title: Promoter competition and Polycomb Response Elements govern transvection efficiency between co-regulated engrailed and invected genes in Drosophila.

status: Public on Sep 25 2025

first: Natalie

middle: Dianna

last: Gehred

address: 650 Charles E Young Dr

department: Anesthesiology & Perioperative Medicine

institute: University of California, Los Angeles

summary: Transvection is a phenomenon where gene regulatory elements interact between different chromosomes, adding an additional layer of regulatory control beyond traditional cis-interactions. Although transvection effects have been characterized for many individual genes in Drosophila, it remains unclear how trans-interactions occur among multiple co-regulated genes where enhancers are shared. Here we demonstrate that transvection is supported at the engrailed-invected (en-inv) locus, where transcription of the two developmental patterning genes is coordinated by common enhancers. Our data show that the presence of the en promoter in cis to the enhancers prevents trans-activation of inv, but removal of this promoter enables robust transvection, demonstrating competition between heterologous promoters in trans. We also find that local Polycomb Response Elements (PREs) enhance transvection reliability but are not strictly required for trans-activation. Furthermore, our analysis reveals that transvection at this locus is developmentally regulated, occurring efficiently in third instar larval tissues and late-stage embryos but not in early embryonic stages. Finally, we show that en-inv transvection can be reconstituted using transgenic constructs at an ectopic chromosomal location where it produces a striking reciprocal expression pattern between en in cis and inv in trans, suggesting that these enhancers can choose to activate one promoter or the other in a stochastic manner.

overall_design: ChIP-seq of H3K27me3 histone post-translational modification in Drosophila melanogaster 3rd instar larval brains and wing imaginal discs from homozygotes of the HAinv84-invdel45 and invdel45 lines.

first: Yuzhong

last: Cheng

first: Adrienne

middle: T

last: Perkins

first: Fountane

middle: W

last: Chan

first: Jack

last: Bateman

first: Judith

last: Kassis


title: Identification of a shared drug-tolerant persister program in triple-negative breast cancer across treatments and patients [CUT&Tag]

status: Public on Sep 22 2025

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acquisition of resistance to anti-cancer therapies is a multistep process, which initiates with the survival of drug tolerant persister cells. Understanding the mechanisms driving the emergence of drug tolerant persister cells remains challenging, primarily because of their limited accessibility in patients. Here, using multiple patient-derived models to isolate persister cells, we show these cells are transcriptionally plastic in vivo and return to a common treatment-naïve like state upon relapse, regardless of the treatment they have been exposed to. We reveal hallmarks of the persister state in TNBC across treatment modalities: high expression of basal keratins together with activation of a stress response and inflammation pathways. HER2+ breast and lunger cancer cells also activate these hallmarks of drug tolerance in response to targeted therapies. Leveraging gene regulatory networks, we identify AP-1, NFKB and IRF/STAT as the key drivers of this hallmark persister state. As a proof of concept, we show that FOSL1 - an AP-1 member - is sufficient to drive cells to the persister state by binding enhancers and reprogramming the transcriptome of cancer cells. On the contrary, cancer cells without FOSL1 have a decreased ability to reach the persister state. By defining hallmarks of drug persistence to multiple therapies of the standard of care in TNBC, our study provides a resource to design novel combination therapeutic strategies to limit resistance.

overall_design: CUT&Tag was performed on a pool of samples of MDA-MB-468, WT or GOF (HA and VPR), treated with DMSO or 5-FU, for H3K27ac and FOSL1.

