by oncogenic IDH1 R132H mutation links fatty acid metabolism to the regulation of IDH1 mutant activities, and is a druggable vulnerability of IDH1 mutant cancers.

overall_design: To study the effects of IDH1 R132H mutant autopamitoylation on downstream gene expressions, we estabilsed U87 cells exogenously expressing PCDH (vector control), IDH1 R13H (IDH1mt), IDH1mt C269S. We then performed gene expression profiling analysis using data obtained from RNA-seq of these three cells.

first: Yang

last: Sun

first: Xu

last: Wu


title: RNA sequencing analysis of control, photon- and proton- irradiated salivary gland organoids at 2 and 6 days post irradiation

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

institute: University Medical Center Groningen

summary: The specific impact of different radiation types, such as photons and protons, and their effects on normal stem cell activity and tissue regeneration are unknown. In this study, we used bulk RNA sequencing to identify differences between photon and proton irradiation using 3 different doses at an early and late timepoint.

overall_design: Organoids derived from 3 different mice were irradiated with either 4, 7 and 15 Gy photons or  4, 7 and 15 Gy protons at day 5. Organoids were collected at 2 or 6 days post irradiation and processed for RNA-seq analysis. Both irradiation types and timepoints have their own control (non-irradiated sample).

first: Rob

last: Coppes

first: Lara

last: Barazzuol


title: Transcriptomic analysis of cardiac remodelling following minimally invasive surgery for aortic regurgitation

city: Guangzhou

first: Xiang

last: Li

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

summary: To explore the signaling pathways  involved in aortic regurgitation (AR)-induced dysregulation from the compensated phase of the heart to the heart failure phase, and to discover the characteristic genes closely related to AR.

overall_design: Aortic valve injury was induced by minimally invasive surgery to construct a mouse model of AR, and hearts were collected for high-throughput sequencing at week2 (compensatory), week 4 (decompensatory) and week 10 (heart failure) after surgery.

first: Weijiang

last: Tan

first: Shuang

last: Zheng

first: FengHua

first: Yunzeng

last: Zou


title: Hypertension promotes hippocampal inflammation and cognitive impairment via sympathetic activation of peripheral immune system

city: Xi’an

first: Jiaxi

last: Xu

address: 76 West Yanta Road

institute: Xi’an Jiaotong University

summary: Hypertension (HTN) has been associated with cerebrovascular dysfunction and cognitive impairment. To understand how HTN affects the brain, the coupling between oxygen consumption and cerebral blood flow in multiple brain regions was firstly analyzed using functional MRI, in patients with HTN and healthy controls. It indicated less functional hyperemia in the cortical areas of HTN group, but showed no difference in their hippocampus. We then used deoxycorticosterone acetate (DOCA)-salt model, in which HTN is developed via sympathetic overactivity, and confirmed HTN-associated cognitive decline and reduction in functional hyperemia of pia arterioles in both male and female mice. Notably, maze test-based cognitive function was partially protected in female mice. In the sensory cortex and hippocampus of male HTN mice, we detected higher reactiveness of glial cells, compared to sham controls. But microglia in the hippocampus reacted more to DOCA-salt, showing a sub-population characterized by high expression of Apoe, B2m, Ramp1, and S100a8/a9, which was not detected in the cortex. With further analyzing the gene profile of immune cells, it revealed disease-associated types of monocyte and macrophage only in the hippocampus, and pinpointed an involvement of peripheral reservoir of immune cells. Next, to determine possible contribution from sympathetic agitation of the peripheral immune system, we tested mice lacking neuron-expressed type 1 angiotensin-II receptors (AT1R), a line that previously showed blunted sympathoexcitation under DOCA-salt treatment. In addition to improved cognitive function, DOCA-salt-induced upregulation of glial reactiveness and pro-inflammatory markers were not seen, and Bdnf expression was preserved in the hippocampus of those mice. To test the role of spleen, which deployed leukocytes upon splenic sympathoexcitation in DOCA-salt HTN, splenectomy was performed and it attenuated hippocampal inflammation and cognitive impairment, in a similar manner as neuronal AT1R knockout. Together, our data provide evidence that the cortex and hippocampus were differently affected by HTN, and proposed a neural mechanism for HTN-associated cognitive impairment that involves sympathoexcitation-induced immune response, thus highlighting that autonomic regulation of the immune system could be a therapeutic target for improving hippocampal health during HTN.

overall_design: The hippocampus and sensory cortex of DOCA-salt- or sham-treated WT mice were rapidly isolated and  analysed by Single-cell RNA sequencing (scRNA-seq).

