title: Effect of over expression RGS6e forward and RGS6e Reverse on gene expression of SK-N-SH cells (Human neuroblastoma cell line)

status: Public on Dec 07 2025

first: Zhongju

last: Wang

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

summary: As fundamental units of transcriptional regulation, enhancers also produce transcriptional products known as enhancer RNAs (eRNAs), whose expression levels reflect their activity. Recently, more studies have demonstrated the function of eRNAs. Therefore, it is important to elucidate the relationship between enhancers and schizophrenia for a deeper understanding of the molecular mechanisms underlying schizophrenia. We here report the enhancer activity and the expression products of RGS6e may contribute to decrease schizophrenia risk. we found that the unregulated genes of over-expression RGS6e  are significantly enriched in psychiatric disorders, suggesting that RGS6e may regulate the expression of nervous system-related genes through trans-acting mechanisms. Taken together, our data supported the notion that RGS6e may impact susceptibility to SZ through trans-acting effects.

overall_design: RNA-seq profiling of over-expression RGS6e Forward and RGS6e Reverse, and their corresponding empty vector in SK-N-SN cells.


title: TP53 Mutation is a Prognostic Biomarker for Patients with Advanced RAS Wild-Type Colorectal Adenocarcinoma Treated with Cetuximab and Pembrolizumab [dataset 2]

status: Public on Dec 04 2025

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

country: USA

institute: Roswell Park Comprehensive Cancer Center

summary: Immunotherapy with checkpoint inhibitors targeting the PD1/PD-L1 and CTLA4 pathways has limited activity in patients with microsatellite stable (MSS) colorectal adenocarcinoma (CRC). In a prior study, the combination of cetuximab and pembrolizumab failed to improve outcomes for patients with advanced RAS wild-type (RASwt) CRC. In this post hoc secondary analysis, we show that patients with TP53 mutant (p53mt) tumors had significantly higher progression-free survival (PFS) and decrease in tumor burden compared to patients with TP53 wild-type (p53wt) tumors. The gene set enrichment analysis showed uniform upregulation in several metabolic gene sets and most immune gene sets including NK-mediated immunity and IL-12 pathway while the IL6 pathway was downregulated. While there were no overlapping transcriptional alterations between the p53mt and p53wt groups with treatment that remain constant despite the therapeutic intervention, we did identify functional overlap with treatment in both groups in proliferative, immune, and metabolic pathways. In the pre-treatment tumor samples, the number of PD-L1+ tumor cells was significantly higher in p53mt tumors while the number of exhausted-1 immune cells (defined as OX40-/AE1_AE3-/PD-L1- cells, positive for 1/3 exhaustion markers, LAG3 or CTLA4 or TIM3) was significantly higher in p53wt tumors. In conclusion, TP53 status was prognostic of improved disease control with cetuximab plus pembrolizumab in RASwt CRC. Future studies evaluating immune-oncology agents in patients with MSS, RASwt CRC should include TP53 as an integrated biomarker and evaluate its performance as a positive predictive biomarker (ClinicalTrials.gov NCT02713373).

overall_design:
Targeted DNA sequencing was performed using the Archer VariantPlex panel
Submitters state "Due to the consenting procedure for this study and NY state law, we are not allowed to release the raw FASTQ files associated with this study"

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

first: Christos

last: Fountzilas

first: Henry G

last: Withers

first: Spencer R.


title: 4-Acetylantrocamol LT3 Suppresses Colorectal Cancer Growth and Metastasis via PI3K/AKT and MAPK Pathway Modulation

status: Public on Dec 03 2025

city: Taipei

first: I-CHUAN

last: YEN

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

department: school of pharmacy

country: Taiwan

institute: National Defense Medical Center

type: Expression profiling by high throughput sequencing

summary:
Background:
Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Despite advances in targeted therapies, drug resistance and limited efficacy in KRAS-mutant CRC continue to present clinical challenges. Antrodia cinnamomea, a medicinal fungus, has demonstrated anti-tumor properties, yet the mechanisms of its triterpenoid compound 4-acetylantrocamol LT3 (LT4) remain unclear.
Methods:
We investigated LT4’s effects in HCT116 CRC cells using cell viability, colony formation, and migration assays. Western blotting was employed to examine key signaling pathways. Transcriptome profiling via RNA sequencing was followed by KEGG/GO enrichment and protein–protein interaction (PPI) network analyses using STRING, CytoHubba, and MCODE. Molecular docking with PI3Kγ (PDB: 1E7U) was conducted to evaluate LT4’s binding affinity.
Results:
LT4 significantly inhibited HCT116 cell proliferation and migration, induced a mesenchymal-to-epithelial transition, suppressed PI3K/AKT/mTOR and ERK signaling, and activated GSK3β/FoxO and p38/p21 axes. It also reduced COX-2 and anti-apoptotic proteins (Bcl-2, Bcl-XL), while impairing mitochondrial stability (COX IV). Transcriptomic analysis identified the PI3K-Akt pathway as the most significantly enriched signaling cascade. Network topology analyses highlighted SLC3A2, CCND1, PSAT1, and CHAC1 as central nodes, linking LT4’s effects to nutrient signaling, redox homeostasis, and serine metabolism. Molecular docking confirmed that LT4 stably occupied the ATP-binding pocket of PI3Kγ with a binding energy comparable to KWT and a conformation similar to Antroquinonol.
Conclusion:
This study is the first to comprehensively demonstrate LT4’s multi-target anti-CRC effects, highlighting its potential as a therapeutic agent, especially in KRAS-mutant CRC.

overall_design: To evaluate the biological effects of LT4 in colorectal cancer, HCT116 cells were subjected to cell viability, clonogenic, and migration assays. Western blotting was performed to assess LT4-induced modulation of key signaling pathways. Transcriptomic analysis was carried out through RNA sequencing, followed by functional enrichment analyses including KEGG and Gene Ontology (GO). Protein–protein interaction (PPI) networks were constructed and analyzed using STRING, CytoHubba, and MCODE to identify central regulatory nodes. Additionally, molecular docking was conducted to assess the binding affinity of LT4 to PI3Kγ (PDB ID: 1E7U), providing insights into potential target engagement.


title: TP53 Mutation is a Prognostic Biomarker for Patients with Advanced RAS Wild-Type Colorectal Adenocarcinoma Treated with Cetuximab and Pembrolizumab [dataset 1]

overall_design:
RNA-sequencing was performed on tumor samples pre and post therapeutic intervention
Submitters state "Due to the consenting procedure for this study and NY state law, we are not allowed to release the raw FASTQ files associated with this study"

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


title: ROS Activated NETosis of Bone Marrow CD55+ Intermediate Mature Neutrophils Through HIF1α-PADI4 Pathway to Initiate Bone Aging.

status: Public on Dec 02 2025

city: Beijing

first: Yutong

last: Guo

address: No.22, Zhongguancun South Avenue, Haidian District, Beijing, 100081, PR China.

country: China

institute: Peking University

summary: Bone marrow neutrophils are highly heterogeneous cells and we used sing cell RNA-sequencing to analyze the diversity of BM neutrophils of SAMP6 and SAMR1 mice femur bone.

overall_design: Femour of 3-month male SAMP6 and SAMR1 mice were separately flushed out, and after lysing red cells, BM cells were analyzed by sc-RNA seq.


title: Comparative analysis of AMOUR and other strategies for profiling surface RNAs

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Conventionally limited to proteins, lipids, and polysaccharides, cell membranes have recently revealed the presence of protein-coding RNAs and glycan small RNAs on the surface of mouse and human cells. Despite glycan-RNA's prevalent presence on the cell exterior, a comprehensive method for accurately mapping all surface RNAs, particularly for rare cell populations has been lacking, leaving their physiological roles largely unexplored. We developed AMOUR, an RNA capture technique coupled with T7-based linear amplification, enabling precise profiling of surface RNAs in mammalian cells while preserving plasma membrane integrity.To ensure both sensitivity and specificity, we developed two supplementary strategies: WGA-Pd and RT-Amp, for surface RNA profiling alongside AMOUR.

overall_design: To ensure both sensitivity and specificity, we developed two supplementary strategies for surface RNA profiling alongside AMOUR. The first employs a wheat germ agglutinin pull-down assay (WGA-Pd), utilizing WGA to capture modified plasma membranes rich in N-acetylglucosamine and N-acetylneuraminic acid (sialic acid), followed by surface RNA extraction. The second involves a modified AMOUR method, substituting T7 RNA polymerase with reverse transcriptase during surface RNA capture. We also compared the surface RNA profiles post-protein deprivation with trypsin treatment (WGA-T).

first: Jiang

last: Xiao

first: Lulu

last: Hu


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [scRNA-seq]

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

summary: Heterogeneity between patients poses a significant challenge in cancer drug development. Although success of a drug candidate in the clinic depends on efficacy across large numbers of diverse patients, only a few in vivo preclinical models are used for assaying a preclinical drug candidate due to the lack of scalability of traditional xenograft models. To address this limitation, we developed GENEVA, a scalable platform that enables the measurement of molecular and phenotypic responses to drug perturbations at single-cell resolution, both in 3D and in vivo. GENEVA models the genetic diversity of cancer by combining multiple patient-derived cell lines and cancer cell lines into pooled 3D cultures and xenograft models, allowing us to study drug responses across a wide range of genetic backgrounds within a single experiment. This platform integrates high-resolution transcriptomics with multiplexed single-cell profiling, providing a unique ability to uncover the interplay between cancer genotypes and drug responses. In this study, we apply GENEVA to investigate KRAS G12C inhibitors and demonstrate that mitochondrial activation is a key driver of cell death following KRAS inhibition. Additionally, we identify epithelial to mesenchymal transition (EMT) as a prominent resistance mechanism to KRAS G12C inhibition using in vivo GENEVA mice. These findings highlight the utility of GENEVA in identifying novel therapeutic targets and optimizing combination therapies, while underscoring its potential to bridge the gap between preclinical cancer models and patient outcomes by modeling the complexity of tumor heterogeneity in a scalable and robust assay.

