title: Transcriptional regulation of abd-A and Abd-B in Drosophila larval adipocytes [RNA-Seq]

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

summary: The Bithorax complex (BX-C) homeobox proteins specify segmental identities along the anterior-posterior axis during Drosophila embryogenesis. We previously showed that heterogeneous expression of the BX-C genes abd-A and Abd-B defines regional differences between thoracic and abdominal adipocytes. However, the mechanisms underlying this heterogeneity in adipocytes remain unclear. Here, we identify cis-regulatory regions and transcription factors that control abd-A and Abd-B expression specifically in abdominal, but not thoracic, adipocytes of the larval fat body. Using a promoter bashing approach, we identified a 627-bp fragment within the Abd-B locus and a ~6-kb region within the abd-A locus that are sufficient to drive heterogeneous expression in larval adipocytes. Yeast one-hybrid screening combined with functional analysis identified the transcription factors Lola (Longitudinals lacking), Lolal (Lola like), and Combgap/Cg as key regulators of Abd-B expression, with Prg Piragua/Prg and Svp (Seven up) acting as transcriptional activators. Furthermore, Lolal negatively regulates the expression of both Abd-B and abd-A in abdominal adipocytes. Together, these findings suggest that the heterogeneous expression of abd-A and Abd-B in the larval fat body is actively regulated by multiple transcription factors rather than passively maintained.

overall_design: We conducted bulk RNA sequencing (RNA-seq) analyses on dissected larval fat body with specific depletions of Abd-B, same batch control sample was submitted earlier at GSE280511

first: Hemba-Waduge

last: Rajitha-Udakara-Sampath

first: Liu

last: Mengmeng

first: Li

last: Xiao

first: Budslick

last: Elisabeth A.

first: Bondos

last: Sarah E.

first: Maggert

last: Keith A.

first: Ji

last: Jun-Yuan


title: Transcriptional regulation of abd-A and Abd-B in Drosophila larval adipocytes [CUT&Run]

status: Public on Jul 09 2026

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&RUN was performed following a previously described protocol (Liu et al., 2024) using an anti-GFP antibody (three biological replicates; AbdB_GFP-1, -2, -3) or control IgG serum (three biological replicates; AbdB_IgG-1, -2, -3).


title: Integrated bulk and single-cell transcriptome analysis reveals the impact of cyclophosphamide on tumor microenvironment in triple-negative breast cancer models

city: Nantong,Jiangsu,China

first: Xiaorong

last: Zhou

state: Jiangsu province

address: 19 Qixiu Road

country: China

institute: Nantong University

type: Expression profiling by high throughput sequencing

summary: Triple-negative breast cancer (TNBC) remains a formidable clinical challenge. Although preclinical investigations utilizing TNBC mouse models have demonstrated that intermittent cyclophosphamide (CTX) treatment yields superior anti-tumor effects, partly through immune stimulation, mechanisms by which CTX modulates the tumor microenvironment (TME) are not yet fully understood. In this study, we assessed the impact of optimal (140 mg/kg every 6 days, C140) and suboptimal (100 mg/kg every 6 days, C100) CTX treatment regimens on 4T1 tumors, a widely utilized orthotopic TNBC mouse model. While the C100 regimen was better tolerated than the C140 regimen, it was less effective in inhibiting tumor growth. Through integrated bulk and single-cell RNA sequencing of tumor tissues, we discovered that CTX treatment not only inhibited cancer cell proliferation and epithelial-mesenchymal transition but also remodeled the TME by recruiting and reprogramming various immune cells, thereby enhancing the anticancer immune response in a dose-dependent manner. Although the C140 regimen demonstrated significant tumor suppression, it also induced notable extracellular matrix remodeling and led to the accumulation of cancer-associated fibroblasts within the tumor microenvironment. Furthermore, the C140 regimen caused considerable exhaustion of CD8+ T cells and was linked to increased expression of various immune checkpoint molecules, including PD-L1/PD-L2, CD39, and CD200. These effects may compromise therapeutic efficacy and potentially contribute to the development of drug resistance. Overall, our findings elucidate both cancer-cell-intrinsic and tumor microenvironment-dependent mechanisms of CTX action at both local and systemic levels, highlighting potential targets for optimizing chemoimmunotherapy in TNBC.

overall_design: In the subcutaneous tumor formation experiment, 4T1 cells resuspended in 100 μL PBS buffer were inoculated into the subcutaneous mammary gland area of each mice (1×10⁶ cells). Nine days later, when the tumor volume reached approximately 100 mm³, the mice were randomly divided into three groups according to the experimental grouping designing. The control group was intraperitoneally injected with 100 μL PBS, and the experimental groups were intraperitoneally injected with 100 or 140 mg/kg CTX in 100 μL PBS, respectively. All groups were injected once every 6 days. On the third day after the third treatment cycle, the mice were euthanized, and the tumor tissues were harvested for bulk RNA sequencing and scRNA-seq.

first: Ling

last: Zuo

first: Jia

last: Ge


title: Transcriptional signatures indicating RB function may predict response to CDK4/6 inhibition in endometrial cancer

city: Boston

first: Sarah

middle: J.

last: Hill

state: MA

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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

overall_design: Refer to individual Series


title: Across Species Identification of Genes Bridging Neurological and Reproductive Functions in Mammals

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

summary: Evolutionary success in mammals depends on coordinated neurological and reproductive functions, likely mediated by shared genes and molecular pathways between the brain and germ cells. However, direct evidence across species remains limited. Here, proteomic and transcriptomic analyses were performed experimentally in Ovis aries and Rattus norvegicus, while transcriptomic datasets from Mus musculus, Macaca mulatta, and Homo sapiens were analyzed in silico. We identified 8,464 protein-coding genes shared between the brain and sperm/testis and conserved across five species. In rats, 8,444 of these genes were also shared between the brain and the ovary. Functional annotation classified 3,890 genes as associated with both neurological and reproductive functions, and 1,752 as uncharacterized in these contexts, highlighting candidates for future studies on reproductive and neurological disorders. These findings identify a set of conserved genes shared between neurological and reproductive systems, implying a potential genetic network underlying evolutionary conservation of molecular functions across these systems.

sample_organism:
Ovis aries
Rattus norvegicus

platform_organism:
Ovis aries
Rattus norvegicus

overall_design: The experimental data consists of brain and sperm RNA-Seq transcriptomic data from 5 post-pubertal male sheep (Ovis aries) and 15 post-pubertal male rats (Rattus norvegicus) as well as brain and ovary RNA-Seq transcriptomic data from 14 female rats. Sheep samples additionally has blood samples (WBC) collected, which altogether were used to perform LC-MS/MS mass spectrometry data produced with bottom-up proteomics approach. Briefly 10 brain dissections (basal ganglia (BG), cerebellum (CB), entorhinal cortex (EC), frontal cortex (FC), hippocampus (HC), motor cortex (MC), prefrontal cortex (PC), pons, posterior parietal cortex (PPC), and visual cortex (VC)) and sperm samples were obtained from 5 male sheep (samples names 687, 688, 690, 694, and 699). Whole brains and seminal fluid were harvested from freshly euthanized male Sprague Dawley rats, and whole brains and ovaries were harvested from freshly euthanized female Sprague Dawley rats. Same hemisphere samples were used for sheep for the further analysis.  RNA were extracted with either TRIzol reagent  (for sheep samples) or  Zymo Quick-RNA miniprep plus extraction kit (rat samples) followed by DNase I treatment before RNA sequencing. RNA sequencing was performed for all samples using the NovaSeq X Plus platform with two 25B lanes, using V1.0 sequencing kits, and as 150 bp paired-end reads. *Ovis aries* RNA-Seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit. *Rattus norvegicus* RNA-Seq libraries were prepared with the Watchmaker Stranded mRNA library kit. The libraries were pooled, quantified by qPCR, and sequenced on one 25B lane for 151 cycles from both ends of the fragments. Fastq files were generated and demultiplexed using the bcl2fastq v2.20 for *Ovis aries* reads and v4.1.17 conversion software for *Rattus norvegicus* reads for downstream analysis. Read quality was checked with MultiQC software, QC trimming was done for adapter sequences and based on an ASCII offset of 33 for quality scores with Trimmomatic v0.39 software. Alignment was performed through STAR v2.7.5a aligner. Rat brain, sperm, and ovary samples aligned to the latest genome assembly ‘GRCr8 (GCF_036323735.1)’ and for the sheep brain and sperm samples, genome assembly ‘ARS-UI_Ramb_v3.0 (GCA_016772045.2)’ was used with the related annotation files. Alignment rates were above 80% for most of the sheep and rat samples. Read counts for each sample were obtained on the R environment v4.4.2 through the ‘Rsubread’ package v2.20.0.

first: Zeynep

last: Kizilaslan

first: Jessica

last: Townsend

first: Christopher

last: Hoffman

first: Andres

last: Mejia Montoya

first: Francisco

last: Penagaricano

first: Mehmet

first: Nagib

last: Ahsan


title: RNA degradation by ribonuclease T2 is required for phosphate homeostasis in S. cerevisiae

status: Public on Jul 20 2026

city: Portland

first: Jennifer

middle: F.

last: Garcia

state: Maine

address: 716 Stevens Avenue

department: School of Biological Sciences, College of Arts and Sciences

institute: University of New England

summary: Inorganic phosphate (Pi) is a critical building block for key biomolecules including ATP, DNA, RNA, and phospholipids. Consequently, cells monitor phosphate levels and acquire phosphate when intracellular levels become low. Here we demonstrate an unanticipated connection between the enzymatic activity of the S. cerevisiae RNase T2 ortholog, Rny1, and inorganic phosphate availability. Rny1 has been studied for its role in autophagy-linked RNA degradation under starvation conditions. Here we find that in nutrient-rich conditions, cells lacking Rny1 function exhibit phosphate starvation phenotypes and aberrantly activate the PHO signaling pathway despite the presence of high levels of inorganic phosphate in the growth media.

overall_design: RNA-seq profiling of wild-type S. cerevisiae (strain SC112) and rny1Δ mutant (strain SC113) grown in standard nutrient-rich synthetic complete (SC) media to log phase. Three biological replicates were sequenced per strain.

first: Allison

middle: M

last: Kee

first: Nusrat

last: Jahan

first: Davion

middle: J

last: McFall

first: Cote

last: Briggs

first: Lucas

middle: R

last: Girard

first: Samuel

last: Spiese

middle: F


title: SETDB1-mediated repression of RhoB promotes EMT and metastatic progression in prostate cancer [RNA-Seq]

city: lexington

first: ka wing

last: Fong

state: KY

address: 760 press ave

institute: University of Kentucky

summary: Metastatic castration-resistant prostate cancer (CRPC) remains a clinical challenge, and epithelial–mesenchymal transition (EMT) contributes to metastatic progression and reduced response to therapy. However, the upstream epigenetic mechanisms that sustain EMT programs in advanced prostate cancer (PCa) are not fully defined. We identify the histone H3 lysine 9 (H3K9) methyltransferase SET domain bifurcated 1 (SETDB1) as a key regulator of EMT and metastasis through direct repression of the small GTPase RhoB. SETDB1 is genomically amplified and transcriptionally upregulated in metastatic CRPC, and SETDB1 depletion reduces cell migration, invasion, and metastatic dissemination. Integrated chromatin profiling and transcriptomic analyses demonstrate that SETDB1 occupies the RhoB promoter and mediates its transcriptional silencing through H3K9 methylation. Restoration of RhoB reverses EMT gene expression and suppresses invasive behavior, whereas RhoB knockdown rescues the effects of SETDB1 depletion, establishing RhoB as a critical downstream effector of SETDB1 function. Androgen signaling inhibitor-resistant PCa models exhibit RhoB loss and EMT activation, linking this axis to therapy-resistant phenotypes. Finally, antisense oligonucleotide-mediated SETDB1 silencing restores RhoB expression and suppresses EMT and invasion in CRPC cell models. Together, these findings define a SETDB1-RhoB epigenetic pathway that promotes EMT and metastatic progression in PCa and may be therapeutically targeted in advanced disease.