first: Léa

last: Baudre

first: Grégoire

last: Jouault

first: Justine

last: Marsolier


title: Endothelins influences the proliferation-migration balance of IDH1-mutant glioma cells and promotes proneural to mesenchymal transition [RNAseq-275HCMEC]

status: Public on Sep 05 2025

city: Montpellier

first: Donovan

last: PINEAU

address: 141 Rue de la Cardonille

institute: IGF

type: Expression profiling by high throughput sequencing

summary: Adult diffuse gliomas are the deadliest brain tumours including IDH-wildtype glioblastomas of worst prognosis and diffuse low grade IDH-mutant astrocytomas and oligodendrogliomas. These glial tumours display distinct tumoral cell population defeating current therapies. Our group has unveiled the role of NOTCH signalling in glioblastoma cell plasticity and in the conversion of oligodendrocytic-like to astrocytic-like tumoral cells in IDH-mutant low-grade gliomas which escalate inevitably to higher grade malignant gliomas. To gain insight into signalling pathways regulating glioma cell plasticity and malignancy, we focused our work on endothelin signalling including endothelin peptide ligands (ET-1, ET-2, ET-3) binding to G-protein coupled endothelin receptors A and B (EDNRA, EDNRB).  Here, using glioma patient samples and glioma patient-derived cell lines, we showed that endothelin reduces glioma cell proliferation while increasing migration initiating a proneural to mesenchymal transition. Mechanistically, EDNRB activation led to IP3-dependent calcium mobilization, apamin-sensitive KCNN2/KCNN3 potassium currents and phosphorylation of ERK1/2 and STAT3 in glioma cells. Finally, we studied endothelin receptor regulation by tumoral microenvironment stimuli highlighting a role for EDNRA induced by NOTCH and hypoxia in perivascular hypoxic area in glioblastoma. Altogether, this study demonstrates endothelin signalling as a key player in mesenchymal transformation of diffuse IDH-mutant gliomas and glioblastomas.

overall_design: RNAseq analyses of a diffuse low-grade glioma LGG275 cells upon cocultures with hCMEC/D3 endothelial cells (human blood brain barrier capillary microvascular endothelial cell line)

first: Jean-Philippe

last: HUGNOT


title: Identification of a shared drug-tolerant persister program in triple-negactive breast cancer across treatments and patients [scRNA-Seq]

overall_design:
scRNAseq of HBCx39, HBCx95, HBCx172, HBCx221 and HBCx218 Patient Derived Xenograft (PDX) of Triple Negative Breast Cancer (TNBC) in response to chemotherapies (Capecitabine and Anthracyclines

***************************************************************
Raw FASTQ files are not publicly available due to patient data privacy considerations.
***************************************************************

first: Elisabetta

last: Marangoni


title: Endothelins positively influences the proliferation vs migration balance of IDH1-mutant glioma cells and promotes proneural to mesenchymal transition [RNAseq-275HUVEC]

overall_design: RNAseq analyses of a diffuse low-grade glioma LGG275 cells upon endothelial cells cocultures with HUVEC cells (Human Umbilical Vein Endothelial Cells)


title: Targeting fatty acid synthase suppresses tumor development in NF2/CDKN2A-deficient malignant pleural mesothelioma

status: Public on Sep 19 2025

city: Nagakute

first: Karnan

last: Sivasundaram

state: Aichi

address: Yazakokarimata

department: Biochemisy

country: Japan

institute: Aichi Medical University

summary: To investigate the effect of cerulenin in NF2/p16 on gene expression, we have emoloyed whole genomic microarray expression profiling using HOMC-B1 and MeT-5Acells

overall_design: The HOMC-B1 and MeT-5A cells were plated at 80% confluence and cultured for 24 hours in vitro.

first: Akinobu

last: Ota

first: Sivasundaram

last: Karnan


title: Exogenous Delivery of Sphingomyelinase Mediates Mesenchymal Stromal Cell-Extracellular Vesicle Biogenesis, Alters Cargo Sorting, and Therapeutic Potency in vitro

status: Public on Sep 03 2025

city: Atlanta

first: Daniel

middle: C

last: Shah

state: Ga

address: 315 Ferst Dr.