overall_design: Lung cancer patient-derived organoids from four genetic backgrounds (KRAS G12C, KRAS G12D, EML4-ALK fusion, and EGFR L858R) were pooled and grown in 3D Matrigel culture. These pooled PDOs were exposed to an ARS-1620 dosage series. After treatment, cells were dissociated and processed using 10x Genomics Chromium Single Cell 3' v3.1 chemistry. Libraries were demultiplexed using SNP-based assignment from scRNA-seq reads and hashed sample tags (MULTI-seq). Single-cell transcriptomes were quantified using Cell Ranger and integrated into downstream analyses to assess differential drug responses.

first: Johnny

middle: X

last: Yu

first: Jung

middle: M

last: Suh

first: Katerina

middle: D

last: Popova

first: Kristle

last: Garcia

first: Tanvi

last: Joshi

first: Bruce

last: Culbertson

first: Jessica

middle: B

last: Spinelli

first: Vishvak

last: Subramanyam

first: Kevin

last: Lou

first: Kevan

last: Shokat

first: Jonathan

last: Weissman


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [xenograft]

overall_design: A total of 11 cancer cell lines with varying genetic backgrounds, including BRAF(V600E) and KRAS G12C mutations, were pooled together into a single experimental setup. These pooled cells were cultured in 3D conditions and then split into three treatment groups:   Vehicle control (DMSO),  Vemurafenib (0.8 µM) targeting BRAF(V600E) mutants,  ARS-1620 (1 µM) targeting KRAS G12C mutants.  After six days of treatment, cells were harvested and subjected to scRNA-seq


title: Reduced TBX5 dosage causes human atrial disease by undermining developmental gene regulation of atrial cardiomyocyte identity [scATAC-seq]

status: Public on Dec 01 2025

first: Benoit

last: Bruneau

address: 1650 Owens St

institute: Gladstone Institutes

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In a TBX5-linked human cellular model of atrial disease, we examined the gene networks controlled by TBX5 during human atrial differentiation using single-cell RNA and ATAC sequencing.

overall_design: Wildtype, TBX5 heterozygous and homozygous mutant iPSCs were differentiated to atrial cardiomyocytes. At day 20 of differentiation, cells were harvested for single-cell ATAC sequencing. Two replicates per genotype per timepoint were harvested. Wildtype iPSCs were also differentiated to ventricular cardiomyocytes and cells were harvested at day 23 for single-cell ATAC sequencing.

first: Kavitha

middle: S

last: Rao

first: Irfan

last: Kathiriya

middle: G


title: Osteocytic FSH inhibition rescues bone mass and boosts fracture healing in ovariectomized mice

city: taiyuan

first: Zemin

last: Liu

state: shanxi

address: wuyi street number 382

department: Orthopedics

institute: Second Hospital of Shanxi Medical University

summary: RNA-seq of femoral cortical bone from osteocyte-specific Fshr knockout mice (Dmp1-CreERT; Fshrfl/fl) identifies PI3K/Akt pathway activation and enhanced osteoblast-osteoclast coupling underlying increased bone mineralization and accelerated fracture repair in ovariectomized mice.

overall_design: In the study, femur samples were collected from three mice in the tamoxifen - induced Fshr knockout group (A1-A3) and three mice in the corn oil - injected control group (B1-B3) for subsequent RNA extraction and high - throughput sequencing procedures.

first: Hongjie

last: Zhou

first: Liben

last: Cheng

first: Xiaoli

last: Li

first: Dong

last: Wang

first: Juan

first: Min

first: Yan

first: Yonghong

last: Zhang

first: Mingxin

last: Sun


title: Gene expression profile in diet-induced HFpEF rat model

city: Nagoya-shi

first: Yuka

last: Kono

state: Aichi

address: 2-1723, Omori, Moriyama-ku

country: Japan

institute: Kinjo Gakuin University

summary: To investigate gene expression changes associated with the development of HFpEF and the preventive effects of pharmacological interventions against HFpEF onset, Wistar rats were administered N(G)-Nitro-L-arginine methyl ester, an inhibitor of nitric oxide synthase, and fed a high-fat diet for 8 weeks. Cardiac tissues were collected at the time of sacrifice.

overall_design: The rats were divided into four groups: a normal group, an HFpEF group, a group treated with the RAS inhibitor captopril (Cap) group, and a group treated with sacubitril/valsartan (Sac/Val) group.

first: Kunihiro

last: Sonoda

first: Shogo

last: Watanabe


title: Small non-coding RNAs encapsulating mammalian cells fuels innate immunity

first: Xu

last: Chu

summary: Our study addresses the void in understanding surface RNAs, notably glycan-RNAs, abundant on the cell exterior yet lacking precise mapping, particularly in rare cell populations. We present AMOUR, a technique uniting RNA capture with T7-based linear amplification, facilitating accurate profiling of surface RNAs while maintaining plasma membrane integrity. Validation via surface fluorescence in-situ hybridization and RNA aptamer imaging confirms their presence on the outer membrane, autonomously associating in vitro, independent of protein scaffolding. Our work reveals non-coding RNAs as integral components of diverse human and murine hematopoietic cell surface RNAs. Single-cell sequencing of human umbilical cord blood mononuclear cells identifies prevalent Y RNAs on monocyte surfaces. Notably, these Y RNAs interact with histones, critically regulating interleukin-6 (IL-6) gene expression and subsequent protein secretion upon histone stimulation. Highlighting the pivotal role of Y RNAs, our findings clarify their involvement in innate immune activation by capturing and presenting extracellular histones.

overall_design:
Surface RNAs are profiled utilizing the AMOUR strategy developed by us across various murine hemotopoietic cell types isolated from C57BL/6 mouse bone marrow cells.
Total RNASeq of mouse PBMC

first: Jiang

last: Xiao

first: Lulu

last: Hu


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [CRISPR screen]

first: Hani

last: Goodarzi

overall_design: Lung cancer cell lines (H358, H2122, H23, H441) transduced with dCas9-KRAB and pooled dual sgRNA libraries targeting approximately 100 genes were injected into the flanks of NSG mice to form mosaic xenografts. Two days post-implantation, mice were treated with Sotorasib ($100~mg/\text{kg}$) or vehicle. Dosing was performed by daily oral gavage for 13 days. Tumors were excised on day 14, and genomic DNA (gDNA) was extracted for subsequent guide RNA sequencing to quantify gene enrichment/depletion (Rho scores) and determine genetic dependencies.

first: Johnny

last: Yu

first: Jung

last: Suh

first: Katerina

last: Popova

first: Kristle

last: Garcia

first: Tanvi

last: Joshi

first: Bruce

last: Culbertson

first: Jessica

last: Spinelli

first: Vishvak

last: Subramanyam

first: Kevin

last: Lou

first: Kevan

last: Shokat

first: Jonathan

last: Weissman


title: H4K16 acylations fine-tune transcriptional response during metabolic perturbations (ChIP-seq)

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: We studied the combined effects of the H4K16 acylations in vivo using a mouse model of the metabolic disorder propionic acidemia (PA), which causes metabolic challenges and systemic shifts in acyl-CoA ratios. Our findings indicate that H4K16 acylations modulate transcriptional responses in a concerted manner, providing insights into an adaptive chromatin regulation in response to metabolic stress.

overall_design: H4K16ac, H4K16pr, H4K16bu, H4K5ac, H4K5pr, H4K12ac, H4K12pr, H3K27ac, H3K9ac ChIP-seq on WT and PA female mouse livers in 2 biological replicates.

first: Sandra

last: Nitsch

first: Eva

last: Richard

first: Lourdes

middle: R

last: Desviat

first: Robert

last: Schneider


title: H4K16 acylations fine-tune transcriptional response during metabolic perturbations (RNA-seq)

summary: We studied the concerted effects of the H4K16 acylations in vivo using a mouse model of the metabolic disorder propionic acidemia (PA), which causes metabolic challenges and systemic shifts in acyl-CoA ratios. Our findings indicate that H4K16 acylations act in vivo in a coordinated manner, allowing fine-tuning of transcriptional responses to metabolic stresses. Our work provides insights into the adaptive mechanisms of chromatin regulation in response to metabolic challenges.

overall_design: RNA-seq on WT and PA female mouse livers in 2 biological replicates.


title: Effect of MetAP2 Inhibitor Evexomostat (SDX-7320) on Gene Expression in MC38 Tumors from Lean and Obese Mice

city: WESTON

first: Pierre

middle: Jean

last: Dufour

state: MA

address: 273 CONANT RD.

institute: SynDevRx, Inc

summary: The objective of this study was to test the anti-tumor activity of the MetAP2 inhibitor evexomostat (SDX-7320) on sub-cutaneous MC38 allografts in lean and obese mice. Mice with established MC38 tumors were treated with evexomostat (SDX-7320) 6 mg/kg by sub-cutaneous injection every 4 days beginning when tumors were 75-100 mm3 for a total of 5 doses. Upon study termination, mice were euthanized and tumor tissue from N=4 mice/group was dissected, weighed, and placed into RNAlater for subsequent isolation of polyA+ RNA, cDNA library construction and sequencing.

first: Peter

last: Cornelius


title: In vivo Spatial Perturb-Seq in the mouse brain

city: South San Francisco

first: Kimberle

last: Shen

address: 1 Dna way

institute: Genentech

summary: Functional genomics that knocks out individual genes is ideal for investigating gene functions. Examining these perturbations in vivo, within native tissue architecture and with spatial context, is crucial for accurately assessing the impact of genetic modifications both within the cell and on its microenvironment.

overall_design: We stereotaxically injected an AAV library targeting 18 genes directly into the mouse hippocampus to induce sparse perturbations, then performed Stereo-seq. The 18 loci that are targeted are: mSafe1, Trem2, Rraga, Flcn, Fasn, Olig2, Gfap, Clu, Dpp6, Tbk1, C9orf72, Cfap410, Stk39, Lrrk2, Ndufaf2, Sh3gl2, Srf, Rbfox3. The data here consists of three chips from three mice.