overall_design: Examine the transcriptome in LNCaP cells with ot without SETDB1 alteration

first: Fong

last: ka wing

first: Jinpeng

last: Liu

first: Ryan

last: Goettl


title: SETDB1-mediated repression of RhoB promotes EMT and metastatic progression in prostate cancer [CUT&Run]

overall_design: Examination of the genomic landscape of SETDB1 and H3K9me3 in human prostate cancer cells LNCaP cells. There are 2 CUT&RUN-seq samples.


title: Soluble DLK1 secreted by telomere-shortening-induced senescent microglia impairs oligodendrocyte functions and alters neuronal activity(ipsc_cell)

city: NEW YORK

first: hao

last: chen

state: NY

address: 413 E 69th ST

department: Brain and mind research institute

institute: Weill Cornell Medicine

summary: Aging is a predominant risk factor of neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Here, we investigated the impact of telomere shortening, a physiological hallmark of aging, on brain function. Telomere-shortened mice exhibited cognitive decline and exacerbated lipofuscinosis, accompanied by the emergence of senescent microglia with a senescence-associated secretory phenotype and oligodendrocyte lineage cells with impaired maturation. Using iPSC-derived microglia with shortened telomeres, we identified DLK1 as a novel senescence-associated ligand secreted by senescent microglia. Elevated soluble DLK1 was detected in the cerebrospinal fluid of both telomere-shortened and physiologically aged mice, and this increase was abolished by microglial depletion, confirming its microglial origin. Functionally, AAV-mediated expression of sDLK1 in mouse brains induced hypomyelination and disrupted oligodendrocyte differentiation in vivo. In human iPSC-derived systems, sDLK1 impaired late-stage oligodendrocyte maturation and disrupted neuronal calcium signaling. Together, these findings establish replicative microglial senescence as a pathological feature of telomere shortening and identify sDLK1 as one key effector linking senescent microglia to oligodendrocyte dysfunction and neuronal dysregulation during brain aging.

overall_design: iPSC-derived microglia were generated following telomerase inhibition with + BIBR1532 (60 µM, 30 days) and subsequent + etoposide treatment (50 µM) to induce senescence. Total RNA was then extracted from microglia for bulk RNA-seq analysis

first: Bangyan

first: Maria

last: Telpoukhovskaia

first: Matthew

last: Mahoney

first: Yilin

last: Feng

first: Alice Maria

last: Giani

first: Eileen Ruth

last: Torres

first: Lihong

last: Zhan

first: Pearly

last: Ye

first: Jingjie

last: Zhu

first: Nessa R

last: Foxe

first: Daphne

first: Xinran

last: Tong

first: Deepak

last: Srivastava

first: Christine V.

last: Theodoris

first: Shiaoching

last: Gong

first: Mingrui

last: Zhao

first: Li

last: Fan

last: Gan


title: Soluble DLK1 secreted by telomere-shortening-induced senescent microglia impairs oligodendrocyte functions and alters neuronal activity [DLK1_snRNA-seq]

first: hao

last: chen

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-nucleus RNA sequencing of hippocampus from 8-month-old male mice injected intravenously with AAV expressing mouse soluble DLK1. Human iPSC-derived oligodendrocytes treated with soluble DLK1. Hippocampus from 8-month-old female G3 Terc⁻/⁻ and wild-type mice

first: Bangyan

last: Liu


title: Mycoplasma infection drives EGFR-TKI resistance through convergent transcriptomic reprogramming in non-small cell lung cancer

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam University Medical Center

summary: Epidermal growth factor receptor (EGFR) mutations are an oncogenic driver in non-small cell lung cancer (NSCLC), but resistance to EGFR tyrosine kinase inhibitors (TKIs) remains a major challenge. Here, we show that mycoplasma infection sustains ERK, AKT, and NF-κB signaling, impairs receptor internalization, and reduces osimertinib sensitivity in EGFR-mutant NSCLC cells. Antibiotic-mediated clearance of Mycoplasma partially restored drug sensitivity, establishing a causal infection-resistance link. Transcriptomic analysis identified converging pathways related to mycoplasma infection and drug resistance, including gene sets enriched for inhibition of receptor internalization and clathrin downregulation at the protein level. Combined inhibition of mTOR and LDHA improved growth suppression in mycoplasma-positive cells. Clinically, mycoplasma infection and higher LDHA expression were associated with poor overall survival of EGFR-TKI-treated patients. These findings establish mycoplasma infection as a causal, non-genetic contributor to EGFR-TKI resistance and support a hierarchical therapeutic strategy combining antibiotic eradication with mTOR and LDHA inhibition.

overall_design: RNA-seq profiling of H1975 and PC9 cells

first: Bing

last: Wang

first: Valentina

last: Donati

first: Alessandro

last: Gregori

last: Leonetti

first: Aldo

last: Pastore

first: Dongmei

last: Deng


title: A highly prevalent lupus risk haplotype increases IRF7-dependent induction of IFN-alpha enhancing antiviral defense and exacerbating autoimmunity

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: Genome-wide association studies have identified polymorphisms at 11p15 associated with Systemic Lupus Erythematosus (lupus). Statistical fine mapping prioritizes a highly prevalent coding haplotype within the IRF7 gene. Analysis of ancient DNA confirms that this risk haplotype has persisted at high frequencies in the global population for millennia. The IRF7 risk haplotype is sufficient to increase nuclear localization of IRF7 and transcriptional activity downstream of pattern recognition receptor pathways. This risk haplotype increased binding strength and altered sequence specificity of IRF7 interactions with DNA, resulting in genotype-dependent increases in IFN-a production in numerous biological systems, including monocytes and airway epithelial cells. CRISPR engineering of a homologous risk variant in mouse Irf7 results in both enhanced innate control virus infection and increased autoantibody titers in a model of autoimmunity. Altogether, we establish a persistent and prominent genetic IRF7 haplotype that amplifies IRF7 activity in a manner that has immunological risks and benefits.

overall_design: We performed RNA-seq in IRF7 deficient (THP-1) monocytes and THP-1 monocytes transduced with IRF7-HA expressing the 1) SLE risk haploptype (QK) and 2) protective (RE) haplotype. We sequenced triplicates of the 3 cell lines both at baseline and after Poly(I:C) transfection. We performed RNA-seq in HEK cells that stably express TLR7 (HEK Blue hTLR7) transduced with IRF7-HA expressing the 1) SLE risk haploptype (QK) and 2) protective (RE) haplotype. We sequenced triplicates of the 2 cell lines after stimulation with TLR7/8 agonist Resiquimod (R848) for 3 hours.

first: Leah

last: Kottyan


title: Transcriptional changes induced by AKR1A1 knocking out in Huh7 cells.

city: Copenhagen

first: Salvatore

last: Rizza

email: salvatoreri@gmail.com, rizza@cancer.dk

address: Strandboulevarden 49

department: Redox Biology

country: Denmark

institute: Danish Cancer Institute

summary: AKR1A1 encodes for the proteinAKR1A1, an aldoketoreductase enzyme acting as a denitrosylase. AKR1A1 reduces S-nitrosoCoenzimeA (SNO-CoA)and indirectly control S-nitrosylated proteins levels

overall_design: RNA-seq profiling of control huh7 cells and their knockdown derivates (siAKR1A1 1 and siAKR1A1 2)

first: Chiara

last: Pecorari

first: Giuseppe

last: Filomeni


title: Transcriptional changes induced by AKR1A1 knocking out in 769-P cells.

overall_design: RNA-seq profiling of control 769P cells and their knockdown derivates (siAKR1A1 1 and siAKR1A1 2)


title: Menin-dependent megakaryocyte proliferation and fibrosis in myeloproliferative neoplasms

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

summary: Menin inhibition, an approved therapy for MLL-rearranged acute myeloid leukemia, is accompanied by decreased platelet counts in 15-20% of heavily pre-treated leukemia patients. While studying the mechanism that accounts for this effect, we discovered that menin inhibition reduced the numbers of megakaryocyte progenitors in human CD34+ cultures and in mice. Given this ability to suppress megakaryopoiesis, which is a key driver of myeloproliferative neoplasms (MPN), we investigated the extent to which menin inhibition ameliorates MPN phenotypes. We found that the menin inhibitor revumenib has potent anti-tumor activity in MPN animal models, leading to significantly increased survival, decreased accumulation of megakaryocytes, normalization of peripheral blood counts, and ablation of bone marrow fibrosis. Revumenib also synergized with the JAK inhibitor ruxolitinib while having subtle effects in healthy mice. Moreover, revumenib suppressed megakaryopoiesis of primary MPN patient specimens in colony forming assays and liquid culture. Importantly, knockout of menin and its target MEIS1 phenocopied the action of revumenib, confirming an on-target effect of the drug. Of note, menin inhibition was not associated with suppression of JAK/STAT signaling indicating that it is a novel dependency. Together we reveal that menin inhibition is a novel therapeutic approach for MPNs.

overall_design: We used 10x genomics platform to profile single-cell transcriptome of human CD34+ cells treated with DMSO or 0.3 μM Revumenib ,or human CD34+ cells electroprated nontargeting sgRNA or sgRNAs targeting MEN1 in the presence of THPO

first: Jeremy

last: Wen

first: Anitria

last: Cotton

first: Trent

last: Hall

first: John

last: Crispino


title: ClC-Kb deficiency inhibits the proliferation and mitochondrial metabolism of renal tubules

city: Iowa City

first: Chih-Jen

last: Cheng

address: 285 Newton Rd, 3270B CBRB

department: Department of Internal Medicine

institute: The University of Iowa

summary: Our previous study demonstrates that ClC-Kb chloride channel deficiency in Bartter syndrome (BS) type 3 not only impairs transport activity but also affects the development of the thick ascending limbs (TALs) and possibly distal convoluted tubules (DCTs). This developmental defect is important to the pathogenesis of BS, with unknown underlying mechanisms. This study investigated the cellular effects of ClC-Kb deficiency and explored potential therapeutic strategies addressing these effects. We isolated TALs and DCTs from Clc-k2(ClC-Kb mouse ortholog)-knockout (Clc-k2-/-) and wild-type mice for multi-omics analyses. The results revealed differential regulations involving cell cycle, cell proliferation, mitochondrial respiration, and metabolism. In vitro studies showed that Clc-k2-/- TALs proliferated less efficiently than wild-type cells, exhibited a G2/M cell cycle delay, had reduced mitochondrial mass and oxidative phosphorylation alongside the suppressed glycolysis and fatty acid oxidation. A gain-of-function D561A mutation in with-no-lysine kinase 4 (WNK4), known to stimulate transepithelial salt transport and mitochondrial biogenesis in TALs/DCTs, significantly restored the salt transport in Clc-k2-/- TALs/DCTs and improved the phenotype of BS. Alternatively, overexpressing Pgc1α, a master activator of mitochondrial biogenesis, also alleviated the disease severity in Clc-k2-/- mice. These findings provide insights into the molecular mechanisms of BS type 3 and suggest novel therapeutic approaches.