first: Hanxue


title: Single-cell genomics highlight MYC-upregulation, metabolic activation, and altered cell interactions in T-PLL progression

city: Koeln

first: Linus

last: Wahnschaffe

address: Kerpener Str. 62

department: Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD)

country: Germany

institute: University hospital of Cologne

summary: T-prolymphocytic leukemia (T-PLL) is a rare T-cell malignancy usually associated with rapid tumor progression already at first diagnosis. A small subset of 15-25% of T-PLL patients, however, presents at a primarily indolent disease stage. These patients feature asymptomatic lymphocytosis with stable tumor load over several months to years, before inevitably progressing into active-stage T-PLL. In this study, we employed single-cell RNA sequencing of longitudinally acquired samples to investigate the pathobiologic mechanism underlying this transition from indolent to active T-PLL. We detected consistent deregulations of relevant cancer-associated pathways, centered around a strong upregulation of MYC target gene signatures that highly correlated with an enhanced energy metabolism in active-stage T-PLL cells. Both in silico and ex vivo analyses identified a marked restriction of cell energy metabolism during the indolent disease stage that strongly confined the outgrowth of T-PLL cells. Active T-PLL cells were capable to surpass this metabolic restriction. Analyses of immune-signaling pathways of T-PLL cells as well as the tumor microenvironment further revealed a progressive detachment from immune-related survival signals and escape from the homeostatic control. In summary, we identified both global alterations of gene expression patterns as well as patient-specific lesions that enabled the transformation into active-stage T-PLL. This study provides the first single-cell-resolved genomic analysis of T-PLL, providing valuable and novel insights into the intra-tumor heterogeneity of T-PLL, mechanisms of tumor evolution, as well as its interaction with the tumor microenvironment.

overall_design: Single-cell RNA expression data comparing PBMCs from indolent stage T-PLL to PBMCs from active stage T-PLL patients.

first: Marco

last: Herling

first: Tea

last: Pemovska

first: Philipp

middle: B

last: Staber

first: Marek

last: Franitza

first: Theodore

last: Georgomanolis

first: Kerstin

last: Becker


title: Transcription factors PLT and chromatin regulators PRC2 and JMJ703 form nuclear condensates to maintain gene repression in bivalent domains controlling cell fate in rice root meristem [RNA-Seq]

city: Wuhan

first: Qi

address: Lion Rock Street

department: Hongshan District

institute: Huazhong Agricultural University

summary: The maintenance of stem cells within root meristem is the foundation for continuous growth of the root system. The PLETHORA (PLT) transcription factors have a function to control patterning of root stem cell niche, but the mechanism by which PLTs regulate root meristem activity remains unclear. In this work we show that rice PLT3, PLT4 and PLT5 function redundantly to maintain the stem cell pool of root meristem by repressing the expression of cell growth/development-promoting genes, which display a bivalent histone methylation feature marked by both H3K27me3 and H3K4me3 in root meristem cells. Mass spectrometry and protein interaction assays revealed that PLT5 could interact with core components of Polycomb Repressive Complex 2 (PRC2) that deposits H3K27me3 and the H3K4me3 demethylase JMJ703 in rice cells. In addition, JMJ703 could also interact with the PRC2 catalytic subunit SDG718. Loss of function of PLT3, PLT4 and PLT5 resulted in decreased H3K27me3, increased H3K4me3, and reduced PRC2 binding in bivalent genes in root meristem. Importantly we show that PLT5, PRC2 and JMJ703 could form a tripartite complex within nuclear condensates likely through PTL5 and/or JMJ703-induced phase-separation. These results uncover a chromatin mechanism by which PLTs control the patterning of stem cell niche in rice root meristem.

overall_design: Toinvestigate PLT function involved in gene expression and chromatin modification in rice root meristem，we  performed CUT&Tag sequencing and RNA-seq using root tip (approx. 0.8 cm) of 7-day wild type and plt345 plants.

first: Junjie

first: Yu

last: Zhao

first: Dao-Xiu

last: Zhou


title: Single cell sequencing analysis of control, photon- and proton- irradiated salivary gland organoids at day 11

first: Davide

last: Cinat

summary: The specific impact of different radiation types, such as photons and protons, and their effects on normal stem cell activity and tissue regeneration are unknown. In this study, we used a scRNA-seq approach to characterize our mouse salivary gland organoid model and to assess the effects of photon and proton irradiation on salivry gland stem/progenitor cells.

overall_design: Mouse salivary gland organoids derived from 4 different animals were irradiated at day 5 with either 7 Gy photons or 7 Gy protons (plateau). Non-irradiated (control), photon- and proton-irradiated organoids were collected at day 11 (6 days after irradiation) and pooled before the sequencing run. After trypsinization, propidium iodide (PI) was used to isolate live cells (PI negative) by flowrescence-activated cell sorting (FACS). Cells were then analysed using scRNA-seq.