first: Wei Leong

last: Chew


title: SAMHD1 depletion restricts SARS-CoV-2 infection by suppressing HNF1-dependent ACE2 expression in lung epithelial cells

status: Public on Nov 30 2025

city: Iowa City

first: Pak Hin Hinson

last: Cheung

state: Iowa

address: 51 Newton Raod

department: Department of Microbiology and Immunology

institute: University of Iowa

summary: Sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1) restricts a broad spectrum of viruses through multifaceted mechanisms. It also limits spontaneous- and virus-induced innate immune responses by suppressing proinflammatory cytokine and type-I interferon (IFN-I) production. Some viruses escape SAMHD1 restriction and utilize SAMHD1-mediated innate immune suppression to establish effective infection through IFN antagonism. Our previous studies showed that SAMHD1 is a proviral factor facilitating replication of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in human macrophages, monocytic THP-1 and epithelial-like HEK293T cell lines by suppressing IFN responses. However, it is unclear about the function of SAMHD1 in lung epithelial cells during SARS-CoV-2 infection. Here, we report that SAMHD1 knockout (KO) restricts SARS-CoV-2 replication in lung epithelial Calu-3 cells by suppressing endogenous expression of the viral receptor angiotensin-converting enzyme 2 (ACE2) via hepatocyte nuclear factor 1-alpha (HNF1α) and HNF1β. Using pseudotyped SARS-CoV-2 and lentiviral vectors, we found that SARS-CoV-2 spike protein-mediated viral entry was suppressed in SAMHD1 KO Calu-3 cells. SAMHD1 KO repressed ACE2 expression in Calu-3 cells at mRNA and protein levels. Functional analyses revealed that HNF1α and HNF1β were crucial for the endogenous ACE2 expression in Calu-3 cells. Additionally, SAMHD1 KO led to a reduction in the expression levels and ACE2-promoting function of HNF1α and HNF1β. Inhibition of IFN antiviral response by baricitinib, a Janus kinase 1 and 2 (JAK 1/2) inhibitor, did not revert the suppression of SARS-CoV-2 in SAMHD1 KO Calu-3 cells. SAMHD1 knock-in and deoxynucleoside supplementation experiments indicated that SAMHD1 expression and dNTP pool balance collectively regulated HNF1-mediated ACE2 expression in Calu-3 cells. Our findings demonstrate that SAMHD1 depletion hinders HNF1-mediated ACE2 expression and SARS-CoV-2 replication in Calu-3 cells via a novel mechanism beyond its IFN-suppressive function.

overall_design: To gain mechanistic insight, mRNA-seq was performed to profile the transcriptome of SAMHD1 knockout Calu3 cells (KO) and compared with that of the control Calu-3 cells (Ctrl). Two clones of KO cells were generated through CRISPR/Cas9 with one single guide RNA having different target sequences. Ctrl cells were mock control treated similarly as the KO cells but were transduced with empty vector. 8 x 105 Calu-3 Ctrl, KO1 and KO2 cells were seeded in 6 well plates in biological triplicate. Cells were cultured in 2mL DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. At 20 hours after seeding, cells were washed once with DPBS and lysed with RLT plus lysis buffer. Cellular RNA was purified with RNeasy Plus kit following manufacturer’s instructions. All RNA samples got RNA integrity Number (RIN) scores equal to or more than 9.9 as determined by Agilent BioAnalyzer by Genomics Division of Iowa Institute of Human Genetics (University of Iowa). RNA samples were processed through Illumina Stranded mRNA Prep (illumina) and sequenced by Element Aviti24 using Cloudbreak FS-High output flow cell at 150 cycle (2x75) by the Genomics Division.

first: Pearl

last: Chan

first: Hua

last: Yang

first: Krisztina

last: Ambrus

first: Shravya

last: Honne

first: Baek

last: Kim

first: Stanley

last: Perlman

first: Li

last: Wu


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [Multiome]

status: Public on Nov 28 2025

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Neural progenitor cells exhibit developmental plasticity, as they are able to commit to different developmental trajectories in response to external stimuli. How these decisions are stabilized at the molecular level remains a highly active area of research. One way to stably integrate external stimuli into cell fate decisions is through epigenetic marks. H4K16ac represents a unique epigenetic mark, as it modulates chromatin compaction and is the only known active histone modification that is transmitted intergenerationally. The deposition of H4K16ac is mediated by the evolutionarily conserved MSL acetyltransferase complex (MSLc), via its catalytic subunit MOF, and mutations in its components have been linked to neurodevelopmental disorders. To dissect the role of the MSLc, we employed a multi-pronged strategy combining both chronic and acute depletion models. Deletion of the MSLc structural backbone Msl1 in vivo resulted in embryonic lethality by E10, and single-cell multi-omics analysis revealed a systemic disruption in lineage commitment within the neuroectoderm. To distinguish primary molecular functions from secondary developmental consequences, we complemented this with a rapid degradation system in vitro, coupled to directed differentiation into two distinct neural lineages. We found that the MSLc facilitates accessibility at regulatory elements in the early stages of lineage commitment during neurogenesis. We observe a significant decrease in enhancer-promoter contacts in a specific subset of neurodevelopmental genes. In the absence of MSLc this gene group fails to reach adequate gene expression levels upon differentiation, resulting in abnormal morphology. Intriguingly, MSLc loss later on during differentiation does not phenocopy this. Our work reveals MSLc-mediated gene priming as a crucial mechanism potentiating the transcriptional activation of neurodevelopmental gene programs. Our study describes a new mode of epigenetic regulation which cements initial cell fate decisions and provides molecular insights into MSLc-associated developmental disorders.

overall_design: Single-cell multiome datasets were generated from a single E9.5 embryo either WT or homozygous Msl1 KO Genotype. Three biological repicates were independently prepared.

first: Arion

last: Foertsch

first: Laura

last: Arrigoni


title: scRNA-seq of a knockout village during hPSC-derived islet differentiation

status: Public on Dec 12 2025

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

summary: This submission consists of processed single-cell RNA-seq data of knockout village samples, provided as filtered feature–barcode matrices generated using Cell Ranger v7.1.0 with default parameters. We previously deposited the same biological samples and data processed by STAR under GEO accession GSE288587. The corresponding raw FASTQ files are available in ENA under accession ERP168459. The supplementary file (reanalysis_samples.xlsx) provides a reference table linking each sample in this submission to its corresponding GSM in GSE288587, which contains the detailed experimental descriptions of culture information, genotypes, and differentiation stages.

relation:
Reanalysis of: GSM8770302
Reanalysis of: GSM8770313
Reanalysis of: GSM8770303
Reanalysis of: GSM8770314
Reanalysis of: GSM8770304
Reanalysis of: GSM8770315
Reanalysis of: GSM8770305
Reanalysis of: GSM8770316
Reanalysis of: GSM8770306
Reanalysis of: GSM8770317
Reanalysis of: GSM8770307
Reanalysis of: GSM8770318
Reanalysis of: GSM8770308
Reanalysis of: GSM8770319
Reanalysis of: GSM8770309
Reanalysis of: GSM8770320
Reanalysis of: GSM8770310
Reanalysis of: GSM8770321
Reanalysis of: GSM8770311
Reanalysis of: GSM8770322
Reanalysis of: GSM8770312
Reanalysis of: GSM8770323
SubSeries of: GSE315753

overall_design: The knockout village consist of 3 WT and 76 knockout lines targeting 30 pancreas developmental regulators and diabetes genes, including GATA6, PDX1, GATA4, FOXA1, FOXA2, MNX1, NEUROD1, NKX2-2, RFX6, GSC, HHEX, HNF4A, PAX6, PBX1, GLIS3, NEUROG3, ARX, OTUD5, BMPR1A, TLE3, BCOR, QSER1, TET1, TET2, TET3, TADA2B, KDM2B, PROSER1, ONECUT1, and NANOG. Edited lines were generated in two hPSC backgrounds (HUES8 and H1). Individual clonal lines were uniquely barcoded by lentiviral infection with GFP-barcode plasmids from the LARRY library and pooled to form a knockout village for differentiation. Samples were collected at five differentiation stages: day -1 (hPSC, 1 day prior differentiation), day 3 (definitive endoderm, DE), day 7 (posterior foregut, PFG), day 11 (pancreatic progenitor, PP) and day 18 (early SC-islet). In addition, WT cells in H1 and HUES8 backgrounds were differentiated and sequenced in parallel at 17 time points: day -1 (hPSC), 3, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 21, 25, 26, 35.

first: Dingyu

last: Liu

first: Dapeng

first: Renhe

last: Luo

first: Wei

last: Li

first: Danwei

last: Huangfu


title: H4K16 acylations fine-tune transcriptional response during metabolic perturbations (ATAC-seq)

first: Tamas

last: Schauer

overall_design: ATAC-seq on WT and PA female mouse livers in 2 biological replicates.

first: Sandra

last: Nitsch

first: Eva

last: Richard

first: Lourdes

last: Desviat

first: Robert

last: Schneider


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [4C]

overall_design: Analysis of locus specific 3D chromatin interactions at genes which showed MSLc primed transcriptomic signatures. Cells underwent directed in vitro Neuronal differentiation in presence or absence of MSL1 (Auxin treatment during Day0-7 of differentiation).

first: Ward

last: Deboutte

first: Janine

last: Seyffert


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [Micro-C]

overall_design: Genome wide analysis of 3D chromatin interactions in NPCs and Day7 Neurons. Cells underwent directed in vitro Neuronal differentiation in presence or absence of MSL1 (Auxin treatment during Day0-7 of differentiation).

last: Seyfferth


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [RNA-Seq]

overall_design: WT vs KO experiments: Global transcriptomic differences in a chronic MSL1 depletion model (MSL1 KO) during Neuronal differentiation. WT vs dN experiments: Global transcriptomic differences in a chronic MSL1 truncation model (dN-MSL1-F) during Neuronal differentiation. MSL1-AID experiments: Global transcriptomic differences in response to MSL1 depletion via the additin of Auxin to the cell culture medium. MSL1 depletion was carried out either in short term, like 24h MSL1 depletion in NPCs, or throughout entire stages of the directed in vitro differentiation (Auxin treatment: Day0-7, Day7-14 or Day0-14 during Neuronal differentiation or Day0-3 during Astrocyte differentiation). At least three replicates were sequenced per condition.


title: The transcriptomic data of TCN1 overexpression in HaCaT cells

status: Public on Nov 27 2025

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: This study aimed to explore the underlying molecular mechanism of TCN1 in driving psoriasis progression. TCN1 has been identified as an autoantigen and an endogenous activator of the IL-17 signaling pathway.

overall_design: The estabilished TCN1 overexpression  and negative control  cell lines (HaCaT cells) were seeded into 6-well plates and grown overnight for total RNA harvest. The differentally expressed genes by TCN1 overexpression were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq X Plus.