overall_design: Microdissected TAL segments were washed in 1× Dulbecco’s PBS with calcium chloride and magnesium chloride under a stereomicroscope. The tubules were transferred into a 1.5 mL microcentrifuge tube containing 2 μL of Dulbecco’s PBS for total RNA extraction using the RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands). Total RNA was eluted in 10 μl of RNase-free water. For RNA-Seq, cDNA was synthesized using a SMART-Seq mRNA LP (Takara Bio, San Jose, CA, U.S.A.) according to the manufacturer’s protocol. The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μl of Elution Buffer. The purified cDNA was quantified fluorometrically using a Qubit 2.0 Fluorometer. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit (Agilent Genomics). The SMART-Seq Library Prep Kit (Takara) was used to generate the libraries, with an input of 1 ng of cDNA. Libraries were pooled and sequenced to obtain 75-base-pair paired-end reads on the Illumina NextSeq550 platform to a depth of >20 million reads per sample.

first: Chiao-Hui

last: Hsieh

first: Yu-Jen

last: Chen

first: Chih-Chien

last: Sung

first: Emily

last: Morrison

first: Chou-Long

last: Huang


title: The NuRD chromatin remodeling complex regulates tRNA genes through direct interactions with RNA polymerase III [Nuclei run-on (nascent RNA) profiling]

city: Urbana

first: Ruiying

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

summary: RNA polymerase III (Pol III) synthesizes noncoding RNAs essential for translation, RNA processing, and transcription regulation. Its activity aligns with cellular growth and nutrient availability, and its dysregulation is linked to diseases like breast cancer and leukodystrophy. Despite its importance, Pol III regulators remain largely unidentified due to a lack of exploration of Pol III-centered protein-protein interactions (PPIs). To address this need, we conducted high throughput proteomic experiments and identified over 300 novel Pol III interactors, including Pol II-related transcription factors, nuclear import factors, and splicing factors. Most notably, our proteomic survey uncovers complex-complex interactions between Pol III and the NuRD (Nucleosome Remodeling and Deacetylase) complex. NuRD complex is a known Pol II co-repressor, but its recruitment to and effect on Pol III remains uncharacterized. Using innovative large-scale NuRD binding pattern meta-study, NuRD ChIP-seq combined with Pol III inhibition, and Pol III activity profiling in mammalian cell lines, we revealed that the NuRD is recruited by Pol III itself and fine-tunes Pol III transcription activity. We found that NuRD exhibits a binding preference for highly active Pol III genes, and inhibition of Pol III transcription reduced the enrichment of NuRD subunits. Functionally, inhibiting NuRD deacetylase activity releases its inhibition on Pol III transcription and increases its dynamic range. In addition, our ATAC-seq analysis suggests NuRD is potentially involved in establishing nucleosome positioning through its ATP-dependent remodeler activity. Beyond identifying NuRD as a novel Pol III regulator, our survey of Pol III interactions unexpectedly identifies physical interactions between Pol III and mRNA splicing factors. We demonstrate that Pol III depletion leads to rewiring of splicing efficiencies for specific mRNA subpopulations, suggesting a previously unrecognized interplay between Pol III and RNA processing factors. Together, these findings advance our understanding of Pol III interactome, uncovering new layers of transcriptional control and unexpected functional consequences of Pol III interactions in human cells.

overall_design: Nuclei run-on (nascent RNA) profiling of wild type THP1 monocyte with or without Pol III inhibitor ML-60218 treatment

first: Kevin

last: Van Bortle


title: TET2 drives myeloid cell fate acquisition through AGO2 modulation

city: Badalona

first: José

middle: Luis

last: Sardina

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

type: Methylation profiling by genome tiling array


title: TET2 drives myeloid cell fate acquisition through AGO2 modulation [RNA-seq, TET2 KD transdifferentiation]

summary: We examine the differential transcriptional dynamics during the C/EBPa-driven transdifferentiation of B-cells into iMacs in cells with reduced TET2 levels.

overall_design: We conducted RNA-seq experiments to examine how gene expression changes during transdifferentiation in cells that presented doxycycline inducible TET2 shRNA mediated gene silencing. We compared the shTET2 to shCTRL cells with a scramble sequence at three different post induction time points (0 hours -B cells-, 27 hours, and 144 hour -iMacs-) using biological duplicates.

first: Aleksey

last: Lazarenkov

first: Anna

middle: V

last: López-Rubio

middle: L


title: Depleting prion protein using splice-switching small molecules

city: Chicago

first: Jingxin

last: Wang

address: Abbott Memorial Hall 210A, 947 E 58th St.

department: Section of Genetic Medicine

institute: University of Chicago

summary: Prion diseases are fatal neurodegenerative disorders driven by prion protein (PrP) misfolding, and lowering cellular PrP represents a promising therapeutic strategy. Here we report a small-molecule approach that reduces PrP by modulating pre-mRNA splicing of the PRNP gene. Through chemical modification of the clinically approved splicing modulator risdiplam, we generated CP3, the first class of compounds that selectively activate a cryptic exon in PRNP and routes its mRNA product for degradation, reducing PrP by ~70% in cells. We demonstrate that CP3 activity critically depends on alternative splicing factor Luc7L, revealing a novel requirement for alternative splicing factors in small molecule splicing modulation. Strikingly, co-administration of CP3 with a Luc7L activator PTC258 significantly lowers PrP levels in the brains of transgenic mice. These results establish splicing modulation as a powerful strategy for PrP reduction and highlight the potential of small-molecule cooperativity for therapeutic RNA targeting.

overall_design: Two RNA-seq experiments. Exp1: titration of splicing-modulator small molecules (Risdiplam, SMSM74, or CP3 with constant 25 µM BPN15477) at increasing doses, plus DMSO vehicle controls, in LN-229 glioblastoma cells treated for 24 h. Exp2: BPN15477 (25 µM) or DMSO vehicle, treated for 24 h, in GM12878 lymphoblastoid cells.

first: Benjamin

last: Fair

first: Bo

last: Liu

first: Zhiling

last: Kuang

first: Junxing

last: Zhao

first: Zhichao

last: Tang

first: Qingyao

last: Kong

first: Xiangbin

last: Ruan

first: Lixian

last: Zhou

first: Frederic

last: Vaillancourt

first: Bryan

last: Dunyak

first: Xiaochang

last: Zhang

first: Ming

last: Xu

first: James

middle: A

last: Mastrianni

first: Rui

first: Yang

middle: I

last: Li


title: TGF-β and IL-2 differentially shape T follicular regulatory cell differentiation and stability in vitro

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

summary: T follicular helper (Tfh) cells and T follicular regulatory (Tfr) cells play critical roles in regulating the activity of the germinal center (GC), which is essential for the generation of high-affinity antibodies. In the GC, Tfh cells help B cells to proliferate and to differentiate into memory B cells and long-lived plasma cells. In contrast, Tfr cells, a specialized subset of regulatory T cells (Tregs), modulate the humoral immune response by suppressing excessive or autoreactive B-cell activity. Here, we established an in vitro differentiation protocol for mouse CD4⁺ T cells that yielded CXCR5⁺FoxP3⁺ Tfr cells that exhibited a Bcl6hiPD-1hiCD25loGITRint phenotype and were distinct from Treg and Tfh cells. Functionally, in vitro-generated Tfr cells potently suppressed Tfh cell-driven B-cell class switching to IgG1 and downregulated the expression of B-cell costimulatory ligands. While in vitro-generated Bcl6-deficient Tfh cells were impaired in providing help to B cells for efficient class switching to IgG1, in vitro-generated Bcl6-deficient Tfr cells failed to inhibit Tfh cell-driven B-cell class switching to IgG1. Mechanistically, we showed that Tfr cells emerged from FoxP3+ precursors in low-IL-2 environments through a TGF-β- and c-Maf-dependent pathway, allowing for reprogramming and reinforcement of the follicular regulatory cell program in CD4+ T cells in vitro.

overall_design: Naive CD4+ T cells obtained from GREAT.Smart-17A.FoxP3hCD2 triple-reporter donor mice were cultured under Treg (anti-IFNg, anti-IL-4, TGF-b, IL-2), Tfr (anti-IFNg, anti-IL-4, TGF-b), and Tfh (anti-IFNg, anti-IL-4, TGF-b, IL-6, IL-21) cell polarizing conditions on anti-CD3/anti-CD28-coated 96-well flat-bottom plates. After 3.5 days of cell culture, T cells were harvested, stained, and sorted on a BD FACSAriaFusion cell sorter for FoxP3+CXCR5– (Treg), FoxP3+CXCR5+ (Tfr), and Foxp3–CXCR5+(Tfh) cells among viable CD8–CD19–CD4+ lymphocytes using a 70-micron nozzle. RNA was isolated using TRIzol™ LS Reagent (Invitrogen, #10296028) according to the manufacturer’s instructions. RNA was cleaned up with a RNeasy Mini Kit (catalog #74104) according to the manufacturer’s instructions. The sequencing library was prepared according to manufacturer´s guidelines with the QuantSeq FWD 3´-mRNA-Seq Kit from Lexogen using 50 ng total RNA as input. Libraries were single-end sequenced with 1x100 bp on a S1 flow cell of an Illumina NovaSeq 6000 instrument to a depth of 10 M raw reads on average at the NGS Core Facility of University Hospital Bonn.

first: Luisa

last: Bach

first: Mohmmadamin

last: Ghasemi

first: Lisa Maria

last: Steinheuer

first: Kevin

last: Thurley


title: The NuRD chromatin remodeling complex regulates tRNA genes through direct interactions with RNA polymerase III

first: Ruiying

last: Cheng

type: Non-coding RNA profiling by high throughput sequencing

overall_design: NuRD complex ChIP-seq in THP-1 monocytes. ATAC seq and smallRNA seq in THP-1 cell, with ML6-induced Pol III inhibition, PMA-induced differentiation or Romidepsin-induced HDAC inhibition

last: Van Bortle


title: RNA seq of mouse tissue samples from ACD animal models : Effect of MMP9 on gene expression.

status: Public on Jul 10 2026

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

summary: In the present study, RNA-seq technique were performed to explore biological significance of MMP9 in the neuro-cutaneous signaling network of chronic itch. We performed high-throughput sequencing of mouse tissue samples from ACD animal models. The study found that the transcription level of MMP9 was highly expressed in the DNFB-induced ACD model, suggesting that MMP9 plays an important role in the process of ACD disease.

overall_design: Mouse ear tissue were from ACD model mice.The gene expression of these cells were investigated utilizing DNBSeq platform.

first: Ruizhen

last: Wang

first: Jianghui

last: Meng


title: Bulk RNA seq data of transcription factor ELF-1 in mouse BMDM derived macrophages.