first: Rob

first: Lara


title: ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development

first: Guanghui

last: Yang

overall_design: Refer to individual Series


title: Transcription factors PLT and chromatin regulators PRC2 and JMJ703 form nuclear condensates to maintain gene repression in bivalent domains controlling cell fate in rice root meristem [CUT&Tag]


title: Single-cell atlas of patient-derived cervical organoids uncovers epithelial immune heterogeneity and intercellular crosstalk during Chlamydia infection

city: Würzburg

first: Cindrilla

last: Chumduri

address: Am Hubland

department: Chair of Microbiology, Biozentrum

institute: University of Wuerzburg

summary: The uterine cervix is a critical mucosal interface that balances immune defense and reproductive function, yet how its distinct epithelial compartments coordinate responses to infection remains unclear. Here, we integrate patient-derived 3D cervical organoids, single-cell transcriptomics and native tissue analysis to construct a high-resolution atlas of epithelial cell diversity and immune dynamics during Chlamydia trachomatis infection. We demonstrate that cervical organoids precisely mirror native tissue at both transcriptional and cellular levels, identifying epithelial subtypes with region-specific immune specializations. Upon infection, ectocervical epithelia reinforce barrier integrity, whereas endocervical epithelia, particularly uninfected bystander cells, exhibit extensive transcriptional reprogramming characterized by robust interferon activation, antigen presentation, and antimicrobial defense. Infection profoundly reshapes epithelial intercellular communication, positioning bystander cells as central signaling hubs that coordinate immune responses and tissue regeneration. Our findings highlight a sophisticated epithelial-intrinsic immune network critical for cervical mucosal defense and establish a physiologically relevant platform for studying human host-pathogen interactions and guiding targeted mucosal therapies against reproductive tract infections and pathologies.

overall_design: Human cervical organoids were cultured as described in Chumduri et al. 2021, Nature Cell Biology. Ecto-and endocervical organoids were infected with Ctr-L2-GFP strain, and then organoids were harvested, and Matrigel was removed. For the human endocervix, organoids were broken down before infection by passing the organoid suspension through a 26G needle 4 times. Organoids were infected at MOI of 5 in an infection medium for 2 hr at 37°C on a shaker (~100 rpm). After infection, organoids were washed, seeded on  Matrigel, and allowed to grow in a 3D media for 36 hr for single-cell RNA-seq analysis. Replicates (3 biological replicates of human ecto- and 2 biological replicates from endocervix)  were pooled, and cell multiplexed using  Cell Multiplexing Oligos (CMOs) based on their tissue region using 10x Genomics 3' CellPlex and Single-Cell 3′ v3.1 RNA-seq kits. CMO-labeled cells were pooled at an equal ratio, made the cell concentration to 2000 cell/µL, and proceeded for the library preparation. Single cells were partitioned into nanolitre-scale Gel-Bead-In-EMulsions (GEMs) using a 10x Chromium Controller. The library was prepared using Single-Cell 3′ reagent kit v3 for reverse transcription, cDNA amplification, and library construction according to the manufacturer's protocol. Sequencing was performed in paired-end mode with an S1 100-cycles kit using Novaseq 6000 sequencer (Illumina)

first: P

last: Prakash

first: N

middle: K

last: Nirchal

first: R

last: K  Gurumurthy

first: C


title: HOXB13 alters chromatin accessibility in prostate cancer through interactions with the SWI/SNF complex [ChIP-seq ]

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

institute: Vancouver Prostate Centre

summary: Homeobox-B13 (HOXB13) is a master transcriptional regulator which is exclusively expressed in the prostate tissue and has been shown to be crucial for its embryonic development. There is extensive clinical and experimental evidence to support the role of HOXB13 in prostate cancer (PCa). Yet, despite this critical role, the function of HOXB13 remains controversial with some studies supporting an oncogenic role and others demonstrating a tumor-suppressive role.  While there is a clear relationship between HOXB13 and AR there are conflicting studies if HOXB13 is itself regulated by AR. Interrogating various AR +ve and AR -ve in-vivo and in-vitro models, in this study, we demonstrate that HOXB13 is crucial for the growth and proliferation of PCa regardless of its androgen dependency. We show that HOXB13 activity in these different models is mediated via interactions with cell-specific transcription factors. Yet despite the diverse transcription factor interactions, HOXB13 activity is commonly modulated by SMARCD2, a member of the mSWI/SNF chromatin remodeling complex. The HOXB13/SMARCD2 interaction is stabilized through interactions with transcription factors. This interaction alters the chromatin accessibility at HOXB13 binding sites which leads to increased proliferation in PCa.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HOXB13 in LNCaP and PC3 cells, for SMARCD2 in PC3 cells, and SMARCD2 in LNCaP cells.