department: Biomedical Engineering

country: USA

institute: Georgia Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Mesenchymal stromal cells (MSCs) are multipotent stromal cells with regenerative, immunomodulatory, and anti-inflammatory properties, making them a promising tool in cell-based therapies. Increasing evidence suggests the therapeutic effects of MSCs are largely mediated by secreted paracrine factors and extracellular vesicles (EVs), which facilitate extracellular communication by transferring bioactive molecules such as proteins, lipids, and nucleic acids to target cells. The lipid composition of EVs is critical for their stability, uptake, and functional activity. Sphingomyelinase (SMase), an enzyme that hydrolyzes sphingomyelin into ceramide, plays a key role in EV biogenesis by influencing membrane curvature allowing for invagination and budding of multivesicular bodies (MVBs). However, the impact of SMase treatment on the characteristics and therapeutic potential of MSC-derived EVs remains largely unexplored. In this study, human MSCs were cultured with SMase for 24 hours and EVs were isolated via ultracentrifugation. EV size distribution was analyzed using nanoparticle tracking analysis (NTA), microRNA (miRNA) profile was determined using RNA-sequencing, while lipidomic and proteomic profiling were assessed using mass spectrometry. Functional assays were conducted to assess changes in bioactivity. NTA revealed a shift in EV production, with a higher vesicle concentration in SMase induced MSCs compared to untreated cells. SMase treatment significantly altered MSC-EV composition, leading to increased ceramide and glycosphingolipids. In addition, the modifications in protein and miRNA EV cargo were found to be associated with pathways involving TNF-α signaling, vesicle trafficking, wound healing, and angiogenesis. Functional assays indicated greater suppression of TNF-α in activated macrophages and greater tubular network formation in HUVECS. These findings provide new insights into distinct biophysical and biochemical changes in MSC-derived EVs following SMase stimulation, potentially enhancing their therapeutic properties and may inform strategies for optimizing future EV-based therapies.

overall_design: MSCs were treated with SMase for 24 hours and the miRNA profile of MSCs and their derived EVs was sequenced.

first: S'Dravious

middle: A

last: DeVeaux

first: Edward

last: Botchwey


title: Identification of transcriptional targets for Dif and Dorsal in intestinal cells of fly

status: Public on Sep 18 2025

city: Changsha

first: peng

middle: guo

last: fan

state: Hunan

address: Lushan Road

country: China

institute: Hunan University

summary: The regulation of Toll signalling pathway in non-immune functions remains unclear. In this study, we found that Toll pathway regulates intestinal stem cells activity of drosophila. To further explore the potential regulation mechanism, we performed cleavage under target and tagmentation (Cut&Tag) analysis to identify candidate genes regulated by Dif and Dorsal (core transcription factors in Toll pathway) in total intestinal cells.

overall_design: Using transgenic flies with Dif-GFP or Dorsal-GFP fusion protein, the transcriptional targets for Dif and Dorsal in total intestinal cells were examined.

first: Guofan

last: Peng

first: Jun

last: Zhou


title: Altered Cell Clusters and Upregulated Aqp1 in Connexin 50 Knockout Lens Epithemium

city: Berkeley

first: Xiaohua

last: Gong

state: CA

address: 695 Minor Hall

department: School of Optometry

institute: University of California, Berkeley

summary: To characterize the heterogeneity and cell clusters of postnatal lens epithelial cellsLens epithelial cells exhibit an intrinsic heterogeneity of different cell clusters in regulating lens homeostasis and lens growth. Upregulated Aqp1 in Cx50KO lens epithelial cells suggests that both connexin 50 and AQP1 likely play important roles in regulating water homeostasis in lens epithelial cells. (LECs) and to investigate the downstream targets of connexin 50 (Cx50) in the regulation of lens homeostasis and lens growth. To determine differentially expressed genes (DEGs) in the connexin 50 knockout (Cx50KO) lens epithelial cells that shed light on novel mechanism underlying the cataract and small size of the Cx50KO lenses.

overall_design:
Single-cell RNA sequencing (scRNA-seq) of lens epithelial cells isolated from one-month-old Cx50KO and wild-type (WT) mice were performed.
Please note that R2 mate file of the 'lens epithelium,cx50ko,biorep1' sample (paired-end) raw data files is corrupted and thus only R1 file is provided as raw data.