city: Beijing

first: Zhaoqi

state: Beijing

address: Peking University People’s Hospital

institute: Peking University People’s Hospital

summary: To define the functional impact of ELF-1 on macrophage-driven AKI, we induce M1 polarization in ELF-1-deficient murine macrophages and perform RNA-seq. Building on clinical correlations between ELF-1 and inflammatory cytokines, this study systematically profiles ELF-1-dependent genes and pathways, with the goal of elucidating how ELF-1 orchestrates M1 polarization and contributes to the pathogenesis of AKI following renal transplantation.

overall_design: Bone marrow-derived macrophages (BMDMs) were isolated and cultured as previously described. BMDMs from wild-type (WT) and ELF-1 knockout (KO) mice were stimulated with or without lipopolysaccharide (LPS) for 6 hours.

first: Yangxiao

last: Hou


title: TET2 drives myeloid cell fate acquisition through AGO2 modulation [RNA-seq, AGO2 KD transdifferentiation]

first: José

last: Sardina

summary: We examine the differential transcriptional dynamics during the C/EBPa-driven transdifferentiation of B-cells into iMacs in cells with reduced AGO2 levels.

overall_design: We conducted RNA-seq experiments to examine how gene expression changes during transdifferentiation in cells that presented AGO2 shRNA mediated gene silencing. We compared two different shAGO2 cell lines (shA2.1 and shA2.2) to shCTRL cells with a scramble sequence at three different post induction time points (0 hours -B cells-, 27 hours, and 144 hour -iMacs-) using biological triplicates.

first: Aleksey

last: Lazarenkov

first: Anna

last: López-Rubio


title: TET2 drives myeloid cell fate acquisition through AGO2 modulation [DNA methylation arrays]

summary: We examine the differential DNA methylation dynamics during the C/EBPa-driven transdifferentiation of B-cells into iMacs in cells with reduced TET2 levels.

overall_design: We used DNA methylation arrays (Illumina Infinium MethylationEPIC Bead-Chip arrays) to examine genome-wide DNA methylation changes during transdifferentiation in cells that presented doxycycline inducible TET2 shRNA mediated gene silencing. We compared the shTET2 to shCTRL cells with a scramble sequence at three different post induction time points (0 hours -B cells-, 27 hours, and 144 hour -iMacs-) using biological triplicates


title: TET2 drives myeloid cell fate acquisition through AGO2 modulation [ChIP-seq, TET2]

summary: We determined TET2 genome-wide occupancy through FLAG-tag based capturing during C/EBPa-driven transdifferentiation of B-cells into iMacs

overall_design: We analyzed the occupancy of TET2 using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). We compared TET2-FLAG tagged versus un-tagged cells using biological duplicates.


title: snRNA-seq profiles distinguish anti-Drebrin- and anti-GAD65-positive encephalitis

first: Daniel Sebastian

last: Galvis Montes

address: Venusberg Campus 1

institute: Universitätsklinikum Bonn

summary: Autoantibodies (ABs) against intracellular proteins, including glutamate-decarboxylase 65 (anti-GAD65), are increasingly recognized in autoimmune and limbic encephalitis (AE/LE). Anti-GAD65 LE frequently progresses into severe temporal lobe epilepsy (TLE), neuropathologically characterized by hippocampal sclerosis (HS) and variable cytotoxic T lymphocytes (CTLs) infiltration. Recently, we have identified Drebrin as a novel intracellular target protein of ABs in patients suspicious for AE. Here, we report on the hippocampal neuropathological sequelae and single-nuclei RNA sequencing (snRNA-seq) of anti-Drebrin- versus anti-GAD65-positive TLE patients, in concert with key clinical parameters from a large patient cohort.

overall_design: Hippocampal tissue from TLE patients who underwent amygdalo-hippocampectomy to remove the epileptic focus for seizure relief and that were seropositive for anti-Drebrin (n = 2) or anti-GAD65 (n = 2) was used as starting material for snRNA-seq. As controls, hippocampi of seronegative patients with HS (n = 2) and brain tissue of patients with lesion associated epilepsy (n = 2) were used.

first: Karen

last: van Loo

first: Daniel

last: Galvis-Montes

first: Annika

last: Breuer

first: Juliane

last: Berns

first: Chiara

last: Hummel

first: Tobias

last: Baumgartner

first: Moritz

last: Freyberg

first: Jan

last: Bauer

first: Theodor

last: Rüber

first: Ashley

last: van Waardenberg

first: Hamed

last: Hamed

first: Valeri

last: Borger

first: Hartmut

last: Vatter

first: Rainer

last: Surges

first: Susanne

last: Schoch

first: Albert

last: Becker

first: Julika

last: Pitsch


title: mRNA signatures of a T-cell driven Limbic Encephalitis mouse model

first: Daniel Sebastian

last: Galvis Montes

summary: To determine the key transcription factors and molecular pathways involved in Limbic Encephalitis (LE), we analyzed immune cell-driven transcriptional changes in a newly developed mouse model of CD8+ T cell-mediated LE. This murine model (OVA-CD8+ LE) recapitulates the essential phenotypic features observed in human cytotoxic T lymphocyte (CTL)-induced LE, including neuroinflammation and seizure susceptibility. In a time series approach 2, 5, 8 and 28 days post-injection hippocampal tissue was harvested for RNA sequencing analysis. These timepoints were selected to capture stage-specific transcriptional changes driven by CD8⁺ T cell activity, thereby providing insights into the molecular events underlying hippocampal dysfunction in LE.

overall_design: OT-I/Rag-/- mice received hippocampal CA1 injections of recombinant AAVs expressing the OVA antigen under a neuron-specific promoter (rAAV-hSyn-OVA-mCherry; rAAV-OVA group) or control AAVs expressing only mCherry (rAAV-hSyn-mCherry; rAAV-control group). Samples were collected 2, 5, 8 and 28 days days post-injection. Hippocampus were dissected and collected for RNA-seq analysis.

first: Karen

last: van Loo

first: Katharina

last: Mair

first: Motaz


title: Effect of Intestinal Microbiome on Chromatin Accessibility in Paneth Cells

city: Newark

first: Dahui

last: Wang

state: NJ

address: 73 Warren st

department: Biological Science

institute: Rutgers University, Newark

summary: To assess epigenetic changes, ATAC-seq was performed on Paneth cells isolated from germ-free (GF) and specific pathogen-free (SPF) mice. The results revealed microbiome-dependent alterations in chromatin accessibility at key genomic loci involved in stemness regulation.

overall_design: ATAC-seq on FACS sorted Paneth cell from germ free and specific pathogen free mice.

first: Michael

middle: P

last: Verzi

first: Oscar

last: Pellon-Cardenas

first: Sohaib

last: Hassan

last: Gao


title: CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [ATAC-seq]

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

summary: Ewing sarcoma is characterized by a chromosomal translocation resulting in the fusion protein EWSR1-FLI1.  To identify small molecules that selectively impair the oncogenic transcriptional program enacted by EWS-FLI1 we employed a novel phenotypic screen. Our screening hits were enriched for inhibitors of cyclin dependent kinase 8/19.  Inhibition of CDK8/19 resulted in a proliferation defect in Ewing sarcoma cells and a reduction in growth of Ewing sarcoma xenografts.  We performed a genome wide pooled CRISPR screen that suggested that small molecule inhibition of CDK8/19 acted in a gain-of-function manner that did not replicate the effects of CDK8/19 genetic knockout.  Through biochemical studies and chromatin profiling, we discovered that CDK8/19 inhibitors act through a novel trapping mechanism in which the inhibitor prevents dissociation of the CDK8 kinase from core Mediator.  This mechanism has broad implications for the development of small molecules to target transcriptional regulation.

overall_design: ATAC-seq analysis in Ewing sarcoma cell lines. The endogenous EWS-FLI fusion was targeted with an AID degron tag. EWS-FLI deletion was induced with 300 nM 5-Ph-IAA treatment for 24 hrs.

first: Ryan

last: O'Hara

first: Xin

last: Zhao

first: Purbita

last: Saha

first: David

last: McFadden


title: CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [ChIP-seq]

overall_design: ATAC-seq analysis in Ewing sarcoma cell lines. The endogenous EWS-FLI fusion was targeted with an AID degron tag. EWS-FLI deletion was induced with 300 nM 5-Ph-IAA treatment for 24 hrs. A673 cells were treated with CDK8 inhibitor SW393109 at 100 nM for 24 hrs.


title: CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [CUT&RUN]

overall_design: CUT&RUN analysis in Ewing sarcoma cell lines. The endogenous EWS-FLI fusion was targeted with an AID degron tag. EWS-FLI deletion was induced with 300 nM 5-Ph-IAA treatment for 24 hrs. For inhibitor studies, cells were treated for 24 hrs with 100 nM SW393109.


title: Peroxisome Proliferator-Activated Receptor Gamma Regulates Invasive Trophoblast Cell Differentiation and Hemochorial Placentation [ChIP-seq]

city: Kansas City

first: Esteban

middle: Mauricio

last: Dominguez

state: Kansas

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

summary: Establishing a successful pregnancy relies on the proper function of trophoblast cells. The expansion and differentiation of trophoblast stem (TS) cells are critical for defining the fundamental properties of the placenta. These include specialized trophoblast cells, which exit the placenta and enter and transform the uterus, including restructuring uterine spiral arteries. In the human these cells are referred to as extravillous trophoblast (EVT) cells, whereas in the rat they are termed invasive trophoblast cells. Mechanisms governing trophoblast cell differentiation into these specialized invasive trophoblast cell lineages remain poorly understood. We investigated the role of peroxisome proliferator-activated receptor gamma (PPARG), a ligand-activated transcription factor, as a potential regulator of EVT/invasive trophoblast cell development and establishment of the uterine-placental interface. In first trimester human placentas, PPARG transcripts and protein were detected in the EVT cell column and increased in amount as human TS cells differentiated into EVT cells. Disruption of PPARG impaired differentiation of human TS cells into EVT cells, including failure to activate their downstream gene regulatory network and migratory capacity. Invasive trophoblast cells of the rat placentation site similarly expressed PPARG. Invasive trophoblast cell-specific conditional inactivation of PPARG was used to assess the in vivo role of PPARG in placentation. PPARG was established as a cell-autonomous regulator of the invasive trophoblast cell lineage with profound effects on placentation, including effects on placental compartmentalization and the integrity and cellular composition of the uterine-placental interface.  In conclusion, PPARG is a conserved regulator of placentation and is essential for directing trophoblast cell-guided uterine transformation

overall_design: CT27 Trophoblast stem (TS- Okae et.al.) after 8 days of extravillous trophoblast cell diferentiation. 3 biological replicates each conditions (IP PPARG and Input)

first: Ayelen

last: Moreno-Irusta

first: Khursheed

last: Iqbal

first: Keting

last: Chen

first: Alex

last: Finlinson

first: Marc

last: Parrish

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Geetu

last: Tuteja

last: Soares


title: Peroxisome Proliferator-Activated Receptor Gamma Regulates Invasive Trophoblast Cell Differentiation and Hemochorial Placentation [RNA-seq]

overall_design: CT27 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PPARG (shPPARG) were used as treatment. RNA-seq was performed in control and treatment cells after 8 days of differentiaiton to extravilous trophoblast cells. 3 biological replicates each conditions (shPPARG and shSCR)

first: Michael


title: RASA3 inhibits Tc1 differentiation and attenuates anti-bacteria immunity by restricting the HCK kinase

city: wuhan

first: Jiayu

last: Song

address: wuhan

institute: WUHAN University

summary: Type I immunity is defined by IFN-γ secretion, with Tc1 cells as a key subset, yet their intrinsic negative regulators remain unclear. We identified RASA3 as a novel negative regulator of Tc1 cells. T cell-specific deletion of RASA3 enhanced Tc1 differentiation and antibacterial immunity. We further revealed the RASA3–HCK–STAT4 axis in the regulatoin of Tc1 cell generation.