first: Shreyas

last: Lingadahalli

first: Betul

last: Ersoy

first: Umut

last: Altintas


title: NRG1-ErbB4 signaling in the medial amygdala regulates sexual motivation in adult male mice

first: yao

last: shan

address: Xinzao

institute: guangzhou

summary: A successful mating relies on appropriate sexual motivation, whose deficits are frequently implicated in numerous neuropsychiatric disorders, including depression and schizophrenia. However, the underlying molecular mechanisms that control sexual motivation are not fully understood. Here we report that NRG1-ErbB4 signaling in the medial amygdala (MeA) plays a pivotal role in regulating sexual motivation. Through transcriptomic analysis combined with immunoblotting verification, we find that the NRG1 expression in the MeA negatively correlates with the sexual motivation levels in adult male mice. Importantly, local injection of NRG1 into MeA and knockdown of NRG1 decreases and increases the sexual motivation levels, respectively. In consistent, Knockdown of ErbB4, the main receptor of NRG1, and genetic inactivation of ErbB4 kinase in the MeA both elevates the sexual motivation levels, suggesting a necessary role of NRG1-ErbB4 signaling. Electrophysiological study indicates that ErbB4 deletion in the MeA causes decreased neuronal intrinsic excitability. Chemogenetic activation and inhibition of ErbB4-positive neurons decreases and increases the level of sexual motivation, respectively. Furthermore, we identify that the expression of hyperpolarization-activated cyclic nucleotide-gated 3 (HCN3) channel is specifically increased in adult male mice when ErbB4 is deleted. Knockdown of MeA HCN3 diminishes the effects of ErbB4 on neuronal excitability and sexual motivation. Together, our study reveals a critical molecular mechanism for the regulation of sexual motivation in adult male mice, which sheds light on developing new interventions for relevant diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MeA tissues from sexual motivation high group and low group mice

first: Jie

last: Huang


title: HOXB13 alters chromatin accessibility in prostate cancer through interactions with the SWI/SNF complex [ATAC-seq ]

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) for HOXB13 over expression in DU145 cells.


title: Effect of silencing of POc04478 gene after adding 5 μM of copper ions  in Penicillium oxalicum strain △PoxKu70 at the transcriptional level.

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

summary: In order to obtain genetically engineering strain of Penicillium oxalicum with high PPDE production,we silenced  POc04478 gene after adding 5 μM of copper ions in Penicillium oxalicum strain △PoxKu70 ,and we want to investigating the function of silencing of POc04478 gene after adding 5 μM of copper ions at transcriptional level.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  at 24 h after tansfer to the enzyme production medium with Avicel (the only carbon source).

first: Ting

last: Zhang

first: Shuai


title: Relative adrenal insufficiency is a risk factor in pediatric sepsis

city: Lexington

first: Xiang-An

last: Li

address: 741 S Limestone

institute: University of Kentucky

summary: Glucocorticoid (GC) therapy had been strongly recommended for pediatric sepsis (grade 1A). However, the recommendation was changed to grade 2C in 2020. Thus, there is an urgent need to determine if GC therapy is beneficial in pediatric sepsis. Relative adrenal insufficiency (RAI) develops in 33.3% of pediatric septic patients. But little is known about the pathogenesis of RAI and whether GC therapy should be based on the status of RAI. In this study, we utilized 21-day-old SF1CreSRBIfl/fl mice as a pediatric RAI mouse model to assess the pathogenesis of RAI and evaluate GC therapy. We found that RAI mice were susceptible to both cecal ligation and puncture (CLP) and cecal slurry induced septic death. SF1CreSRBIfl/fl mice featured persistent inflammatory responses, and they were effectively rescued by GC therapy. RNA-seq analysis revealed that RAI leads to the persistent inflammatory responses mainly due to transcriptional dysregulation of AP-1 and NF-κB. A number of prognostic biomarkers reported in pediatric septic patients were also identified in RAI mice. Our findings support a precision medicine approach to guide GC therapy for pediatric patients - use of GC based on the status of RAI.

overall_design: Bulk RNA sequencing of liver from 21-day-old SRBIfl/fl and SF1CreSRBIfl/fl mice (n=3) at CLP 6h

first: Dan

last: Hao


title: RNA-seq of B16F10 tongue xenografts with or without inhibition of LN-innervating nociceptive nerves

city: Shanghai

first: Yu

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

summary: We analyzed the transcriptomes of murine B16F10 tongue xenografts from immune-competent C57/B6J mice with or without inhibition of LN-innervating nociceptive nerves using AAV2/retro-Trpv1-hM4D(Gi)-mCherry and Deschloroclozapine.