first: Shanshan

last: Qin

first: Dandan


title: Integrated analysis of differential m6A methylation and transcriptome profiles in ovaries of young and aged Cele black sheep

city: Alar City, Xinjiang Uygur Autonomous Region

first: linlin

last: pei

state: Aral

address: Alar City Happy Road Street

institute: Tarim university

summary: Ovarian aging results in follicular failure and atresia, leading to a decline in both the quantity and quality of oocytes. N6-methyladenosine (m6A) has been demonstrated to play a regulatory role in the reproductive functions of female animals; however, the regulatory mechanisms of m6A in the ovaries of sheep remain unclear. In the present study, ovarian tissues from 1~2 year-old and 5~6 year-old Cele black sheep were collected and analyzed using MeRIP-seq and RNA-seq sequencing. A total of 109 differentially methylated genes were identified, including 7 genes that were up-regulated in both methylation and mRNA expression, 55 genes that were up-regulated in methylation while down-regulated in mRNA expression, and 33 genes that were down-regulated in both methylation and mRNA expression. Additionally, 14 genes exhibited down-regulation in methylation and up-regulation in mRNA expression. Differential methylation peaks (DMPs) were found to be significantly enriched in the BMP signaling pathway, uterine embryonic development, histone acetyltransferase activity, and VEGF signaling pathway by GO and KEGG enrichment analysis. Differentially expressed genes (DEGs) were significantly enriched in negative regulation of the I-kappaB kinase/NF-kappaB signalling pathway, positive regulation of leukocyte adhesion to vascular endothelial cells, histone methyltransferase binding, transcriptional co-repressor activity, and cellular senescence. The results suggest that differentially expressed genes may influence various biological functions, including transcription, translation, aging, development, regeneration, and immune responses in the ovary of sheep. In this study, we constructed the first comprehensive whole transcriptome analysis map of the sheep ovary, which provides a theoretical foundation for investigating the transcriptional regulation mechanisms of m6A modification in the ovary.

first: Linlin

last: Pei

first: Chunjie


title: Quantitative analysis of small RNA pseudouridylation reveals interplay of PUS enzymes in tRNA anticodon stem-loop

first: Wenqing

address: No. 5, Yiheyuan Road, Haidian District, Beijing

summary: Pseudouridine (Ψ) is an abundant modification in small RNA and is catalyzed by multiple pseudouridine synthases (PUSs). However, the substrate specificity of human PUSs are not fully understood. In this study, we adopted PRAISE, a quantitative Ψ detection method, to profile pseudouridylation in small RNA, including cytosolic and mitochondrial tRNAs, snRNA, and snoRNA. We found that pseudouridylation of snoRNAs can be mediated not only by RNA-guided DKC1, but also stand-alone enzyme PUS7. Interestingly, we found that several PUS enzymes, which install nearby Ψ sites within tRNA anticodon stem-loop, can influence pseudouridylation level catalyzed by other PUSs. Typical examples include PUS1, RPUSD1, and PUS7, revealing a novel interplay among human PUSs during Ψ formation. For the three RluA family enzymes, we found that in addition to the canonical substrate Ψ30, RPUSD1 also catalyzes Ψ72 of tRNA-Arg isoacceptors. RPUSD2 pseudouridylates Ψ31 of mt-tRNALeu(CUN), and Ψ32 of mt-tRNAPro and mt-tRNACys, and hence is functionally similar to yeast Pus9. RPUSD3 does not modify tRNA at all, consistent with its lack of a catalytic residue. Together, using quantitative Ψ profiling, our study characterized the tRNA substrates of PUS enzymes and revealed unexpected interplay among human PUSs in tRNA pseudouridylation.

overall_design: We detected the Ψ sites in small RNAs of HEK293T cells to profile the quantitative landscape. We then identified the DKC1-dependent sites of snRNA and snoRNA in DKC1 knockdown cell lines. After that, we identified substrates of 6 PUS enzymes in PUS1, PUS7, TRUB1, RPUSD1, RPUSD2, and RPUSD3 cell lines.


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [RELACS]

first: Asifa

last: Akhtar

overall_design: Genome wide patterns of multiple active and repressive histone marks in steady state NPCs in ctrl or MSL1 depleted conditions (24h Auxin treatment). Three replicates were sequenced per condition.

first: Arion

last: Foertsch


title: Effect of depletion of ANAPC1P2  on OVCAR3 cells.

status: Public on Nov 26 2025

city: Pune

first: Dr. Sharmila

middle: A

last: Bapat

state: Maharashtra

address: NCCS campus, SPPU, Ganeshkhind road.

country: India

institute: National Centre for Cell Science

summary: ANAPC1P2 is a chimeric pseudogene that gives rise to a novel chimeric long non-coding transcript, vA-202 (RMND5A-ANAPC1). Notably, vA-202 functions as a γ-irradiation–responsive lncRNA, becoming induced under genotoxic stress conditions. In this study, we generated ANAPC1P2-knockdown OVCAR3 cell lines (OVCAR3_KD) and performed RNA-sequencing alongside their corresponding control lines. The resulting transcriptomic datasets reveal the global changes in gene expression that occur upon loss of this lncRNA, including both upregulated and downregulated targets.

overall_design: RNA-seq profiling of OVCAR3 cells and its derivative having shRNA knockdown of ANAPC1P2 (OVCAR3_KD).

first: Sharmila

first: Jadhav

last: Amruta


title: The transcriptomic data of HaCaT cells with and without DNA methyltransferase inhibitors (DNMTi) treatment

summary: This study aimed to explore the genes repressed by DNA methylation, since their expression will be activated by DNMTi treatment.

overall_design: DNA methylation negatively regulates gene expression at pre-transcription level. Thus, we aimed to identify potent genes upregulated by 5-Aza-CdR (25, 50 μM) in HaCaT cells.

last: Li


title: Protocol for quantifying silent ribosome induction in yeast and mammalian cells using polysome profiling

city: Basel

first: Attila

last: Becskei

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: Translationally silent ribosomes have become an important focus in RNA biology, yet their quantification remains challenging. Lacking mRNAs, they represent a hibernating ribosome state. This protocol outlines how to measure silent ribosome induction under diverse conditions by analyzing RNA from polysome-profiling fractions in yeast and mammalian cells, using RNA-seq with removal of anomalously amplified rRNAs and qPCR for validation.

overall_design: For an example of the execution of this protocol, please refer to Rahaman, et. al.1

first: Sayanur

last: Rahaman

first: Samuel

last: Mondal

first: Nicole

last: Schiffelholz


title: Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [RRBS]

status: Public on Nov 25 2025

city: New York City

first: Richa

last: Singh

state: NY

address: 413 East, 69th street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: Acquired changes in DNA methylation have been proposed as a mechanism underlying epigenetic plasticity in several cancer types. In prostate cancer, methylation changes are dynamic, with preclinical studies pointing to a tumor suppressor role of the DNA methyltransferase DNMT1 in early stage, in contrast to an oncogenic function of DNMT1 in later stage. The importance of DNA methylation dynamics during normal development and cell lineage fate decisions also points to DNA methylation having a critical function in lineage plasticity, yet the mechanisms by which DNA methylation changes drives lineage transitions in prostate cancer is not well understood. DNA methylation can directly repress gene expression but also cooperate with other epigenetic pathways to modulate downstream transcriptional activity. The enhancer of zeste homolog 2 (EZH2) protein is a subunit of the polycomb repressive complex 2 (PRC2) and catalyzer of the repressive histone 3 lysine 27 tri-methylation (H3K27me3) mark that also acts to suppress downstream transcriptional activity and has also been implicated in lineage plasticity. EZH2 is overexpressed in castration-resistant prostate cancer (CRPC) including NEPC and is an emerging therapeutic target. Although, the compensatory relationship between DNA methylation and EZH2 has been shown in embryonic stem cell studies and in some cancer types during acquired treatment resistance or immune evasion, how DNA methylation and EZH2/PRC2 interact to modulate prostate cancer lineage plasticity has not been characterized. In this study, we address the potential crosstalk between epigenetic pathways in advanced prostate cancer and demonstrate how DNA methylation and H3K27me3 profiles overlap and cooperate to reprogram the epigenome during prostate cancer lineage plasticity. Using both mouse and patient-derived models, we highlight the compensatory roles of these two repressive machineries during progression of CRPC towards a NE-lineage state. We predict their specific impact on NEPC progression by assessing the associated molecular alterations following genetic and pharmacological perturbations of each.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RRBS in mouse prostate tumors, patients' tumor derived organoids and LNCaP cells

first: David

last: Rickman


title: Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [RNA-Seq]

overall_design: RNA-Seq in mouse prostate tumors


title: Distinct contributions of Etv2+ and Flk1+ progenitors to endothelial, hematopoietic, and cardiac lineages [RNA-seq]

status: Public on Nov 21 2025

city: St. Louis

first: Dereck

last: Alleyne

state: MO

address: 425 South Euclid Avenue

department: Department of Pathology and Immunology

institute: Washington University School of Medicine

summary: The ETS family transcription factor ETV2, VEGFA and its receptor FLK1 are essential for hematopoietic, vascular and cardiac development. Here, we combine dual Etv2 and Flk1 lineage tracing with molecular profiling to define how mesoderm progenitors are allocated to hematopoietic, endothelial, cardiomyocyte and smooth muscle lineages. We demonstrate that hematopoietic, endothelial, and cardiac valves arise from dual Etv2+ and Flk1+ lineages and that Etv2+ and Flk1+ mesoderm contributing to the hemangiogenic fate is molecularly distinct from those generating muscle. Mechanistically, we show that ETV2 cooperates with the BAF chromatin remodeling complex to establish accessibility at ETV2 target loci. Loss of Baf155 expression reduces chromatin accessibility at ETV2 target loci and impairs hemangiogenic lineage specification. This work defines lineage relationships and the molecular circuitry underlying hemangiogenic specification during cardiovascular development.

overall_design: RNA-seq profiling of day 4 embryoid bodies (EBs) derived from wildtype, iEtv2 and T-GFP;Etv2-tdTomato mouse ES cells. Etv2 overexpression was induced by treating day 2.5 EBs with 2ug/ml doxycline. EBs were sorted by FACS to sort PDGFRalpha+FLK1+ (DP) and PDGFRalpha-FLK1+ (SP) mesodermal cells.