first: Chun-Hong

last: Xia

first: William

last: Lin

first: Rachel

last: Li

first: Xinfang

last: Xing

first: Guangdu

middle: J

last: Shang

first: Haiwei

last: Zhang


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [MPRA_shRBMS3]

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet post-transcriptional regulation likely influences these patterns as well. However, the quantitative contribution of post-transcriptional mechanisms to cancer transcriptome dynamics remains unclear. Here, we systematically measured mRNA dynamics across diverse breast cancer models, revealing that mRNA stability significantly shapes gene expression variability. To decipher the regulatory grammar underlying these dynamics, we developed GreyHound, an interpretable multimodal deep-learning framework integrating RNA sequence features and RNA-binding protein (RBP) expression. GreyHound identified an extensive network of RBPs and their regulons underlying variations in mRNA stability. Among these, we uncovered a metastasis-suppressive regulatory axis centered on the RNA-binding protein RBMS3 and its post-transcriptional control of the redox regulator TXNIP. Functional and molecular analyses revealed that RBMS3 depletion resulted in targeted transcript destabilization, which was associated with poor clinical outcomes and enhanced metastatic potential in xenograft models. Using in vivo epistasis studies, we confirmed that RBMS3 regulation of TXNIP mRNA stability drives this metastasis-suppressive program. These findings position the RBMS3-TXNIP regulatory axis as a key post-transcriptional mechanism in breast cancer and illustrate how interpretable models of RNA dynamics can uncover hidden regulatory programs in disease.

overall_design: To validate RBMS3 binding sites, we applied a dual mCherry/GFP reporter assay for 13 RBMS3 binding site sequences and respective scrambled controls. This parallel reporter library was expressed in RBMS3 knockdown and control MDA-MB-231 cells to evaluate differential stability of transcripts containing RBMS3 binding sites.

first: Heather

last: Karner

first: Tabea

last: Mittmann

first: Vicky

last: Chen


title: Sex-related differences in gene expression in early-stage bladder cancer revealed by whole-transcriptome sequencing

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Bladder cancer (BC) is significantly more prevalent in men than in women, yet female patients often experience higher recurrence rates and poorer prognosis. Our study aimed to investigated sex-specific gene expression differences in early-stage BC using whole-transcriptome sequencing. A total of 51 patients diagnosed with low-grade Ta stage non-muscle-invasive bladder cancer were recruited. Paired tissue samples from tumor lesions and adjacent healthy bladder mucosa were analyzed to identify differentially expressed genes (DEGs). Among the top 100 most significant DEGs, overwhelmingly more upregulated were in male than female tissues (90% vs. 19%). The most significantly altered expression in female BC tissues included MT-ND6, ARL4C, ASGR1, MYBL1, and SCAMP5, whereas in males, ONECUT2, SPEG, CTSE, GJB2, and SYNM. Notably, 753 DEGs were unique to female patients, while 3989 were specific to males, with 1633 shared between both sexes. Functional annotation revealed that female-unique DEGs were significantly enriched in immune-related pathways, including regulation of leukocyte activation and cell-cell adhesion, and lymphocyte differentiation. Whereas male-unique DEGs were predominantly associated with pathways related to cell cycle regulation, mitochondrial function, and androgen receptor signaling. Immune-related gene expression indicated that female-specific DEGs were involved in leukocyte activation and antigen receptor signaling, whereas male-specific DEGs were linked to B-cell activation and neutrophil-mediated immune responses. A two-factor interaction model identified S100A14 as the only protein-coding gene whose expression exhibited a significant sex-dependent pattern, with four additional genes (GJB2, DSC2, TM4SF and ALOX15B) showing a probable interaction effect. These findings highlight the necessity for sex-specific therapeutic strategies in BC management.

overall_design: Patients  diagnosed with bladder tumors were recruited to the study. Paired tissue samples of bladder tumor and adjacent healthy-appearing bladder mucosa were collected from men and women. The gender-related differences in gene expression were determined using whole transcriptome sequencing.