overall_design: The immune-competent C57BL/6J mice underwent retrogradly labeled of LN-innervating nociceptive nerves through injection of eithor AAV2/retro-Trpv1-mCherry or AAV2/retro-Trpv1-hM4D(Gi)-mCherry in cervical LNs. Six weeks later, the B16F10 murine melanoma cells were innoculated into the submucosal region of mouse tongues. Mice were given Deschloroclozapine treatment twice per day for 12 days. The tongue xenografts were harvested and the non-tumoral tissues were removed. The RNA of entire xenografts was extracted and underwent RNA-seq.

first: Tong

last: Ji


title: The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA Biology [smallRNA-Seq]

status: Public on Nov 17 2025

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: Accurate genome assemblies are critical for understanding small RNA-mediated genome defense. In animals, the PIWI-interacting RNA (piRNA) pathway protects genome integrity by silencing transposable elements. Studying how piRNAs are generated and how they guide heterochromatin formation requires complete reconstruction of genomic piRNA source loci and detailed transposon maps. Here, we present a high-quality de novo genome assembly of Drosophila melanogaster ovarian somatic cells (OSCs), a widely used cell line that recapitulates nuclear piRNA biology. The OSC genome differs substantially from the reference genome, with major differences in transposon content and piRNA cluster composition. Our assembly resolves the 700 kb flamenco locus, the primary piRNA cluster in OSCs, and provides a genome-wide transposon map. Using this resource, we characterize piRNA source loci, reveal how piRNA cluster composition determines transposon-derived piRNA profiles, and clarify the widespread impact of the nuclear piRNA pathway on heterochromatin. Finally, we provide an open platform for integrating user-generated datasets with the OSC genome, creating a community resource for studying transposon control and piRNA biology.

overall_design: Sequencing of Argonaut bound small RNAs from wildtype and Armitage depleted cells. In addition small RNA data of an experiment where flamenco transcription is reduced by promoter proximal tethering of silencing domains.

first: Julius

last: Brennecke


first: Cindrilla

last: Chumduri

type:
Expression profiling by array
Third-party reanalysis

overall_design: Patient-derived human ecto- and endocervical epithelial stem cells were cultured as 3D organoids as described in Chumduri et al. 2021, Nature Cell Biology. These 3D organoids were either uninfected or infected with Chlamydia trachomatis for 5days, respectively as described in this manuscript. Total RNA was extracted from samples and hybridized on Agilent-8x60k Human custom arrays as single-color hybridizations.

first: P

first: N

first: S

last: Koster

first: R

last: Gurumurthy


title: The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA Biology [RNA-Seq]

overall_design: Sequencing of total-RNA using Illumina to determine splice-patterns in piRNA clusters and Nanopore direct RNA sequencing of polyA-RNAs to determine cell-line specific 3' UTR isoforms.


title: The long noncoding RNA Peanut promotes neurogenesis and rod photoreceptor differentiation during postnatal retinal development.

city: Saint Louis

first: Jade

middle: Olivia Enright

last: Hostetler

state: MO

address: 660 S Eucllid Ave

department: Ophthalmology

institute: Washington University in St. Louis

summary: Long noncoding RNAs (lncRNAs) display pervasive expression and function in the developing nervous system. Temporal profiling of gene expression in the retina has demonstrated differential expression of lncRNAs throughout development, however determinations of lncRNA function during retinal development remain limited. In this study, we identify numerous lncRNAs with dynamic temporal expression and characterize the function of the lncRNA Gm11454, which we have named Peanut. Using an overexpression model in mice, we determine that Peanut promotes rod photoreceptor fate and neurogenesis of retinal progenitor cells (RPCs) via inhibition of Notch signaling and regulating expression of neighboring gene Tox2. A novel Peanut knockout mouse model demonstrates that Peanut is required for proper visual function and photoreceptor gene expression. Finally, we determined that Peanut is necessary for proper cell cycle progression and neurogenesis. Our results characterize the function of a novel lncRNA as a regulator of RPC neurogenesis and differentiation and support the importance of lncRNAs in the developing retina.

overall_design: RNAseq profiling of Peanut heterozygote and knockout mouse retinas at P0 and P22.

last: Enright Hostetler

first: Philip

last: Ruzycki

first: Brian

last: Clark


title: The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA Biology [HiC]

overall_design: Hi-C DNA conformation caputre from wt OSC cells


title: The Drosophila OSC Genome: A Resource for Studies of Transposon and piRNA Biology [PRO-Seq]

overall_design: Transcriptional output of wt OSC cells measured using PROseq.