first: Alleyne

last: Dereck

first: Kim

last: Minseo

first: Wu

last: Jun

first: Kwon

last: Yoojung

last: Ye-Ram

first: Ul Kabir

last: Ashraf

first: Ishahak

last: Matthew

first: Millman

last: Jeffrey R.

first: Fan

last: Changxu

first: Lee

last: Hyung Joo

first: Krchma

last: Karen

first: Xing

last: Xiaoyun

first: Lavine

last: Kory

first: Wang

last: Ting

first: Choi

last: Kyunghee


title: Distinct contributions of Etv2+ and Flk1+ progenitors to endothelial, hematopoietic, and cardiac lineages

overall_design: ATAC-seq profiling of day 4 embryoid bodies (EBs) derived from wildtype, Etv2 overexpressing and Etv2KO mouse ES cells. Etv2 overexpression was induced by treating day 2.5 EBs with 2ug/ml doxycline. EBs were sorted by FACS to sort PDGFRalpha+FLK1+ (DP) and PDGFRalpha-FLK1+ (SP) mesodermal cells.


title: Gene expression and chromatin accessibility in human embryonic stem cells with partial deletion of PDHB during DE differentiation [ATAC-seq]

status: Public on Nov 24 2025

city: WuHan

first: liming

last: meng

address: No. 115, Donghu Road

institute: WuHan university

summary: We established a PDHB heterozygous cell line in human embryonic stem cell HUES8. Then we performed definitive endoderm (DE) differentiation using both WT and PDHB partial deletion cell lines, and assessed gene expression and chromatin accessibility changes during this process by RNA-seq and ATAC-seq. Differentially expressed genes and regions with altered chromatin accessibility showed that in the PDHB-deleted cell line, the efficiency of endoderm differentiation was significantly inhibited. This alteration primarily occurred through changes in chromatin accessibility at BAF complex binding sites on DNA, which is a major ATP-dependent chromatin remodeling complex. And we also detected the SMAD2/3 binging by ChIP-seq.

overall_design: We performed the DE differentiation in WT and PDHB partial deletion cells. The DE differentiation medium was based on DMEM and supplemented with 100 ng/mL Activin A, 1x penicillin/streptomycin, and 0.2% bovine serum albumin. After the differentiation, we performed the RNA-seq and ATAC-seq in both cells. Besides that, we performed the SMAD2/3 ChIP-seq in WT cells. Detection was carried out after 3 days of induction using the same system.

first: Liming

last: Meng

first: Jie

last: Yang

first: Wei

last: Jiang


title: Mouse sperm: Control vs Cd treatment

city: Hefei

first: Jin

last: Zhang

address: Anhui Medical University, No. 81 Meishan Road, Shushan District, Hefei City, Anhui Province, China

institute: public health

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

summary: Compare the RNA m6A methylation profiles of sperm from control-treated mice and cadmium (Cd)-treated mice. The aim is to investigate the impact of the common environmental toxicant Cd on RNA m6A modification levels in sperm, and whether such alterations impair the healthy development of offspring

overall_design: Two-condition experiment, control-treated mice vs. Cd-treated mice. Biological replicates: 3 control replicates, 3 Cd replicates.

first: Yong-Wei

last: Xiong


title: Gene expression and chromatin accessibility in human embryonic stem cells with partial deletion of PDHB during DE differentiation [RNA-seq]


title: Coordinated Gene Family Evolution Shapes the Genome of Dimorphic Organisms

status: Public on Nov 20 2025

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

summary: Dimorphic organisms possess the remarkable ability to encode within their genomes the information necessary to alternate between two distinct life forms, a choice unavailable to most monomorphic species. However, the evolutionary solution that allows for the integration of genetic information from two divergent life forms into a single dimorphic organism remains unresolved. Here, we investigated this phenomenon using species of Mucorales fungi that are not only capable of growing as either yeast or mycelium but also able to transition reversibly between these forms depending on environmental cues. We have discovered that hundreds of gene families have undergone convergent evolution to adapt their paralogs to the dimorphic lifestyle. This adaptation manifests as the functionalization of paralogs and expression, with some paralogs expressed in the yeast form and others in the mycelial form. Although each of these dimorphic gene families performs distinct and specialized functions, they are all coordinately regulated to achieve differential expression of yeast and mycelium paralogs. Furthermore, distinct gene families with related functions have organized their paralogs into head-to-head (H2H) structures, further enhancing the coordination of their differential expression. This striking coordinated regulation is controlled by two new genes identified in this study (dkl and dfl). Loss of function of these genes results in global dysregulation of gene expression and the consequential loss of dimorphism. Dimorphic gene families, H2H marker loci, and the dfl gene are conserved across various dimorphic species but are absent in closely related monomorphic species. Collectively, dimorphic gene families, their genomic organization, and their specific regulation represent a novel evolutionary mechanism that integrates and optimizes the genetic information required for two distinct life forms within a single organism.

overall_design: RNA-seq experiment to analyze the differences in gene expression at the mRNA levels in the yeast-to-hyphae and from mycelium-to-yeast transitions in M. lusitanicus. Total RNA was extracted using the NYZ total RNA kit (NYZtech) and subjected to on-column DNase I treatment (Sigma). Three biological replicates were analyzed for each expression experiment.

first: Ghizlane

last: Tahiri

first: Maria Isabel

last: Navarro-Mendoza

first: Gabriel

last: Navarro del Saz

last: Peréz Arques

first: Victor

last: Garre

first: Francisco

last: E. Nicolás


title: Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

city: San Francisco

first: Elphege

last: Nora

state: California

address: 555 Nelson Rising Lane

department: CVRI

institute: UCSF

summary: Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without confounding cell cycle defects. Transcriptional dysregulation is cell type-specific, and not all loci with distal enhancers depend equally on cohesin extrusion. Using comparative genome editing, we demonstrate that enhancer-promoter communication over just 20 kilobases can require cohesin. However, promoter-proximal elements can support long-range, cohesin-independent enhancer action – even across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of embryonic cell types remain largely robust despite disrupted extrusion. Beyond establishing novel strategies to study cohesin in enhancer biology, our work provides mechanistic insight into cell type- and genomic context-specificity.

overall_design:
Stranded mRNA-seq and CUT&Tag for H3K27ac and H3K27me3 in mouse ES cells, ES cells exiting pluripotency, neural progenitors, and neural progenitors differentiating into astrocytes in control (DMSO/untreated) and NIPBL-depleted (dTAG-13/IAA) cells.
Bulk ATAC-seq from control (NIPBL) and NIPBL-depleted (dTAG-13) gastruloids. NIPBL depletion was initiated either 48, 72, or 96 hours after aggregation of mouse embryonic stem cells.
ChIP-seq for CTCF in ES cells with a mutation of the CTCF-binding site in the Car2 promoter.
4C-seq in ES cells (WT SRR2 and homozygous SRR2 deletion) from control (DMSO/untreated) and NIPBL- or RAD21-depleted (dTAG or IAA) cells. Viewpoints include the Sox2 promoter, Sox2 SCR, Car2 promoter, Car2 enhancer 1, and Car2 enhancer 2.
Cells harboring an dTAG-inducible (FKBP) or auxin-inducible degron (AID) on endogenous Nipbl or Rad21 alleles and were treated with either DMSO (control) or dTAG-13/IAA (NIPBL or RAD21 depletion). WT parental cells are E14Tg2a (129 X,Y background).

first: Karissa

middle: L

last: Hansen

first: Elphège

middle: P


title: Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [ChIP-Seq]

first: Richa

last: Singh

overall_design: H3K27me3 and H3K4me3 ChIP-Seq in mouse prostate tumors and in decitabine-treated NEPC patients' tumor derived xenografts

first: David

last: Rickman


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run]

first: Asifa

last: Akhtar

summary: Precise regulation of epigenetic marks is critical for proper lineage commitment throughout neurodevelopment. Mutations in members of the MSL acetyltransferase complex (MSLc), specific for H4K16ac, are associated with neurodevelopmental disorders in humans. However, the precise gene targets and enzymatic contributions of the MSLc during neural differentiation remain unclear. Through single-cell multi-omics analysis, we demonstrate that Msl1 deletion leads to severe neurodevelopmental defects, culminating in embryonic lethality by E10.5. Using a rapid depletion system, we uncoupled acute transcriptional effects from epigenetic memory and found that MSLc-mediated gene priming is responsible for faithful upregulation of crucial neurodevelopmental gene programs. The priming of the MSLc target genes is limited to the initial stages of differentiation following neuronal induction, where the MSLc facilitates chromatin accessibility at regulatory regions to, allowing for selective enhancer-promoter interactions and subsequent gene activation. Our study identifies the MSLc as a crucial epigenetic regulator during neurodevelopment, providing molecular insights into MSLc-associated developmental disorders.

overall_design: Neural progenitor cells exhibit developmental plasticity, as they are able to commit to different developmental trajectories in response to external stimuli. How these decisions are stabilized at the molecular level remains a highly active area of research. One way to stably integrate external stimuli into cell fate decisions is through epigenetic marks. H4K16ac represents a unique epigenetic mark, as it modulates chromatin compaction and is the only known active histone modification that is transmitted intergenerationally. The deposition of H4K16ac is mediated by the evolutionarily conserved MSL acetyltransferase complex (MSLc), via its catalytic subunit MOF, and mutations in its components have been linked to neurodevelopmental disorders. To dissect the role of the MSLc, we employed a multi-pronged strategy combining both chronic and acute depletion models. Deletion of the MSLc structural backbone Msl1 in vivo resulted in embryonic lethality by E10, and single-cell multi-omics analysis revealed a systemic disruption in lineage commitment within the neuroectoderm. To distinguish primary molecular functions from secondary developmental consequences, we complemented this with a rapid degradation system in vitro, coupled to directed differentiation into two distinct neural lineages. We found that the MSLc facilitates accessibility at regulatory elements in the early stages of lineage commitment during neurogenesis. We observe a significant decrease in enhancer-promoter contacts in a specific subset of neurodevelopmental genes. In the absence of MSLc this gene group fails to reach adequate gene expression levels upon differentiation, resulting in abnormal morphology. Intriguingly, MSLc loss later on during differentiation does not phenocopy this. Our work reveals MSLc-mediated gene priming as a crucial mechanism potentiating the transcriptional activation of neurodevelopmental gene programs. Our study describes a new mode of epigenetic regulation which cements initial cell fate decisions and provides molecular insights into MSLc-associated developmental disorders.