overall_design: Naive CD8+ T cells, which were purified from spleen and lymph nodes, were cultured under Tc1  polarization conditions from WT and RASA3 KO Mice for 2 days. Then, RNA was extracted from the Tc1 cells.

first: Bing

last: Wu


title: Isoform-Specific Splicing of ANK2 by PTBP2 Orchestrates Retinal Pigment Epithelial-to-Neuron Fate Conversion

city: Chongqing

first: BINGLIN

last: ZHU

address: 313 Jinyue Road

institute: Jinfeng Laboratory

summary: Direct lineage reprogramming represents a promising strategy to convert somatic cells into functional neurons, offering potential for regenerative medicine. While transcription factor-based approaches have been extensively studied, the role of post-transcriptional regulation, particularly alternative splicing (AS), in neuronal fate acquisition remains poorly defined. Here, we demonstrate that the concurrent knockdown of the splicing regulator PTBP2 and the barrier protein p53 synergistically enhances the neuronal conversion of human retinal pigment epithelial (hRPE-19) cells when combined with ASCL1 and MiR-9/9*-124 (AMnp). Transcriptomic and splicing analyses reveal that PTBP2 depletion induces widespread AS changes, most notably promoting near-complete inclusion of exon 36 in the ANK2 gene, which encodes a key regulator of axon initial segment assembly. Functional assays confirm that the loss of exon 36 significantly impairs neuronal induction, establishing ANK2 isoform switching as a mechanistic requirement for reprogramming. Moreover, AMnp-reprogrammed neurons display upregulation of photoreceptor markers (RHO, L/M-opsin, and recoverin) and transcriptional signatures of epigenetic remodeling, suggesting that chromatin memory may interact with AS to influence subtype identity. These findings identify the PTBP2-ANK2 splicing axis as a molecular switch for RPE-to-neuron conversion, offering a novel isoform-level strategy to enhance the precision and efficiency of neuronal reprogramming.

overall_design: Transcriptomic profiling of induced neurons mediated by ASCL1, miR124-9/9*, p53 shRNA and PTBP2 shRNA at day 7 using human RPE-19 cells.

first: Wenxi

last: Ma

first: Jun

last: Li

first: Yanke

last: Zhang

first: Lan

last: Tang

first: Binglin

last: Zhu


title: EPAS1 knockdown in infantile hemangioma endothelial cells

city: Jinan

first: Zheren

last: Su

address: No. 324, Jingwu Road

department: Plastic and Cosmetic Surgery

institute: Shandong Provincial Hospital

summary: This dataset contains RNA-seq data from primary infantile hemangioma endothelial cells (HemECs) comparing EPAS1 knockdown and non-targeting control conditions. EPAS1 knockdown was associated with transcriptional changes related to cell cycle, DNA replication, and MYC/E2F-related signatures.

overall_design: RNA-seq profiling was performed using primary infantile hemangioma endothelial cells (HemECs) cultured under normoxic conditions. Samples were from two groups: sh-NC and sh-EPAS1 (n = 3 samples per group).

first: Ran

last: Huo


title: Mycobacteria infection induced cascade of epigenetic alterations promote training in bystander macrophages

city: Bangalore

first: Bharath

last: Saravanan

state: Karnataka

address: Bellary Road

department: Genetics and Development

country: India

institute: National centre for Biological Sciences

summary: Mycobacterium tuberculosis (Mtb) actively remodels host cell functions to promote its intracellular survival. Emerging evidence suggests that Mtb also significantly affects uninfected bystander cells within the host. However, the mechanisms underlying bystander cell modulation and their functional consequences during Mtb infection remain poorly understood. In this study, we show that Mtb infection alters the host epigenome, resulting in correlated gene expression changes not only in infected cells but also in bystander cells. We demonstrate that cytokines secreted by Mtb-infected cells, particularly interleukin-1 beta (IL-1β), mediate these epigenetic changes in bystander cells, creating an intracellular environment similar to that of infected cells. These epigenetic alterations in bystander cells lead to population-wide trained immunity, enhancing the response of both infected and bystander cells to subsequent secondary stimuli. Our findings provide a mechanism for the propagation of trained immunity in a cell population and highlight bystander cells as active participants in shaping the innate immune response to Mtb infection. Understanding these intercellular communications presents a new frontier for developing comprehensive strategies that target both infected and bystander cells to modulate the broader cellular and immune response to tuberculosis.

overall_design: Using ChIP-seq and RNA-seq , we establish that the major upregulated genes upon mycobacteria infection fall under the catergory of cytokines and growth factors

first: Varadharajan

last: Sundaramurthy

first: Dimple

last: Notani

first: Shah-e-Jahan

last: Gulzar

first: Ibrahim

last: Umar

first: Dhruv

last: Sheth

first: Umer

last: Farooq

first: Sahanawaz

last: Molla

first: Aditi

last: Ravikumar


title: DNA Methylation and Hydroxymethylation Profiles in Paneth cell from Germ-Free and SPF Mice

first: Dahui

last: Wang

summary: To assess epigenetic effects, Paneth cell–specific Nanopore sequencing was performed on germ-free (GF) and specific pathogen–free (SPF) mice. Our analysis reveals microbiome-driven changes in 5mC and 5hmC at key genetic loci involved in stemness regulation.

overall_design: Nanopore direct DNA-seq for FACS sorted Paneth cell from germ free and specific pathogen free mice.

first: Subhasree

last: Kumar


title: Comprehensive Expression Profiles of mRNAs, LncRNAs, and CircRNAs in Colon Specimens of Patients with Slow Transit Constipation

city: Suzhou

first: Shuai

last: Yan

state: Jiangsu

address: 18 Yangsu Road

institute: Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

summary: Slow transit constipation (STC) is a complication of depression, which can be commonly seen, that can have a negative impact on STC patients’ prognosis and quality of life. Nonetheless, the pathogenesis of STC is principally uncertain. In this work, colon tissues from STC and non-STC patients were utilized to identify transcriptome expression patterns (mRNAs, lncRNAs, and circRNAs) by high-throughput sequencing.

overall_design: This study comprised a total of 10 participants: 5 individuals diagnosed with STC who underwent subtotal colectomy, and 5 control subjects who underwent radical surgery for colon cancer.

first: Yanghui

first: Xiaopeng


title: Autophagy Inhibition Sensitizes Radiotherapy Responses in High-grade Mutant IDH1 Glioma

city: Ann Arbor

first: Maria

middle: G

last: Castro

state: MI

address: 1150 East Medical Center Drive

department: Neurosurgery

institute: University of Michigan Medical School

summary: Mutant isocitrate dehydrogenase 1 (mIDH1) catalyzes 2-hydroxyglutarate production which leads to epigenetic reprogramming in astrocytomas with TP53/ATRX loss. RNA-seq, scRNA-seq, and ChIP-seq analysis revealed that human and mouse mIDH1 gliomas exhibit downregulated gene ontologies (GOs) related to mitochondrial metabolism and upregulated autophagy-related GOs. Decreased mitochondrial metabolism was accompanied by decreased glycolysis, rendering autophagy a source of energy in mIDH1 gliomas. Mutant IDH1 glioma cells exhibited increased expression of autophagy-related proteins and enhanced LC3 I/II conversion, indicating augmented autophagy. Inhibiting autophagy in vivo by administration of synthetic protein nanoparticles encapsulating ATG7-siRNA sensitized mIDH1 glioma cells to radiation, resulting in tumor regression, long-term survival, and immunological memory. This work uncovered autophagy as a critical pathway for survival in mIDH1 gliomas and its inhibition elicits radiosensitivity in vitro in human and mouse mIDH1 glioma cells, and in vivo in mIDH1 models. Thus, autophagy inhibition emerges as an attractive therapeutic target for mIDH1 gliomas.

overall_design: We utilized a  patient-derived glioma cell culture SF10602, which retained the endogenous mutations in IDH1-R132H, ATRX and TP53 after adaptation to in vitro culture. In order to identify pathwaysaltered by mIDH1 inhibition in SF10602, we performed scRNA-seq by administering 5µM AGI-5198 every 2 days for 1 week.

first: Kaushik

last: Banerjee

first: Ziwen

first: Pedro

last: Lowenstein


title: A transcriptomic atlas of the parasitoid wasp Nasonia vitripennis across ploidy, sex, and tissue [RNA-seq WPL]

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

institute: Nanjing Agricultural University

summary: The parasitoid wasp Nasonia vitripennis is a major insect model for morphology, behavior, and genetics. It has haplodiploid sex determination: unfertilized eggs develop into haploid males and fertilized eggs develop into diploid females. Additionally, polyploids (diploid males, triploid females) occur in Nasonia, representing gene expression mechanisms regulating sexual maintenance outside of standard haplodiploidy. Here, we generated a transcriptomic atlas for N. vitripennis across two tissues (head and abdomen) for typical haploid males and diploid females and polyploid diploid males and triploid females. These data are a resource for analyses on transcriptomic differences across sex, tissue type, ploidy, strain, and temporal change.

overall_design: Whiting Polyploid Line, WPL is a spontaneously arisen polyploid line. For transcriptome sequencing, both head and abdomen tissues of females (diploid and triploid) and  males (haploid and diploid) were sampled.

first: Kelley

last: Leung


title: BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

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

overall_design: Refer to individual Series


title: A transcriptomic atlas of the parasitoid wasp Nasonia vitripennis across ploidy, sex, and tissue [RNA-seq WOM]

overall_design: The WOM line is an artificially induced neo-polyploid line, resulted from knocking down wasp-overruler-of-masculinization (wom). For transcriptome sequencing, diploid and triploid females from generations F2 and F14, and haploid and diploid males from generations F3 and F15 were used. Both head and abdomen tissues were sampled.


title: Transcriptome of MLL-AF9 blast sensitive and resistant to chemotherapy

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: Chemotherapy resistance in acute myeloid leukemia (AML) remains a significant challenge, and understanding its molecular basis is crucial. Using multi-omic profiling and in vivo functional genomics, we identified splicing perturbations as a major determinant of chemoresistance in AML. We pinpointed a splicing-associated network involving the splicing regulator SRRM1 and two kinases, CLK and PAK1, as critical vulnerabilities in chemoresistant AML cells. Both kinases are hyperactivated in chemoresistant AML cells and we discovered a point variant in PAK1, c.1429G>T p.(Ala477Ser), that conferred resistance to chemotherapy in a patient undergoing relapse post-treatment. Combinatory inhibition of PAK1 and CLK kinases exhibited partially similar splicing perturbations to SRRM1 loss, preferentially targeting chemoresistant AML cell lines, primary cells, and multiple mouse models of AML and potentiating anti-leukemic effects of chemotherapy. Our study provides a new therapeutic rationale for targeting this splicing network to circumvent AML patient relapse and maximize the therapeutic benefit of chemotherapy.