title: Preclinical evaluation of antisense oligonucleotide therapy in a mouse model of HNRNPH2-related neurodevelopmental disorder

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Mutations in HNRNPH2 are associated with an X-linked disorder characterized by developmental delay, intellectual disability, motor and gait disturbances, and seizures. Murine models that reproduce key clinical features of HNRNPH2-related neurodevelopmental disorder suggest that it may result from a toxic gain of function of the mutant protein or a complex loss of normal HNRNPH2 function with impaired compensation by its homolog, HNRNPH1. In this study, we tested gapmer antisense oligonucleotides (ASOs) that target murine Hnrnph2 in a non-allele-specific manner. The lead ASO reduced Hnrnph2 mRNA and protein levels while inducing compensatory upregulation of Hnrnph1 in both WT and Hnrnph2 mutant mouse brains. A single intracerebroventricular injection of the Hnrnph2 ASO into neonatal mutant Hnrnph2 mice rescued molecular and audiogenic seizure phenotypes and improved motor and cognitive functions. ASO treatment at the juvenile stage also rescued audiogenic seizures and motor deficits. In contrast, Hnrnph2 ASO administration did not improve survival, body weight, or hydrocephalus. In human iPSC-derived neurons, a human-specific HNRNPH2 research ASO reduced HNRNPH2 and upregulated HNRNPH1 mRNA levels.

overall_design: Gene expression profiling analysis were performed while treated Hnrnph2 P209L and R206W hemizygous males and WT littermates with a single bolus ICV injection of 30 µg control ASO or Hnrnph2 ASO at PND 2-4 and collected whole brains at 3 weeks of age or 8 weeks of age (n=3 per grpup).

first: Ane

last: Korff

first: Xiaojing

last: Yang

first: Ozan

last: Ozdemir

first: Ananya

last: Samanta

first: Tushar

last: Patni

first: Alfonso

last: Lavado

first: Anoop Murthy

last: Kavirayani

first: Joseph

last: Ochaba

first: Berit

last: Powers

first: C. Frank

last: Bennett

first: Hong Joo

last: Kim

first: J. Paul

last: Taylor


title: Erbb2 establishes the timing of progesterone priming required for uterine receptivity

city: Cincinnati

first: Bo

last: Li

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: This project investigates the role of Erbb2 in regulating uterine stromal progesterone responsiveness during the peri-implantation period in mice. Using bulk RNA sequencing of stromal tissues collected on day 4 of pregnancy, we examined transcriptional alterations caused by uterine Erbb2 deletion. The data provide insight into how Erbb2 enables timely progesterone receptor activation, promotes stromal preparedness, and ensures normal implantation and decidualization. These findings contribute to understanding the molecular mechanisms governing uterine receptivity.

overall_design: RNA-seq profiling of day 4 mouse endometria from Erbb2f/f and Erbb2d/d females.


title: GFP Reporter System Reveals Cell-to-Cell Variability in Aquaporin-2 Expression

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Vasopressin regulates transcription of the aquaporin-2 gene (Aqp2) in collecting duct principal cells. To investigate regulatory mechanisms in Aqp2 gene transcription, we engineered an Aqp2 reporter cell line using CRISPR/Cas9 to insert a green fluorescent protein (GFP) cassette at the endogenous Aqp2 gene locus in mpkCCD cells. In the absence of dDAVP, a vasopressin analog, these cells exhibited low or undetectable GFP and Aqp2 expression in all cells. dDAVP stimulation (1nM dDAVP for 48hrs) markedly increased both GFP and Aqp2 expression together with reversal upon dDAVP removal. These observations demonstrate that GFP faithfully tracks Aqp2 expression. Interestingly, fewer than 50% of cells express GFP and Aqp2 after dDAVP or forskolin, indicating significant variability even though they were clonally-derived. We flow-sorted  the GFP- cells (Aqp2-) and GFP+ cells (Aqp2+), regrew them, and restimulated them separately with dDAVP.  Cells originating from GFP- cells gave rise to both GFP- cells and GFP+ cells, and GFP+ cells similarly regenerated both GFP- and GFP+ populations in the same proportion. Flow cytometry analysis of the DNA content showed variability in cell cycle phases, with most GFP+ cells in G0/G1, and more GFP- cells in G2/S. RNA-seq analysis of the GFP- and GFP+ cells revealed increased abundance of cell-cycle related transcripts in the GFP- cells. We conclude that: 1) heterogeneity in Aqp2 expression is related to cell cycle state; and 2) the newly generated reporter cell line will likely serve as a useful tool to study Aqp2 transcriptional regulation.