first: Arion

last: Foertsch

first: Janine

last: Seyfferth


title: Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [ATAC-Seq]

overall_design: WT vs MSL1 KO experiments: Global changes in chromatin accessibility in response to chronic MSL1 depletion (MSL1 KO) at different timepoints of the directed in vitro Neuronal differentiation. MSL1-AID experiments: Global changes in chromatin accessibility in response to acute MSL1 depletion in NPCs or prolonged MSL1 depletion throughout the directed in vitro Neuronal differentiation (Auxin treatment from Day0-Day7 of Neuronal differentiation).

first: Ward

last: Deboutte


title: Gene expression and chromatin accessibility in human embryonic stem cells with partial deletion of PDHB during DE differentiation [ChIP-seq]

first: liming

last: meng

first: Liming

last: Meng

first: Jie

last: Yang

first: Wei

last: Jiang


title: Identification of differentially expressed genes in psoriasis by RNA sequencing

first: Qin

last: Shanshan

summary: This study aimed to explore the novel differentially expressed genes in psoriasis.

overall_design: 6 normal skin tissues and 8 psoriasis tissues were collected for RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq X Plus.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: Distinct spatial organization governs oral mucosal immunity

status: Public on Nov 18 2025

city: Bethesda

first: Niki

last: Moutsopoulos

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Immune responsiveness at barrier surfaces is tailored to the exposures of each tissue. In the oral mucosa, mechanisms by which a permeable epithelium coexists with diverse microbiota and maintains integrity during inflammatory pathology remain poorly understood. We compile a multi-omics spatial map of this exposed mucosal microenvironment and uncover remarkable immune zonation with organization that is preserved even during inflammatory disease. At steady state, we identify a dynamic epithelium at the tooth interface marked by a tonic inflammatory signature which is underlined by a layer of neutrophils and a zone of APC-lymphocyte aggregates. During disease, inflammatory zones expand and organize into immature tertiary lymphoid structures, suggesting local antibody production.  This spatial immune organization meets the demands for continuous protection in health and expands in function and complexity during disease while preserving key elements of zonation. Our work provides insights into tissue-specific wiring of immunity at a vulnerable human mucosal barrier.

overall_design: Periodontitis cells from four samples (P5, P8, P9, P16) were profiled by CITE-seq using TotalSeq-A Human Universal Cocktail panel of 154 antibodies.


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

status: Public on Nov 17 2025

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

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

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

first: Ane

last: Korff

first: Xiaojing

first: Ozan

last: Ozdemir

first: Ananya

last: Samanta

first: Tushar

last: Patni

first: Alfonso

middle: J

last: Lavado

first: Anoop Murthy

last: Kavirayani

first: Joseph

last: Ochaba

first: Berit

last: Powers

first: C. Frank

last: Bennett

first: Hong Joo

last: Kim

first: J. Paul

last: Taylor


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

city: guangzhou

first: shi

last: hang

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

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

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

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

first: Hang

last: Shi

first: Jiang

middle: H

last: Tang


title: TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment

status: Public on Nov 16 2025

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

summary: Metastasis is a major cause of breast-cancer-related death and frequently occurs following paclitaxel neoadjuvant chemotherapy failure. Tumor microenvironment contributes to metastasis, while the role of specific host cells in lung metastases induced by paclitaxel (PTX) treatment remains poorly understood. Here, we demonstrate that PTX neoadjuvant chemotherapy promotes triggering receptor expressed on myeloid cells-2 (TREM2)-positive macrophage infiltration in the breast cancer tissues of patients. Meanwhile, we also show that more TREM2-positive macrophage infiltrates in breast cancer tissues of patients with lung -metastasized. Genetic TREM2 deficiency decreases breast cancer lung metastases induced by PTX treatment in vivo, suggesting that TREM2-positive macrophages are essential for PTX-promoting lung metastasis of breast cancer. We further reveal that PTX promotes tumor cell secretion of fibroblast growth factor 2 (FGF2), triggering TREM2 transcription via upregulating its transcriptional factor early growth response-1 (EGR1) in macrophages. Increased TREM2 activates epithelial-mesenchymal transition (EMT)-related cytokine secretion in macrophages, inducing tumor cell lung metastases. Targeting TREM2 significantly suppressed lung metastasis in breast-cancer-bearing mice. Our findings establish that tumor-cell-derived FGF2 induced by paclitaxel treatment upregulates TREM2 in myeloid macrophages, which in turn promotes the EMT of neighboring tumor cells through cytokine secretion. Our results highlight TREM2 as a potential therapeutic target to mitigate lung metastasis due to PTX treatment.

overall_design: RNA-seq of BT549-D, BT549-P, SUM159-D, SUM159-P, MDA-MB-231-D and MDA-MB-231-P were harvested and analyzed

first: Hongquan

last: Zhang

first: Jun

last: Zhan


title: Metabolic quiescence of naïve-like memory T cells precedes and maintains antigen-specific T-cell memory

city: Erlangen

first: Kilian

last: Schober

address: Wasserturmstraße 3/5

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

institute: Uniklinikum Erlangen/ Friedrich-Alexander-Universität Erlangen-Nürnberg

summary: Metabolic activity shapes cell fate but remains challenging to capture in vivo with high resolution. We performed longitudinal metabolic and phenotypic profiling of human antigen-specific CD8+ T cells after yellow-fever vaccination on the single-cell level. During the acute phase, T cells upregulated glycolysis to fuel anabolic needs of proliferation, but predominantly used oxidative phosphorylation for energy production, as assessed via protein translation rates. Central memory T cells were the most active subset, while effector cells underwent metabolic shut-down. In contrast, weakly differentiated naïve-like memory T cells showed minimal activity, relying solely on oxidative phosphorylation already during the acute phase. Reinforcing the link between cellular quiescence and longevity, naïve-like memory cells were preferentially maintained even 26 years post vaccination. This association between differentiation degree and metabolic activity was conserved after SARS-CoV-2 vaccination and in two murine infection models. Our study dissects the metabolic profile of antigen-specific T-cell responses ex vivo, highlighting quiescence as a key feature for long-term immunological memory formation in humans.

overall_design: Yellow Fever Virus (YFV)-specific CD8+ T cells from human blood before and after YFV-vaccination were were identified by DNA-baroded pMHC multimers (Dextramers) in three independent experiments. Cells were stained with DNA-barcoded CITEseq antibodies for surface markers (among them CD45RA,CD62L,CD95), cells from 27 different donors and  11 time-points were labelled with TotalSeq-C anti-human hashtag antibodies and samples were pooled for further processing. CD8+ T cells specific for eight different  YFV-epitopes (including the HLA-A2-restricted NS4B214 epitope)  and five different control-virus epitopes, as well as cells without dextramer staining were sort-isolated by FACS. Cells were subjected to 5' scRNAseq on a 10x Genomics platform including VDJ-sequencing and  CITEseq for Dextramers, hashtag and surface marker antibodies.

first: Sina

last: Frischholz

first: Ev-Marie

last: Schuster

first: Myriam

last: Grotz

first: Christine

last: Schülein

first: Julia

last: Benz

first: Katharina

last: Kocher

first: Lucia

last: Klotz

first: Szilard

last: Varga

first: Theresa

last: Hiltner

first: Rayya

last: Alsalameh

first: Jan

last: Esse

first: Johannes

last: Träger

first: Jürgen

last: Held

first: Frederik

last: Graw

last: Pahle

first: Bernd

last: Spriewald

first: Luca

last: Gattinoni

first: Veit

last: Buchholz

first: Felix

last: Drost

first: Benjamin

last: Schubert

first: Simon

last: Rothenfußer

first: Dirk

last: Busch

first: Christian

last: Bogdan


title: A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin

status: Public on Nov 19 2025

city: Genève

first: Kimberly

last: Kline

address: 1 Rue Michel Servet

institute: University of Geneva

summary: Daptomycin resistance in Enterococcus faecalis is due to consecutive acquisition of two types of mutation: a primary mutation that constitutively activates the LiaFSR two component system followed by secondary mutations in phospholipid biosynthetic genes. Here, we study how E. faecalis remodels its membrane composition in response to the antibiotic as part of a cell envelope stress response. We show that cell membrane remodelling is due to LTA synthesis by LtaS1. LTA production is under the control of the two component systems LiaFSR, SapRS, and BsrRS and contributes to baseline daptomycin resistance. We propose an updated model of how E. faecalis responds to daptomycin and provide a framework to understand the sequential acquisition of mutations that lead to clinical high-resistance daptomycin resistance.

overall_design: We wanted to understand a) if membrane remodelling in wild-type E. faecalis is regulated on the transcriptional level, and b) uncover the LiaFSR regulon during daptomycin stress. Thus, we determined transcriptional changes in wild-type, ∆liaR, and ∆liaFSR strains exposed to daptomycin. We included three biological replicates of each strain and treated with a subinhibitory concentration of daptomycin for 15 min prior to RNA-Seq analysis. Untreated cultures were used as controls.

first: Cristina

last: Colomer Winter

first: Zeus

last: Nair

first: Jerome

last: Chua

first: Soukayna

last: Jabli

first: Mélanie

last: Roch

first: Amaury

last: Cazenaeve-Gassiot

first: Roberto

last: Sierra

first: Diego

middle: O

last: Andrey

first: Shu Sin

last: Chng


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance

city: La Jolla

first: Randal

middle: J.

last: Kaufman

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program, Center for Genetic Disorders and Aging Research NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

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

overall_design: Refer to individual Series


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance [bulk RNA-seq of TG-AAV-GFP/CRE, DEN/HFD]