overall_design: Total RNA from chemotherapy resistant and chemotherapy sensitive murin MLL-AF9 blasts was extracted to generate TruSeq libraries that were sequenced on HiSeq2500 to assess for transcriptome variations.

first: Alexandre

last: Puissant


title: Transcriptome changes in Grin2b-C456Y-mutant mice with foot-shock stimulation

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Grinb-C456Y-mutant mice show behavioral sensory hypersensitivity, including exaggerated response to electric foot shock. To illustrate the molecular mechanisms underlying the hypersensitivity, we conducted RNA-sequencing and found out that foot-shock stimulation futher increases the genotypic difference in the gene expression pattern.

overall_design: Transcriptome analysis of foot-shock treated Grin2b heterozygous and wild-type mice at adult ages

first: Wangyong

last: Shin

first: Gina

last: Lee

first: Hyojin

last: Kang


title: Transcriptomic changes in Grin2b-C456Y-mutant mice with NMDAR activation

summary: Our previous study reported a Grin2b-mutant mouse line carrying a point mutation identified in individuals with ASD (Grin2b+/C456Y mice), which show suppressed long-term depression and anxiolytic-like behavior that are responsive to early chronic D-cycloserine (DCS) treatment (postnatal day 7 to 16) for pharmacological activation of NMDARs. To figure out the rescue mechanism, we attempted RNA-Seq analysis of wild-type (WT) and Grin2b+/C456Y mice that are early and chronically treated with vehicle and DCS.

overall_design: Transcriptome analysis of DCS-treated Grin2b heterozygous and wild-type mice at P17 ages


title: Longitudinal whole transcriptomic profiling of live cells through domain adaptation

status: Public on Jul 08 2026

city: Toronto

first: Gregory

last: Schwartz

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

summary: Tracking transcriptomic profiles of cells over time in response to developmental cues and environmental stimuli can reveal critical insights into the fundamental mechanisms of development and disease. However, longitudinal molecular profiling at the global tran- scriptome level remains a major challenge, as RNA sequencing fundamentally alters or destroys cells. To overcome these limitations, we developed PENNE, a deep-learning framework that infers whole-transcriptomic profiles directly from live-cell images. Using gated attention mechanisms, PENNE trains on spatial transcriptomic datasets to align morphological features with gene expression. To enable inferences from images, our model performs domain adaptation to eliminate discrepancies between stained and unstained tissue images, effectively transferring molecular information from tis- sue sections to live-cell imaging. PENNE accurately identifies cell-type-specific and radiation-response markers via imputed expression. Furthermore, using only live-cell images stained with a G2/M cell cycle marker, our model captures temporal gene dynamics, evidenced by strong correlations between predicted expression and both ground-truth cellular confluency and cell-cycle progression. By bridging the gap be- tween data-rich spatial transcriptomics and the practicality of live-cell imaging, PENNE provides a powerful new framework for monitoring molecular temporal dynamics di- rectly through morphological information. This approach enables a paradigm-shifting workflow, fusing transcriptome-wide data with live-cell microscopy to fuel the discovery of novel gene programs via scalable, non-invasive, real-time interrogation of cellular states.

overall_design: We established a validation dataset using MCF10A and HCT116 cell lines. We cultured H2B-GFP-expressing MCF10A cells (ATCC, CRL-10317) in 1:1 mixture of F12:DMEM media supplemented with 5% horse serum (Wisent Bioproducts, 098150), 20 ng/mL human EGF (Cedarlane Labs, AF-100-15), 0.5 mg/mL hydrocortisone (Sigma-Aldrich, H0888), 100 ng/mL cholera toxin (Sigma-Aldrich, C8052), and 10 mg/mL recombinant human insulin (SAFC, 91077C). We also cultured unlabeled HCT116 p53-null cells in McCoy’s 5A medium, and 10% fetal bovine serum. All media were supplemented with 1% penicillin-streptomycin. We then analyzed H2B-GFP-expressing MCF10A cells and unlabeled HCT116 p53-null cells both as monocultures and as a 50-50 mixed co-culture under non-irradiated (NIR) and 10 Gy irradiated (IR) conditions, with three biological replicates per group. We harvested the total RNA at 72 hours post-irradiation using TriZol reagent (Life Technologies, 15596018) for poly(A)-selected mRNA-seq using NovaSeq X Plus paired-end 150-bp sequencing (Novogene). We obtained an average of 20 million reads per sample across 18 samples (3 replicates for each of the 6 conditions: MCF10A NIR, MCF10A IR, HCT116 NIR, HCT116 IR, 1:1 MCF10A:HCT116 NIR, and 1:1 MCF10A:HCT116 IR).

first: Zhi Fei

last: Dong

first: Shreya

last: Mishra

first: Maha Mohamed

last: Tageldein

first: Chris

last: McIntosh

first: Shane

last: Harding

middle: W


title: Determining the Translational Potential of Human Pericardial Fluid to Improve Clinical Outcomes in Cardiac Surgery

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

summary: The pericardial space, which contains pericardial fluid (PF), maintains homeostatic conditions that facilitates optimal heart function. PF can carry biomarkers for different cardiac diseases. PF can also play a central role in delivering targeted therapeutics. The loss of PF during surgery perturbs the equilibrium of this environment, contributing to postsurgical complications, including postoperative pericardial adhesion formation (PPAF) and postoperative atrial fibrillation (POAF), both of which involve immune-mediated pathways. We have yet to fully understand the exact pathophysiology of these adverse events. This study aimed to establish the immune profile of human PF, determine whether specific markers can drive inflammatory processes, such as fibrosis, and elucidate the underlying mechanisms that can result in such phenomena.

overall_design: PF was collected from patients undergoing elective cardiac surgery. Multiplex analysis was performed on the PF to determine the composition of inflammatory chemokines, cytokines, growth factors, matrix metalloproteinases (MMP), and tissue inhibitors of matrix metalloproteinases (TIMP). To explore the source of these mediators, multiplex analysis was conducted on cultured media from the pericardium, right atrial appendage, and pericardial adipose tissue. Mass spectrometry revealed the proteomic content of PF. Collagen gel contraction assay was used to investigate the fibrotic potential of PF. RNA-sequencing was used to elucidate the mechanisms driving the pro- or anti-fibrotic properties of PF. Single-cell RNA-sequencing was performed on the PF cells. Collagen gel contraction was also used to assess the impact PF cells have on human cardiac fibrosis in vitro. Enrichment studies and trans-well experiments were performed to identify the role of specific cell subpopulations and potential paracrine mechanisms. Proteomic analysis was also done using PF cells.

first: Ali

last: Hassanabad

first: Nicole

last: Rosin

first: Sarthak

last: Sinha

first: Elodie

last: Labit

first: Arzina

last: Jaffer

first: Justin

last: Deniset

first: Paul

last: Fedak


title: Sturgeon Cartilage–Derived Peptides Promote Cartilage Repair-Associated Responses in Osteoarthritis via Integrin αvβ3–PI3K/Akt Signaling

city: Qingdao

first: yinghuan

last: jing

address: No. 238, Songling Road, Laoshan District

department: College of Food Science and Engineering

institute: Ocean University of China

summary: Osteoarthritis (OA) features progressive cartilage loss with no effective regenerative therapies. This study investigated sturgeon cartilage peptides (SCPs) for OA repair and identified key bioactive peptides and mechanisms. SCPs, prepared by trypsin hydrolysis, were evaluated in in vitro and in vivo OA models. SCPs markedly improved cartilage damage, reduced matrix degradation, and increased chondrocyte proliferation to 126%.

overall_design: Multi-omics and docking analyses revealed integrin αvβ3-mediated PI3K/Akt pathway activation as the core mechanism, and four bioactive peptides were screened, they promoted S/G2 cell-cycle progression, reducing IL-1β–induced apoptosis from 33% to 19–28%, and restored Col2A1 and proteoglycan synthesis, Mechanistically, these effects occurred via binding to integrin αvβ3 and upregulation of αV, β3, PI3K, AKT, SOX9, and CCND1, and were abolished by Cyclo(-RGDfK). Therefore, SCPs improve the OA phenotype by promoting synthesis and repair responses through the αvβ3-PI3K/Akt pathway, and GDR6 (GDFGER) is a lead peptide, providing insights for marine peptide-based OA treatment.

first: Yinghuan

last: Jing


title: Satb1

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine


title: RAI1 safeguards fidelity and tempo of human neurodevelopmental gene expression.

first: Shigeki

last: Iwase

address: 1241 E. Catherine St., 5815 Medical Science II

department: Department of Human Genetics

summary: Human brain development proceeds on an unusually long timeline, fostering the species' cognitive advantages. Retinoic Acid Induced 1 (RAI1) gene encodes a nucleosome-binding protein haploinsufficient in Smith–Magenis Syndrome (SMS), a neurodevelopmental disorder characterized by cognitive deficits with autistic features. However, the role of RAI1 in human neurodevelopment remains unexplored experimentally. Here, we generated isogenic heterozygous and homozygous RAI1 loss-of-function human embryonic stem cell lines and interrogated the roles of RAI1 in neurodevelopmental gene regulation. A longitudinal transcriptome study during in vitro cortical development revealed that RAI1 deficiency accelerates developmental transcriptome progression, as indicated by the induction of synaptic genes. Single-cell RNA-seq analysis revealed that RAI1-deficient neuroprogenitors acquire a transient mesoderm-like gene expression signature followed by pro-neuronal maturation gene expression in postmitotic neurons. Unexpectedly, the developmental acceleration signature was exacerbated during NGN2-induced excitatory neuron differentiation, suggesting functional interplay between RAI1 and NGN2-driven programs. Together, these results identify RAI1 as a suppressor of the mesodermal lineage program and as a novel brake that slows the tempo of human neurodevelopmental gene expression.

overall_design: Bulk mRNA-seq was performed on newly generated mouse embryonic stem cell samples and DIV7 cortical neuron cultures prepared from E16.5 mouse embryos. These samples represent pluripotent and mature neuronal reference states, respectively. The new RNA-seq data were analyzed together with public Kasper et al. mouse ESC-derived NPC/neuron RNA-seq data to place Rai1-deficient mouse cells within a developmental PCA trajectory. Additional public ENCODE postnatal mouse cortex data and public Huang et al. Rai1 conditional knockout cortex data were used for separate analyses of in vivo neuronal maturation.

first: Bo

last: Zhou

first: Paris

last: Riggle

first: Michael

last: Sutton

first: Satabdi

last: Mohanty

first: Louis T.