overall_design: To provide a surrogate marker for Aqp2 expression and to investigate the mechanisms of vasopressin-mediated heterogeneity, we developed an Aqp2-GFP reporter cell line using CRISPR/Cas9-mediated gene editing—a technique that has revolutionized genetic engineering. By tagging the endogenous Aqp2 gene with GFP in mouse collecting duct cells (mpkCCD), we were able to directly visualize and quantify Aqp2 expression in living cells. Here, we show that GFP faithfully tracks the Aqp2 expression and could servers as a reporter for Aqp2 transcriptional regulation. We further investigate the heterogeneity of Aqp2 expression using RNA-seq and FACS analysis and show that the heterogeneity is partially driven by the cell cycle. Finaly, our reporter cell line could provide as a powerful tool for studying Aqp2 transcriptional regulation in future studies screening for both positive and negative regulators.

first: Mark

last: Knepper


title: Spatial transcriptomic profiling of FFPE and frozen colorectal cancer tissues

city: Bangkok

first: Thanawat

last: Suwatthanarak

address: 2 Wanglang Road, Bangkok-Noi

country: Thailand

institute: Mahidol University

summary: This dataset contains spatial whole-transcriptome profiles from colorectal cancer (CRC) tissues preserved using formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF) methods. Samples were obtained from a patient with stage IV CRC during surgical resection at Siriraj Hospital, Mahidol University, Thailand. Each tissue type was sectioned, stained for Pan-cytokeratin (PanCK), CD45, and SYTO13, and analyzed using the NanoString GeoMx Digital Spatial Profiler with the Human Whole Transcriptome Atlas panel. A total of 36 areas of illumination (AOIs) representing epithelial (PanCK⁺), immune (CD45⁺), and stromal (PanCK⁻/CD45⁻) compartments were collected. Sequencing was performed on an Illumina NovaSeq 6000 platform, and raw counts were processed using NanoString DSP Analysis Suite v3.1 and R for normalization and quality control. This dataset provides spatially resolved gene-expression information across different preservation conditions of CRC tissues to support comparative analysis and method evaluation in spatial transcriptomics.

overall_design: This study compares spatial transcriptomic profiles of colorectal cancer (CRC) tissues preserved using three methods: formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF). All samples were obtained from a patient with stage IV CRC to evaluate how preservation methods affect spatial whole-transcriptome measurements. Spatial gene-expression data were generated using the NanoString GeoMx platform, covering epithelial, immune, and stromal regions within each tissue type. The dataset includes 36 spatially resolved transcriptomic profiles and provides a resource for assessing consistency and data quality across different preservation approaches in CRC research.

first: Kullanist

last: Thanormjit

first: Vitoon

last: Chinswangwatanakul

first: Pariyada

last: Tanjak


title: Baculovirus-mediated expression of a maleness gene in female Anopheles gambiae cells [CUT&Tag]

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

summary:
Background: Rising global temperatures are expected to increase the burden of infectious diseases, including the expansion of mosquito-borne illnesses into new regions. The Anopheles mosquito, the vector of malaria, is a highly sexually dimorphic species; only females require blood meals for egg production and thus transmit disease. Understanding the molecular basis of sex differences in mosquitos may contribute to the design of novel tools for controlling disease transmission. Here, we established baculovirus as a gene delivery tool in female Anopheles cells to investigate the cellular effects after ectopic expression of Yob, the male-determining gene and upstream regulator of sex-specific pathways.
Methods: Ag55 cells were infected with different concentrations of baculovirus and incubated for different timepoints and the effects on the number of EGFP+ and viability were assessed by flow cytometry. Comparison of the transcriptome and proteome of Ag55 cells upon ectopic Yob expression was performed. CUT&Tag and microscopy experiments were done to assess Yob chromatin association and location within the cells. Immunoprecipitation of Yob followed by mass spectrometry was used to understand which proteins Yob interacts with. Results were compared using an empty baculovirus.
Results: We found that the proportion of detectable EGFP+ cells after infection is promoter-dependent and that the baculovirus blocks cell cycle progression in infected cells. Modest transcriptome changes occurred upon Yob ectopic expression. Yob is a nuclear protein, but did not directly associate with chromatin by CUT&Tag. Proteomics experiments revealed that it upregulates and stabilizes proteins involved in RNA metabolism. In addition, Yob interacts with RNA helicases whose Drosophila orthologues are implicated in dosage compensation.
Conclusions: Together, these results demonstrate that the baculovirus system provides a versatile platform for studying mosquito gene biology in vitro.