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. In contrast to the well-characterized role of ATF6α-activation as an adaptive response to ER-stress, we here demonstrate its hitherto unknown function as an ER stress-inducing oncoprotein and metabolic master-regulator restricting cancer-immunosurveillance. In human HCC, ATF6α-activation significantly correlated with reduced patient-survival, tumor-progression, local immunosuppression, and higher recurrence rates of liver-cancer upon hepatectomy. Hepatocyte-specific ATF6α-activation in mice induced progressive hepatitis with ER-stress, immunosuppression, and hepatocyte-proliferation. Concomitantly, activated-ATF6α increased glycolysis and repressed gluconeogenic enzyme fructose-1,6-bisphosphatase 1 (FBP1). Restoring FBP1 expression prevented ATF6α-activation-related pathologies. Prolonged ATF6α-activation in hepatocytes triggered hepatocarcinogenesis, intratumoral T-cell infiltration, and nutrient-deprived immune-exhaustion. Immune-checkpoint blockade (ICB) efficiently restored immunosurveillance and dramatically reduced HCC. In line, HCC patients with a significantly higher ATF6α-activation signature presented complete response to ICB monotherapy. Targeting Atf6 via germline, hepatocyte-specific ablation, or therapeutic delivery of antisense-oligonucleotides dampened HCC in preclinical liver-cancer models. Thus, prolonged ATF6α-activation drives ER-stress, leading to aberrant glucose metabolism-dependent immunosuppression in liver cancer. Our findings propose persistently activated ATF6α as an oncoprotein, stratification-marker for liver-cancer ICB, and targetable therapeutic strategy against HCC.

overall_design: Gene expression analysis of TG-AAV-GFP/CRE, DEN/HFD mice using RNA-seq

first: Xin

last: Li

first: Cynthia

last: Lebeaupin

first: Mathias

last: Heikenwälder


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance [bulk RNAseq of TG-AAV-GFP/CRE/FBP1]

overall_design: Gene expression analysis of TG-AAV-GFP/CRE/FBP1 mice using RNA-seq


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [RNA-Seq]

status: Public on Nov 13 2025

city: Montrreal

first: Javier

last: Di Noia

state: Quebec

address: 110 Av des Pins Ouest

country: Canada

institute: Institut de Recherches Cliniques de Montreal

summary: Activation-induced deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation of immunoglobulin genes, which are required for efficient antibody responses. Collaterally, AID can also mutate a set of off-target genes with oncogenic consequences. The mechanisms that make such loci susceptible to AID are not fully understood. We find that the H3K79 histone methyltransferase DOT1L is located close to AID in the nucleus. Not only does DOT1L activity facilitate CSR, but it also facilitates AID off-target activity, including Igh-cMyc translocations. Genes mutated by AID display high DOT1L activity. DOT1L deficiency causes mostly increased nascent transcription, accompanied by a modest reduction in RNAPII occupancy. By integrating different genomic approaches, we discovered that DOT1L restricts the velocity of transcription elongation proportionally to the level of higher order H3K79 methylation (H3K79me2/3) and favors RNAPII pausing. These transcriptional conditions enhance AID occupancy and, consequently, its activity. Our data indicate a role for DOT1L and H3K79me2/3 in limiting transcription and highlight stronger RNAPII pausing and attenuated RNAPII elongation velocity as critical steps for productive AID association and mutagenesis at target loci. Furthermore, increased transcription elongation velocity could explain both upregulation and downregulation of genes in DOT1L-deficient cells.

overall_design:
To investige gene expression changes upon Dot1l depletion, CH12F3-G Dot1l knockout cells were generated by CRIPSR.
We then perform paired-end RNA-seq of unstimulated WT and Dot1l-/- CH12F3 cells, using Kc167 cells as spike-in controls.
Differential gene expression for WT vs Dot1l-/- CH12F3-G cells. Normalized counts, log2 fold changes and DESeq2 padj values are in the supplementary file "norm_counts.txt".

first: Poorani

last: Subramani

first: Noé

last: Seija

first: Jana

last: Ridani

first: Jonathan

last: Boulais

first: Paul

last: Donnelly

last: Provencher

first: Halil

last: Bagci

last: Poitras

first: Jean-François

last: Côté

first: François

last: Robert


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [CUT&RUN]

overall_design: CUT&RUN for Rpb1 and CTCF in WT and Dot1l-/- CH12F3-G cells; and CUT&RUN for H3K27me3 in WT CH12F3-G cells.

first: Mélanie

first: Christian


title: Chemoradiation Reprograms Tumor Cells and Immune Microenvironment In Cervical Cancer [bulk RNA-seq]

status: Public on Nov 10 2025

first: Julie

middle: K.

last: Schwarz

department: Radiation Oncology

institute: Washington University in St. Louis

summary: Despite advances in screening and prevention, cervical cancer remains a leading cause of cancer-related deaths worldwide, underscoring the need for better treatments. Here, we present a multi-cohort longitudinal study of human cervical tumors and the tumor microenvironment during chemoradiation therapy (CRT). Integrating RNA sequencing, single-cell transcriptomics, and in vivo validation, we define the cellular and molecular programs shaping cell interactions and document how CRT alters them. We identify multiple therapeutic targets in CRT-resistant tumors, notably MDM2, a key mediator of radiation responses in tumor and immune cells. MDM2 inhibition enhanced radiotherapy effects in HPV-positive, TP53 wild-type cervical cancer cells, improved radiation response and reshaped the immune landscape in preclinical models. These findings highlight the potential of combining MDM2 inhibition with CRT to overcome resistance and improve patient outcomes. Our data provides novel insights into therapy-induced changes in tumor and immune compartments, guiding new strategies against treatment-resistant HPV-positive cancers.

overall_design: RNA-seq profiling of biopsies of primary cervical tumors from patients treated with definitive chemoradiation collected at pre-treatment and at week 3 of treatment

first: Tito

last: Sandoval

first: Yize

first: Naoshad

last: Muhammad

first: Tresha

last: Desai

first: Reyka

last: Jayasinghe

first: Saman

last: Zeeshan

first: Kay

last: Jayachandran

first: Matthew

last: Inkman

first: Michael

last: Waters

first: Naomi

last: Msengi

first: Tyler

last: Mckinnish

first: Ibrahim

last: Hatipoglu

first: Ana

middle: C

last: Paschoalini Mafra

first: Muyassar

last: Anwar

first: Donghua

last: Hu

first: Dhaval

last: Bhatt

first: Varintra

last: Lander

first: R. Jay

last: Mashl

first: Liyun

last: Chen

first: Jessika

last: Contreras

first: Clifford

last: Robinson

first: Sherri

last: Davies

last: Belmar

first: Shunqiang

first: M. Benjamin

last: Major

first: David

last: DeNardo

first: Stephanie

last: Markovina

first: Brian

middle: T

last: Edelson

first: Jin

last: Zhang

first: Li

last: Ding

middle: K


title: Developmental convergence and divergence in human stem cell models of autism spectrum disorder

status: Public on Nov 12 2025

city: Santa Monica

first: Lucy

last: Bicks

address: 1033 3rd street, apartment 106, apartment 106

department: Neurology

institute: UCLA School of Medicine

summary: Two decades of genetic studies in autism spectrum disorder (ASD) have identified over a hundred genes harboring rare risk mutations. Despite this substantial heterogeneity, transcriptomic and epigenetic analyses have identified convergent patterns of dysregulation across ASD post-mortem brain. To identify shared and distinct mechanisms of ASD-linked mutations, we assembled the largest patient hiPS cell cohort to date, consisting of 70 hiPS cell lines after stringent quality control representing 8 ASD-associated mutations, idiopathic ASD, and 20 lines from non-affected controls. We used these hiPS lines to generate human cortical organoids (hCO), profiling by RNAseq at four distinct timepoints up to 100 days after in vitro differentiation. Early timepoints harbored the largest mutation-specific changes, but different mutations converged on shared transcriptional changes as development progressed. We identified a shared RNA and protein interaction network, which was enriched in ASD risk genes and predicted to drive the observed down-stream changes in gene expression. CRISPR-Cas9 screening of these candidate transcriptional regulators in induced human neural progenitors validated their downstream molecular convergent effects. These data illustrate how genetic risk can propagate via transcriptional regulation to impact convergently dysregulated pathways, providing new insight into the convergent impact of ASD genetic risk on human neurodevelopment.

overall_design:
To investigate the effects of ASD-linked mutations on gene expression changes across development in human cortical organoids.

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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first: Aaron

last: Gordon

first: Se-Jin

last: Yoon

first: Sergiu

last: Pasca

first: Daniel

last: Geschwind


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [ChIP-seq]

first: Javier

middle: M

last: Di Noia

overall_design: Quantitative ChIP-seq for RNAPII, S2P-RNAPII, S5P-RNAPII, Rad21 and Nipbl in WT and Dot1l-/- CH12F3-G cells; and ChIP-seq for H3K79me2 and H3K79me3 in WT CH12F3-G cells.

first: Poorani Ganesh

last: Subramani

first: Noé

last: Seija

first: Jana

last: Ridani

first: Jonathan

last: Boulais

first: Paul

last: Donnelly

first: Mélanie

last: Provencher

first: Halil

last: Bagci

first: Christian

last: Poitras

first: Jean-François

last: Côté

first: François

last: Robert


title: PDE4B deficiency aids macrophage Trojan horses to transfer Cryptococcus neoformans into the brain

status: Public on Nov 06 2025

city: nanjing

first: ying

last: gong

address: The Jiangning Campus of Nanjing Medical University is located at No. 101 Longmian Avenue, Jiangning District, Nanjing, China.

institute: nanjing medical university

summary: Cryptococcal meningitis (CM) is a fatal compliation. Macrophages work as Trojan horses transferring Cryptococcus neoformans (C. neoformans) into the brain. Mechanisms for C. neoformans Trojan horses are largely elusive. In this study, we performed scRNA-Seq on immune cells infiltrated into the brain in a murine model of CM. Bioinformatics analysis reveals that phosphodiesterase 4B (PDE4B) ranks top in regulating macrophage Trojan horses. Melanin, a virulence factor for Cn, decreased PDE4B in macrophages. PDE4B inhibitor promoted the Cn Trojan horse across the blood-brain-barrier (BBB) in vitro and in vivo. As similar, PDE4B knockout increased fungi burden in the brain, which is, at least partially, rescued by macrophages depletion. In contrast, PDE4B activation diminished C. neoformans brain infection. Mechanistically, PDE4B inhibition increased CXCR4 and CCR7 on C. neoformans macrophage Trojan horses, a process regulated by the cAMP/PKA signaling pathway. Dexamethasone, commonly used to treat Pneumocystis infections in AIDS patients, significantly decreased PDE4B expression in macrophages. Overall, this study reveals that PDE4B plays a crucial role in C. neoformans macrophage Trojan horses and serves as a potential therapeutic target for CM.