first: Natalia

last: Zeber-Lubecka

first: Konrad

last: Bilski

first: Michalina

last: Dąbrowska

first: Jerzy

last: Ostrowski

first: Jakub

last: Dobruch

first: Ewa

middle: E

last: Hennig


title: Engineering a superactivator of smooth muscle gene expression with the Myocardin condensate forming region [RNA-seq]

status: Public on Sep 02 2025

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: Differentiation of smooth muscle cells (SMCs) is accompanied by the expression of a battery of genes controlled by serum response factor (SRF), a ubiquitous transcription factor with weak intrinsic transcriptional activity. Myocardin (MYOCD) is a potent transcriptional coactivator that activates smooth muscle differentiation through its association with SRF. MYOCD forms condensates through its highly disordered transcription activation domain (TAD), whereas SRF displays a diffuse distribution within the nucleus. SRF is recruited to nuclear condensates by the TAD of MYOCD (MYOCD-TAD), thereby triggering the smooth muscle gene program. Swapping the weak TAD of SRF with that of MYOCD enables SRF to form condensates and acquire the ability to reprogram fibroblasts to SMCs. SRF-MYOCD-TAD chimeric protein exhibits stronger transcriptional activity on smooth muscle genes than MYOCD. Using protein proximity labelling, quantitative proteomics and super-resolution confocal microscopy, we show that MYOCD-TAD condensates aggregate chromatin remodelers, RNA polymerases, and mRNA processing factors to drive smooth muscle gene expression. These findings provide insights into the mechanisms whereby nuclear condensates promote tissue-specific gene expression and point toward a strategy for engineering superactivators leveraging transcriptional condensates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data and chromatin occupancy and chromatin accessibility (H3K27ac) by ChIP-seq data for 10T1/2 cells reprogrammed by GFP (control), SRF, and SRF chimeric mutants (SRF-MYOCD-TAD, SRF-MYOCD-TAD-FWY/A, SRF-FUSN).

first: Peiheng

last: Gan

first: Akansha

middle: M

last: Shah

first: Svetlana

last: Bezprozvannaya

first: Kenian

first: Qianqian

last: Ding

first: Hui

first: Xinyi

last: Zhou

first: Ning

last: Liu

first: Eric

middle: N

last: Olson


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

first: Hani

last: Goodarzi

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

overall_design: Refer to individual Series


title: RNA-seq in parental and resistant non-small cell lung cancer (NSCLC) cells

status: Public on Sep 16 2025

city: Shenyang

first: sihong

address: Wenhua Road

institute: Shenyang Pharmaceutical University

summary: Crotonylation is a crotonyl-coenzyme A (CoA)-mediated post-translational modification best known for its roles in epigenetic regulation. Histone lysine crotonylation (Kcr) has been reported to be involved in tumor-related biological functions such as DNA damage repair and immune infiltration. Here we find that abnormal reduction of histone Kcr significantly correlates with a poor response to epithelial growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in resistant models of lung cancer cell lines, and in cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. The crotonyl-CoA-producing enzyme ACSS2 is the key regulator of the resistance-related change of crotonylation. Quantitative crotonylomic, transcriptomic and epigenomic analyses reveal that EGFR-TKI resistance is accompanied by reduced levels of histone 3 lysine 56 crotonylation (H3K56cr) on chromatin, which inhibits transcription of HNF1A and activates the PI3K/AKT signaling pathway.

overall_design: To uncover how histone Kcr regulates target genes and downstream signaling pathways to mediate EGFR-TKI resistance, RNA-seq was performed to analyze transcriptional changes in HCC827 and HCC827_Er cells with 3 replicates.