overall_design: CUT&Tag samples are analyzed. Each group has two biological replicates. The samples infected with the empty baculovirus are a negative control for Yob-HA expression, whereas the IgG antibody is a negative control for unspecific binding of the antibodies

first: Fritz García

last: José Héctor Gibrán

first: Agata

middle: I

last: Kalita

first: Annika

last: Fox

first: Rachel

last: Mullner

first: Falk

last: Butter

first: Maria Felicia

last: Basilicata

first: Claudia

last: Keller Valsecchi


title: Baculovirus-mediated expression of a maleness gene in female Anopheles gambiae cells [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ag55 cells.  Each group has four biological replicates. The samples infected with the empty baculovirus are a negative control for Yob-HA expression.


title: Expression data from lesions and non-lesions before and after treatment in patients with atopic dermatitis

city: Seoul

first: Seo Hyeong

last: Kim

address: 97, Uisadang-daero, Yeongdeungpo-gu

country: South Korea

institute: Cutis Biomedical Research Center Co. Ltd.

summary:
Individual differences in treatment response remain an unmet need. This study aimed to identify biomarkers that can evaluate disease activity and treatment response and predict treatment efficacy by precisely analyzing gene expression changes in patients with atopic dermatitis using a minimally invasive microneedle-based skin sampling method.
To identify the molecular effects of atopic dermatitis treatment, we used microarrays on lesional and non-lesional skin samples before and after treatment.

overall_design: Skin samples from six patients with moderate-to-severe atopic dermatitis were collected using minimally invasive skin sampling using microneedle pathes, and RNA was extracted and hybridized to Affymetrix microarrays.

first: Kwang Hoon

last: Lee

first: Jiyoung

last: Ahn


title: Limb-on-a-Chip: An All-Hydrogel Platform for Scalable and Reproducible Engineering of Neuromuscular Tissues

city: Cambridge

first: Ritu

last: Raman

address: 77 Massachusetts Avenue

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

summary: Disease or damage that impacts neuromuscular tissues thus has a severe negative impact on health, mobility, and quality-of-life, motivating the development of tissue engineered models of the motor control system. Here we present a 1-step fabrication method for manufacturing an all-hydrogel organ-on-a-chip with a spinal cord-inspired design, enabling reproducible patterning of multiple independent motor units.

overall_design: C2C12 myoblasts, wild type(WT) and genetically encoded calcium indicator line(RGECO), grown on a methacrylated gelatin hydrogel and differentiated for 14 days before RNA extraction.

first: Angel

last: Bu

first: Laura

last: Schwendeman

first: Sonika

last: Kohli


title: Intrinsic RB activation induces tumoral and stromal anti-tumor responses that limit triple-negative breast cancer [RNA-Seq]

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

summary: The RB tumor suppressor is a key regulator of cell cycle progression that is often inactivated in triple-negative breast cancer (TNBC). Recent studies indicate that drugs activating RB have multiple tumor-suppressing effects on the tumor and the tumor microenvironment (TME). Here, we utilize a constitutively active RB protein incapable of being phosphorylated and inactivated by CDKs (RBΔCDK) to assess the intrinsic sufficiency of RB activation on tumor suppression. Expression of RBΔCDK in TNBC cell lines uniformly inhibited proliferation. Transcriptomic analysis revealed suppression of cell cycle genes and the induction of genes associated with interferon response. Similarly, tumor growth and metastasis were suppressed in RBΔCDK expressing human xenograft and mouse syngeneic tumor models. RB activation was sufficient to dramatically alter the TME, wherein tumor growth suppression was mediated by CD8+ T cells. Together, these data indicate that active RB suppresses TNBC progression in cancer cell-autonomous and non-autonomous mechanisms.

overall_design: Patient derived TNBC cell lines (HCC1806 and MDA-MB 231) with RBΔCDK isoform and mouse derived TNBC cell lines (AT-3 and 4T1) with RBΔCDK isoform were seeded in 6 well dish at a denisty of 100,000 cells/well. Following 24 hours, the cells were treated with 0.1% DMSO and Doxycycline (1 μg/mL). The tretments were done in triplicates. The cells were exposed to the Doxycycline for 48 hours and RNA was extracted using Quiagen RNeasy plus kit.

first: Yin

last: Wan

first: Thomas

middle: N

last: O’Connor

first: Vishnu

last: Kumarasamy

first: Ioannis

last: Sanidas

first: Scott

last: Abrams

first: Agnieszka

last: Witkiewicz

first: Erik

last: Knudsen


title: Intrinsic RB activation induces tumoral and stromal anti-tumor responses that limit triple-negative breast cancer [scRNA-Seq]