last: Dang


title: On the state of chromatin in mammalian sperm

city: Atlanta

first: Katerina

last: Tsimaratou

state: GA

address: Whitehead Biomedical Research Building,615 Michael Street

department: Human Genetics

institute: Emory Univeristy

summary: Mammalian sperm chromatin carries epigenetic information with the potential to influence offspring phenotype, making its faithful characterization essential. It has been suggested that cauda sperm preparations are contaminated by somatic chromatin, that this contamination dominates genome-wide profiles, and that valid results require pretreatment with somatic cell lysis buffer (SCLB), DNase I, and dithiothreitol. Here we show that properly purified cauda sperm contain no detectable somatic cells or cell-free DNA and that this pretreatment disrupts sperm chromatin organization. SCLB permeabilizes the sperm nucleus, allowing DNase I to fragment the sperm genome in situ, while DTT treatment causes chromatin to leak out of the nucleus. Using ATAC-see, we further demonstrate that Tn5 transposase can access intact protamine-condensed sperm chromatin without DTT, refuting the premise that profiles from untreated sperm reflect contamination. Pretreatment therefore damages the chromatin it claims to purify, and published profiles of untreated cauda sperm are valid and require no systematic re-examination.

overall_design: Genome binding/occupancy profiling by high throughput sequencing

first: Victor

last: Corces


title: Macrophage-Derived IL-18 Drives M1 Polarization via IFN-γ/JAK1-STAT1 Axis to Promote Myocardial Injury in Fulminant Myocarditis

city: Wuhan

first: Jin

last: Wang

address: 1095# Jiefang Ave.

institute: Huazhong University of Science and Technology

summary: Fulminant myocarditis (FM) is a rapid, severe form of myocarditis requiring urgent mechanistic insight. While anti-interleukin-18 (IL-18) antibodies show promise in other inflammatory diseases, IL-18’s role in FM remains unknown. Here, we found that plasma IL-18 levels in FM patients negatively correlated with ejection fraction and positively with NT-proBNP. Elevated IL-18 was confirmed in a coxsackievirus B3 (CVB3)-induced murine FM model, with macrophages identified as the primary cellular source. Exogenous IL-18 promoted M1 macrophage polarization without affecting cardiomyocytes or fibroblasts. Neutralizing IL-18 antibodies (IL-18nAbs) suppressed M1 polarization and chemokine secretion in vitro, and improved survival, reduced myocardial M1 infiltration, and preserved cardiac function in vivo. Mechanistically, IL-18 activated the JAK1-STAT1 axis in macrophages; STAT1 silencing abrogated IL-18-driven M1 polarization. IL-18 also induced IFN-γ, and IFN-γ neutralization blocked Stat1 and Nos2 upregulation. Myeloid-specific IL-18R1 deletion alleviated CVB3-induced cardiac dysfunction and inflammation. Collectively, IL-18, primarily from macrophages, drives FM progression via JAK1-STAT1, representing a key pathogenic factor and therapeutic target.

overall_design: Primary BMDMs were stimulated with rIL-18 (100 ng/mL, Sigma) for 24 h, and RNA-seq was performed on control and treated groups. Three biological replicates per group were included.

first: Zheng

last: Wen

first: Chen

last: Chen

first: Daowen


title: p300/CBP inhibition promotes apoptosis in mouse embryos by impairing H1K75ac-mediated DNA repair from the 4-cell to blastocyst stage

first: Nannan

last: WANG

state: Hubei Province

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Defective pre-implantation embryonic development is a major cause of implantation failure and early embryonic arrest. p300/CBP is known to influence blastocyst formation; nevertheless, its molecular regulatory cascades mediating murine embryonic development from the 4-cell to blastocyst stage are poorly understood. Here, we show that pharmacological inhibition of p300/CBP markedly reduced morula and blastocyst rate, increased embryonic fragmentation, and disrupted markers of compaction, polarization, and first lineage segregation from the 4-cell to blastocyst stage. Smart-seq2 analysis showed that differentially expressed genes were enriched in pathways related to apoptosis, cell-cycle regulation, DNA modification, and embryonic development. Consistently, immunofluorescence analyses showed that p300/CBP inhibition increased apoptosis, suppressed cell proliferation, and promoted DNA damage accumulation. Mechanistically, p300/CBP inhibition reduced histone H1 lysine 75 acetylation (H1K75ac), leading to impaired DNA repair and subsequent activation of p38 signaling, thereby triggering apoptosis. Collectively, our findings identify a p300/CBP-H1K75ac-DNA repair-p38 MAPK signaling axis that maintains genome integrity and developmental competence in mouse pre-implantation embryos.

overall_design: A485 (HY-107455, MCE) was dissolved in dimethyl sulfoxide (DMSO; 60313ES60, Yeasen, China) and diluted in KSOM to a final concentration of 2 μM. Embryos in the control group were cultured in KSOM containing 0.1% DMSO from the 4-cell  to blastocyst stage, whereas embryos in the treatment group were cultured in KSOM containing 2 μM A485 from the 4-cell  to blastocyst stage.

first: Qianhui

last: Zeng

first: Rong

last: Zheng


title: scRNAseq of LCMV-specific P14 cells: WT, P2RX7-KO and NKG7-KO

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

department: Immunology

institute: Mayo Clinic Arizona

summary: We have used Parse Biosciences to generate single-cell RNAseq libraries from P14 CD8+ T cells (wild-type - WT, P2RX7-KO and NKG7-KO) collected from mice infected with either LCMV-Armstrong or LCMV-Clone 13 (days 0, 7 or 30 post-infection). The goal of this study was to determine the transcriptional alterations in memory or exhausted CD8+ T cells driven by the absence of either P2RX7 (a purinergic receptor that senses extracellular ATP) or NKG7 (a metabolic regulator that can downregulate mTORC1 and simultaneously induce cytotoxicity).

overall_design: Following adoptive transfer of WT, P2RX7-KO or NKG7-KO P14 cells and infection with either LCMV-Armstrong or LCMV-Clone 13, P14 cells were isolated from spleens of infected mice via FACS sorting, and analyzed by scRNAseq. OBS: Parse Biosciences libraries mix all samples together and barcodes representing each sample sublibrary can be identified using further analyses (split-pipe file has a guideline).

first: Salgado

last: Caio L.

first: Borges da Silva

last: Henrique


title: RAI1 safeguards fidelity and tempo of human neurodevelopmental gene expression

first: Shigeki

last: Iwase

overall_design: Bulk RNA sequencing was performed to investigate the effect of RAI1 loss on gene expression during human cortical neurodevelopment. Isogenic wild-type (RAI1+/+), heterozygous (RAI1+/-), and homozygous (RAI1-/-) CRISPR-edited H9 human embryonic stem cell lines were differentiated into cortical neurons using a dual-SMAD inhibition protocol. Cells were collected at four developmental stages (day 0, day 20, day 34, and day 60) to capture pluripotent, neural progenitor, and neuronal differentiation stages. Two independent clones per genotype were analyzed with biological duplicates at each time point. Bulk RNA sequencing was performed to compare temporal gene expression changes associated with RAI1 deficiency during cortical development.

first: Bo

first: Louis

middle: T


title: RAI1 safeguards fidelity and tempo of human neurodevelopmental gene expression [scRNA-Seq]

overall_design: Single-cell RNA sequencing was performed to investigate the impact of RAI1 deficiency on human cortical neurodevelopment. Isogenic wild-type (WT), heterozygous (RAI1+/−), and homozygous (RAI1−/−) CRISPR-edited H9 human embryonic stem cell (hESC) lines were differentiated into cortical neurons using a dual-SMAD inhibition protocol. Cells were collected at differentiation days 20 and 60 to capture neural progenitor and neuronal maturation stages. Fixed cells were profiled using the 10x Genomics Chromium Fixed RNA Profiling (Flex) platform. Sequencing libraries were generated according to the manufacturer's protocol and sequenced on an Illumina NovaSeq 6000. Downstream analyses included quality control, clustering, cell-type annotation, differential gene expression, pseudobulk analysis, and pseudotime trajectory analysis to determine how RAI1 deficiency affects lineage specification and neurodevelopmental gene expression.

last: Zhou

first: Satabdi

first: Paris


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [RNA SCIENCE]

city: Boston

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

summary: The human genome is pervasively transcribed into protein-coding and regulatory non-coding RNAs whose functions are coordinated within higher-order nuclear architectures. However, direct mapping of RNA–RNA and DNA–DNA interaction networks in complex human tissues at single-cell resolution has remained a major challenge. Here, we present SCIENCE-seq, a multimodal single-cell interactomics platform enabling simultaneous detection of RNA–RNA interactions and chromatin DNA–DNA contacts within individual cells. Applied to primary glioma specimens, SCIENCE-seq reveals cancer-specific interactions organized by lncRNAs and centered on key oncogenic drivers, including EGFR, hTERT, SOX2, CDK6, CDC42, CD47, and HOX loci. These datasets uncover previously unrecognized molecular relationships between premature lncRNAs and pre-mRNAs that regulate transcription, alternative splicing, and polyadenylation. Notably, we identify a glioma-specific trans-chromosomal HOX hub driven by five interacting lncRNAs. Targeting these RNA and DNA interactions with steric antisense oligonucleotides (ASOs) or CRISPRi enables selective inhibition of oncogenic programs in malignant cells while sparing normal tissue, establishing chromatin interactomes as actionable therapeutic targets.

overall_design: RNA-RNA interactomics (RNA SCIENCE) technique was applied to primary glioma tumors to profile RNA-RNA interactions between glioma oncogenes and glioma-specific lncRNAs.


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scBarcode sequencing]

overall_design: Barcode Uptake was quantified with scBarcode-seq in human brain organoids.


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids]

overall_design: polyA mRNA scRNA-seq was performed on human brain organoids.


title: CD300A drives glioblastoma progression by orchestrating M2 macrophage polarization via the JAK2/STAT3 signaling axis

city: Taiyuan

first: Fengjing

address: 56 Xinjian South Road, Yingze District, Taiyuan, Shanxi, 030001, China

institute: 山西医科大学

summary: Glioblastoma (GBM) is the most lethal primary intracranial malignancy, characterized by aggressive recurrence and a dismal prognosis. Despite the implementation of multimodal standard-of-care therapies, including maximal surgical resection, radiotherapy, and chemotherapy, clinical outcomes remain unsatisfactory. A critical determinant of therapeutic resistance is the highly immunosuppressive tumor microenvironment (TME). Tumor-associated macrophages (TAMs), which constitute 30-50% of the tumor mass, are the predominant immune population within the TME and key orchestrators of GBM-associated immunosuppression. While TAMs predominantly acquire a protumoral M2-like phenotype to facilitate tumor progression via the secretion of cytokines, angiogenic factors, and matrix metalloproteinases, the molecular mechanisms governing this polarization remain elusive. Herein, we identify the immunoregulatory receptor CD300A as a critical driver of M2 macrophage polarization in GBM. Analysis of clinical specimens demonstrated that CD300A is significantly upregulated in GBM tissues and positively correlates with the M2 marker CD163. In a macrophage model, we found that upon M2 induction, CD300A expression was markedly upregulated, paralleling the induction of canonical M2 markers, including CD206 and Arg-1. Functionally, ectopic overexpression of CD300A markedly upregulated canonical M2 markers CD206, Arg-1, and FIZZ1, whereas CD300A knockdown attenuated this phenotype. Mechanistically, we demonstrate that CD300A promotes M2 polarization by activating the JAK2/STAT3 signaling axis. Furthermore, CD300A-mediated M2 polarization was found to enhance the proliferation, migration, and invasion of GBM cells via the induction of VEGFA secretion. Collectively, our findings delineate a novel CD300A-JAK2/STAT3-VEGFA signaling axis that couples immune modulation with malignant progression, highlighting CD300A as a potential therapeutic target for modulating TAMs in GBM.