overall_design: To elucidate the characteristics of Trojan cells during Cryptococcus neoformans brain infection, we isolated CD45+ cells from the brain tissue of mice infected with the H99Tdtomato strain and conducted single-cell RNA sequencing (scRNA-Seq) analysis. Clustering analysis of the transcriptomic data, based on known marker genes and literature, followed by UMAP dimensionality reduction, revealed the composition of infiltrating cells in the brain tissue post-infection. To further identify the cell types associated with Cryptococcus infection, we analyzed the distribution of fungal RNA across different cell types.


title: RNAseq data of frontal cortex of 4 months high fat diet fed WT, AKO,  4 months high fat diet fed conditional human amylin expressing mice followed by vehicle and Tamoxifen injection, and 2 months high fat diet fed WT mice

status: Public on Nov 15 2025

city: Lexington

first: Nirmal

last: Verma

state: Kentcuky

address: 900 S Limestone

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

summary: We performed gene expression profiling analysis using data from RNAseq of brain frontal cortex from four months high fat diet fed WT (n=10), AKO (n=10), four months high fat diet fed condition human amylin mice followed by vehicle (n=10) or Tamoxifen (n=10) injection for another two months, and 2 months high fat diet fed WT mice (n=10).

overall_design:
Expression profiling by high throughput sequencing
CreVE: four months high fat diet fed condition human amylin mice followed by vehicle
CreTM: four months high fat diet fed condition human amylin mice followed by Tamoxifen
4MHFW: four months high fat diet fed WT
4MHFA: four months high fat diet fed AKO
2MHF: 2 months high fat diet fed WT mice

first: Davargaon

last: Ravichandra

first: verma

last: nirmal

first: Kotiya

last: Deepak

first: Leibold

last: Noah

first: Despa

last: Sanda

first: despa

last: florin


title: Metabolostasis failure thresholds are linked with network topology, metabolite solubility, and translational control

status: Public on Nov 05 2025

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Cells maintain metabolite homeostasis (metabolostasis) by buffering fluctuations in metabolite levels, yet the limits of this buffering and the mechanisms underlying metabolic toxicity remain poorly understood. To study this, we systematically overfed metabolites in Saccharomyces cerevisiae and quantified associations with growth inhibition, intracellular aggregation, and multiomic perturbations. We identify metabolite-specific failure thresholds at which amyloid-like aggregates are observed, with graded growth inhibition detectable at sub-threshold concentrations, suggesting toxicity mechanisms beyond transporter saturation. Metabolites with higher network influence and broader pathway participation are associated with higher failure thresholds and smaller pathway disturbances. These patterns are associated with chemical properties and solubility: more soluble metabolites, while broadly tolerated, are associated with localised aggregates at their failure thresholds, whereas less soluble metabolites are associated with larger systemic pathway disruptions. Multiomic integration identifies a two-tiered translational regulatory architecture characterising cellular resilience to metabolic overfeeding. General resilience is associated with transcriptional commitment to resource conservation via attenuation of anabolic pathways. Metabolite-specific defense is characterised by high-magnitude translational regulatory events; for example, engagement of aromatic catabolism under phenylalanine overfeeding and energetic control pathways under glycine overfeeding. Together, our results operationally define metabolostasis as a cellular system associated with constraint of metabolite concentrations, coordination of network and pathway-level regulation, and buffering against amyloid-like aggregation, highlighting how network topology, pathway architecture, and chemical properties are associated with metabolic resilience and toxicity thresholds.

overall_design: We systematically characterise metabolostasis through controlled metabolite overfeeding in Saccharomyces cerevisiae, quantifying failure thresholds for twenty-three metabolites alongside metabolomic, transcriptomic, and proteomic responses. While single-metabolite perturbations do not fully recapitulate the complexity of physiological metabolite mixtures, this framework enables systematic mapping of metabolite-specific buffering capacity and exposes failure modes that may be obscured under combinatorial conditions. Integrating these data, we find that failure thresholds are associated with metabolic network topology and metabolite solubility, and that cellular resilience is characterised by a two-tiered post-transcriptional regulatory architecture, which emerges as a general resource-conservation program superimposed by metabolite-specific high-magnitude translational responses.

first: Shon

last: Levkovich

first: Christine

last: Lim

first: Emi

last: Marzini

first: Hanaa

last: Adsi

first: Maoz

last: Lahav

first: Ilana

last: Sogolovsky-Bard

first: Myra

last: Gartner

first: Keila

last: Kaplan

first: Yasmin

last: DeRowe

first: Alexander

last: Brandis

first: Michele

last: Vendruscol

first: Ehud

last: Gazit

first: Dana

last: Laor Bar-Yosef


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [TT(chem)-seq]

first: Javier

last: Di Noia

overall_design:
To investigate changes in nascent transcription upon Dot1l depletion, CH12F3-G Dot1l knockout cells were generated by CRIPSR.
We then perform paired-end TT(chem)-seq of unstimulated WT and Dot1l-/- CH12F3 cells, using S. cerevisiae (strain BY4741) cells as spike-in controls.

first: Poorani Ganesh

last: Subramani

first: Noé

last: Seija

first: Jana

last: Ridani

first: Jonathan

last: Boulais

first: Paul

last: Donnelly

first: Mélanie

last: Provencher

first: Halil

last: Bagci

first: Christian

last: Poitras

first: Jean-François

last: Côté

first: François

last: Robert


title: Single-cell transcriptomic characterization of immune cells from livers of wild type and ATF6 transgenic mice

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We isolated CD45+ cells from livers of wild type and hepatocyte-specific nATF6 overexprerssion mice for scRNAseq to decrible the the immune cell population.

overall_design: In total 8 samples were included, 4 from wild type mice and 4 from ATF6 transgenic mice.

first: Mathias

last: Heikenwälder

first: Xin

last: Li


title: MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

address: 4515 McKinley Ave

department: Genetics

summary: More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, Multiplexed Analysis of Short Tandem Repeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses.

overall_design: Multiplexed STR analysis by target nanopore sequencing in human iPSC or  ESC samples modeling human pathological STR expansion related neurological diseases, like fragile-X-syndrome and huntington diseases.

first: Chuanbin

last: Su

first: Han-Seul

last: Ryu

first: Keerthivasan

last: Chandradoss

first: Thomas

last: Malachowski

first: Ravi

last: Boya

first: Kristen

last: Brennand

middle: E


title: Liver transcriptomic profile of 3 months old wild type and hepatocyte-specific ATF6 overexpression mice

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination. At 3 months age, livers from the transgenic mice and their wild type controls were harvested for RNA isolation and followed with RNA-sequencing.

overall_design: In total 12 samples were included, 5 from wild type mice and 7 from ATF6 transgenic mice.


title: Chemoradiation Reprograms Tumor Cells and Immune Microenvironment In Cervical Cancer [scRNA-seq]

first: Julie

last: Schwarz

overall_design: scRNA-seq of primary tumor samples from 10 cervical cancer patients treated with definitive chemoradiation obtained before treatment (pre-RT), and at 1–2 weeks (on-RT#1) and 2–3 weeks (on-RT#2) after the initiation of chemoradiation

first: Tito

last: Sandoval

first: Yize

first: Naoshad

last: Muhammad

first: Tresha

last: Desai

first: Reyka

last: Jayasinghe

first: Saman

last: Zeeshan

first: Kay

last: Jayachandran

first: Matthew

last: Inkman

first: Michael

last: Waters

first: Naomi

last: Msengi

first: Tyler

last: Mckinnish

first: Ibrahim

last: Hatipoglu

first: Ana

last: Paschoalini Mafra

first: Muyassar

last: Anwar

first: Donghua

last: Hu

first: Dhaval

last: Bhatt

first: Varintra

last: Lander

first: R. Jay

last: Mashl

first: Liyun

last: Chen

first: Jessika

last: Contreras

first: Clifford

last: Robinson

first: Sherri

last: Davies

last: Belmar

first: Shunqiang

first: M. Benjamin

last: Major

first: David

middle: G

last: DeNardo

first: Stephanie

last: Markovina

first: Brian

last: Edelson

first: Jin

last: Zhang

first: Li

last: Ding


title: Liver transcriptomic profile of 6 months old wild type and hepatocyte-specific ATF6 overexpression mice

first: Kristian

last: Unger

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination. At 6 months age, livers from the transgenic mice and their wild type controls were harvested for RNA isolation and followed with RNA-sequencing.

overall_design: In total 13 samples were included, 6 from wild type mice and 7 from ATF6 transgenic mice.

first: Mathias

last: Heikenwälder

first: Xin

last: Li


title: Bovine host transcriptomics to evaluate how markets and vaccines influence health and disease

status: Public on Nov 07 2025

city: Canyon

first: Matthew

last: Scott

state: TX

address: 3201 Russell Long Blvd

institute: Texas A&M University

summary: To evaluate how commercially available vaccines and marketing strategy affect the host transcriptome of commercial beef cattle overtime, we sequenced the whole blood RNA of 73 commercial beef bull calves enrolled in a split plot study. Calves were randomized to one of four groups, having received a commercially available vaccine during the cow-calf phase or not, and placed in a commercial salebarn system after weaning (auction) or directly shipped to backgrounding (direct). Samples were acquired from six time points: T1 (modified live viral (MLV) vaccination; age: ~107 d.), T2 (seven days post-vaccination; age: ~114 d.), T3 (revaccination; age: ~183 d.),  T4 (abrupt weaning; age: ~230 d.), T5 (arrival to backgrounding after marketing decision; age: ~233 d.), and T6 (45 days post-arrival to backgrounding; age: ~278 d.). Further evaluation was made based on whether calves were clinically diagnosed with bovine respiratory disease (BRD) after weaning.

overall_design: Whole blood from 73 randomly selected individuals with relative equal allocation across study group and disease acqusition were used for gene expression profiling and differential analysis across six time points (T1-T6).

first: Robert

last: Valeris-Chacin

first: Sarah

last: Capik

first: Bradly

last: Ramirez


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID

first: Javier

last: Di Noia

overall_design: Refer to individual Series


title: Genomic copy number number characterisation of liver tissues in wildtype mice and ATF6-transgenic mice.

summary: We compared the genomic copy number profiles of liver tissues of wild type mice with that of ATF6-transgenic mice after 3 and 12 months, respectively.

overall_design: Genomic DNA from tissue samples was hybridised against a pooled reference DNA from healthy mice.