overall_design: To investigate the transcriptional regulatory effects of CD300A overexpression on THP-1 cells, total RNA was extracted from THP-1 cells transfected with either the empty vector (vector group) or the CD300A-overexpressing construct (oeCD300A group), and subsequently subjected to high-throughput RNA sequencing (RNA-seq) to compare the global gene expression profiles between the two groups.

first: Chunfa

last: Wu

first: Ying

last: Shao

first: Xile

last: Pei

first: Boyuan

last: Zhang

last: Sui

first: Tao

last: Yang

first: Dahai

last: Wan


title: Pannexin 1 inhibition reduces tumorigenic properties of patient-derived glioblastoma cells through the HIPPO and Wnt signalling pathways

city: London

first: Silvia

last: Penuela

state: Ontario

address: 1151 Richmond St DSB00066

institute: University of Western Ontario

summary: Glioblastoma (GBM) is the most common primary brain tumour, with a median survival of 12-18 months, highlighting a need for new treatment targets. We observed that pannexin 1 (PANX1), a channel-forming glycoprotein important in purinergic signalling, is upregulated in GBM compared to normal tissue and expressed throughout patient tumours. Western blot analysis of patient-derived GBM cell lines revealed significantly increased PANX1 expression in these primary lines compared to brain tissue and control glial cells. Immunofluorescent staining indicated mostly intracellular localization of PANX1 in GBM cells. Bulk RNA-sequencing compared the gene expression of GBM cells devoid of PANX1 via CRISPR/Cas9 deletion (PANX1-KO) compared to controls. Gene Ontology and KEGG gene set analyses revealed PANX1-KO in GBM cells affects cell surface and cell junction components, processes, and pathways, including the HIPPO pathway, in addition to critically downregulating β-catenin mRNA and other components of the Wnt pathway. The deletion of PANX1 resulted in a disruption of the β-catenin protein and a dramatic reduction in migration and cell growth. Pharmacological inhibition of PANX1 in GBM cells with Probenecid (PBN) and Spironolactone (SPIR) demonstrated a significant reduction in live cell numbers and migration via scratch assay. The intracellular PANX1 staining was unaffected by channel inhibition; however, both blockers dramatically decreased F-actin filament formation. PANX1 and b-actin protein levels remained unchanged with blocker treatment, but the cellular localization of b-catenin became more intracellular compared to controls upon drug treatments. Xenografted GBM tumours grown on a chick chorioallantoic membrane model showed a reduction in tumour cell viability by bioluminescent imaging and reduced hemorrhaging incidence when treated with PBN. PBN-treated tumours had reduced pro-inflammatory IL-8 mRNA expression, a cytokine involved in vascular leakage. We provide evidence that PANX1 is upregulated in GBM, and PANX1 inhibition or deletion reduces several tumorigenic properties of GBM cells across multiple model systems. These new insights support further investigation of PANX1 as a potential GBM therapeutic target and its role in multiple cancer signaling pathways that regulate this devastating disease.

overall_design: RNA-seq profiling of patient derived glioblastoma cells with and without PANX1 knocked out. 3 controls samples (G9, G11, H5) and 3 PANX1-KO samples (BC12, BD6, BG1)

first: Danielle

last: Johnston


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [DNA SCIENCE]

overall_design: DNA-DNA interactomics (DNA SCIENCE) technique was applied to primary glioma tumors to profile DNA-DNA interactions between glioma oncogenes and glioma-specific lncRNAs.


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [GRO-Seq]

overall_design: bulk GROseq were performed in NHA followed by treatment with all-trans-retinoic acid.


title: RAI1 safeguards fidelity and tempo of human neurodevelopmental gene expression [RNA-seq]

overall_design: RNA-seq profiling of WT, RAI1+/−, and RAI1−/− H9-derived iNeurons at Day 0, Day 3, and Day 7 of NGN2-induced neuronal differentiation.

last: Mohanty

last: Riggle

first: Grace

last: Lin

first: Louis T.

last: Dang

first: Michael

last: Uhler


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [4C-Seq]

overall_design: Bulk 4Cseq was used to detect and quantify DNA-DNA interactions between promoters of HOTAIRM1, HOXB-AS1, HOTAIR, HOXD-AS2 and LINC01116 lncRNAs and the rest of the genome in Glioma stem cells (GBM8) or Normal Human Astrocytes (NHA).


title: Forced Notch2 signaling instructs TLR and BCR responsiveness in B cells [RNA-Seq]

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary: Marginal zone (MZ) B cells optimize protection against blood-borne bacteria by rapidly producing plasma cells in response to Toll-like Receptor (TLR) ligands. Here, we demonstrate that forced Notch2 instructs this responsiveness for Notch2-independent follicular B cells. Upon stimulation with either TLR4 ligand LPS or B cell receptor crosslinking via anti-IgM, access to Notch2 ligands promoted early transcriptional changes to numerous activation programs. These changes include augmenting TLR response programs, early and late mitotic pathways, and key cell growth and protein secretion pathways critical for plasma cell differentiation. We conclude that t uniquely robust hyper-responsiveness can be ascribed to any B cell with access to Notch2 ligands.

overall_design: Purified FO B cells from Blimp1-GFP+ mice were cultured for 20, 44, or 68 hours on OP9 or OP9-DL1 monolayers alone or with 10 ug/mL LPS or anti-IgM. At the end of culture, cells were removed from the plate and sort purified for viability directly into Trizol with 0.5% 2-ME and held at -80°C until RNA preparation. RNA was prepared by published Trizol RNA-extraction protocol (Thermo-Fisher Scientific). RNA was co-precipitated using glycogen as a carrier. RNA was quantified using Qubit RNA high sensitivity flurometric assay. cDNA was prepared using Takara Clonetech SMART-Seq v4 Ultra Low Input RNA kit according to protocol using 500-1000 ng RNA as input. cDNA was quantified using HSDNA assay on Agilent 2200 bioanalyzer. RNA-seq libraries were constructed using the Illumina Nextera XT kit with 150ng cDNA input. Libraries were quality controlled and quantified by bioanalyzer and pooled at equal molar ratio preceding sequencing with Illumina Hiseq (50bp SE v4 high output) and Illumina Nextseq500 (75 bp SE v2) machines.

first: Jennifer

last: Londregan

first: Isaiah

last: Rozich

first: Sarah

last: Naiyer

first: David

last: Allman


title: A non-enzymatic role for METTL3 as an Androgen Receptor co-regulator promoting prostate cancer proliferation.

city: Maywood

first: Steven

last: Kregel

state: IL

address: 2160 S. First Avenue

department: Cancer Biology

institute: Loyola University Chicago

summary: Metastatic prostate cancer (PCa) continues to be a major cause of death in males, despite advances in treatment. Most treatment focuses on targeting the Androgen Receptor (AR), the main oncogene responsible for driving most tumors, and despite these therapies targeting AR, majority of patients still succumb to AR-driven disease. Therefore, there is a critical need for understanding how AR functions to promote prostate cancer growth and identify alternative therapeutic targets in AR-driven PCa. One avenue garnering attention is targeting epigenetic regulators that promote AR-activity, however, the importance of epitranscriptomic regulators is less understood. Here, we identify a new role for the key catalytic subunit of the RNA N6-methyladenosine (m6A) transferase complex, METTL3, as an AR-coregulator. METTL3 is overexpressed in prostate tumors compared to normal tissue, and METTL3 protein is elevated in AR-expressing cell lines. Depletion of METTL3 significantly reduces proliferation of cancer

overall_design: ChIP-sequencing experiemnts on AR and METTL3 proteins in LNCaP PCa cells with a dox-inducible METTL3-targeted shRNA knockdown, +/- AR pathway activation (EtOH/R1881)

first: Kregel

last: Steven

first: Kostlan

last: Raymond J

first: Phoenix

last: John T


title: Differential chromatin accessability in follicular B cells, marginal zone B cells and newly formed plasma cells. [ATAC-Seq]

summary: Marginal zozne B cells are poised to rapidly differentiate into plasma cells through biochemical pathways activated by Notch2 signaling. We sought to determine differences in chromatin accessability at plasma cell program-relevant loci between these cells and follicular B cells also located within the spleen but less receptive to Notch signaling. To ths end, we prepared ATAC-seq libriaries from steady state marginal zone and follicular B cells as well as newly formed plasma cells generated in Blimp1GFP/+ reporter mice 4 days post immunization with LPS.

overall_design: Fifty thousand follicular B cells (CD19+, CD93-, CD23+, CD21int) and marginal zone B cells (CD19+, CD93-, CD23-, CD21high) were sorted from individual C57BL6 animals. Fifty thousand plamsa cells (IgD-, lineage[CD4, CD8a, F4/80, Ter119]-, CD138+, GFP(Blimp1)+) were sorted from B6.Blimp1GFP/+ mice 4 days after immunization with 50 ug LPS i.p. Samples are coded by experimenal day and mouse number (eg. 83-1). ATAC-seq libraries were prepared by published protocol (Buenrostro et al Curr Protoc Mol Biol 2015) with minor modificaitons.


title: A guardian role of TagA in protecting Mycobacterium tuberculosis from nitrosative killing

city: Shanghai

first: Ruiqing

last: Ma

address: 2901 Caolang Rd., Jinshan District

institute: Shanghai Public Health Clinical Center

summary: Upon activation, macrophages generate substantial levels of reactive nitrogen species (RNS), which can induce alkylating damage in the DNA of intracellular Mycobacterium tuberculosis (Mtb) and thereby restrict bacterial replication. However, the molecular mechanisms by which Mtb repairs such DNA lesions remain poorly understood. Here, we identified genes required for Mtb survival in distinct macrophage subsets using transposon insertion sequencing (Tn-seq). Among these, tagA displayed a specialized role in Mtb survival in M1-polarized macrophages, as well as in mice at 4 weeks post-infection, a stage when macrophages are biased toward an M1-polarized state. Mechanistically, TagA conferred resistance to the DNA alkylating agent methyl methanesulfonate (MMS) through its 3-methyladenine (3-MA) excision activity, and substrate binding in Mtb depended on the conserved catalytic residue Glu48. Critically, TagA was found to inhibit the alkylated damage to Mtb genome from nitrosative stress characteristic of M1 polarized macrophages. Furthermore, pharmacological inhibition of iNOS with S-methylisothiourea sulfate (SMT) in mice or genetic deletion of nos2a in zebrafish markedly rescued the survival defect of ΔtagA, further supporting that this phenotype is primarily driven by host nitrosative stress. Together, these findings reveal a previously unappreciated mechanism by which the DNA repair enzyme TagA protects Mtb against 3-MA DNA damage under nitrosative stress, thereby promoting bacterial survival in M1-polarized macrophages and during in vivo infection.

overall_design: We constructed a transposon mutant library in Mycobacterium tuberculosis H37Rv that covered 49,821 TA sites, corresponding to 66.8% of all TA sites (74,604) in the genome.The H37Rv transposon mutant library was then used to infect M0, M1, and M2 macrophages

first: Ying

last: Zhang

first: Hao

last: Wang

first: Yatong

last: Liu

first: Ziyao

last: Qin

first: Xiao-yong

last: Fan