first: Sihong

last: Chen

first: Xiaoyuan

last: Wang

first: Youwei

last: Su


title: Disrupting YAP phase separation attenuates the development of primary liver cancer in animal models

city: Xiamen

first: Lijun

last: Cai

address: No. 668, Jinhu Road

department: Central Laboratory,

institute: Zhongshan Hospital (Xiamen), Fudan University

summary: In these murine liver cancer samples, we used specific antibody detection to find endogenous YAP formation condensates in the focal area, a phenomenon also observed in human liver cancer tissues. Deletion, mutagenesis and replacement assays of the coiled-coil (CC) domain demonstrate a critical role of activated YAP condensation in c-Myc-induced hepatoma, myr-AKT-induced intrahepatic cholangiocarcinoma, and N90-CTNNB1-induced hepatoblastoma. Transcriptome sequencing revealed that YAP phase separation inhibits AMPK activation and promotes c-Myc-induced hepatoma development. Our research indicates that condensates driven by YAP phase separation enrich TAK1, an AMPK-activated upstream kinase, potentially creating a physical barrier to AMPK phosphorylation activation. In addition, we further demonstrated that a specific peptide derived from TEAD1 disrupts the formation of YAP condensates and attenuates the development of these primary liver cancers.

overall_design: Transcriptomic sequencing was conducted on liver cancer tissues induced by YAP-S127A/c-Myc and YAP-S127A-4LE/c-Myc.

first: Shuang-zhou

last: Peng

first: Fu-quan

last: Jiang

first: Jia-jia

last: Liang


title: Multi-step genomics on single cells and live cultures in sub-nanoliter capsules

status: Public on Sep 09 2025

city: Boston

first: Ignas

last: Mazelis

state: MA

address: 210 Longwood Avenue

department: System Biology

institute: Harvard Medical School

summary: Single-cell genomics encompasses a set of methods whereby hundreds to millions of cells are individually subjected to multiplexed assays including sequencing DNA, chromatin accessibility or modification, RNA, or combinations thereof 1,2. These methods enable unbiased, systematic discovery of cellular phenotypes and their dynamics 1–3. Many functional genomic methods, however, require multiple steps that cannot be easily scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells, mRNA, and gDNA, while allowing free diffusion of media, enzymes and reagents. CAGEs enable carrying out high-throughput assays that require multiple steps, including combining genomics with live-cell assays. We establish methods for barcoding CAGE DNA and RNA libraries, and apply them to measure persistence of gene expression programs by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extend them to live-cell assays.

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus

overall_design:
RNA-seq data for the establishment of Capsule-based multi-step processing of single-cell in cultures. Data includes inC-RNAseq of fresh, frozen, and fixed cell lines, frozen PBMCs and cell lines cultured in CAGES. Washed cells were encapsulated into CAGEs, lyzed, washed, followed by mRNA capture via oligo-dT RT. cDNA was amplified in CAGEs, barcoded using split-pool implementation. Barcoded cDNA was used for 3’ end RNA-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Data also included single-cell inC-ATACseq data of cell lines, GFP-RFP gDNA amplicon sequencing of individual cells as well as plasmid barcoding test. Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT/ATAC/PCR barcode and UMI [for RNAseq].

Plasmid_sequencing: Sequencing data for the establishment of Capsule-based multi-step processing of single-cell and cultures. Data includes inC-seq barcoding of plasmid DNA processed in CAGES. DNA containing CAGEs were washed and plasmid DNA were amplified in CAGEs, barcoded using split-pool barcode addition. Barcoded DNA amplicon were indexed and sequenced using Illumina
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - gDNA amplicon; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1 and CMV gDNA loci.

Fresh_Fixed: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of fresh and PFA fixed K562 cells processed in CAGES. Washed cells were encapsulated into CAGEs, lyzed (decrosslinked in PFA case), washed, followed by mRNA capture via oligo-dT RT. cDNA was amplified in CAGEs, barcoded using split-pool implementation. Barcoded cDNA was used for 3? end RNA-seq library preparation using NEBNext® Ultra? II DNA Library Prep Kit for Illumina.
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT/ATAC/PCR barcode and UMI [for RNAseq].

gDNA_Amplicons: Sequencing data for the establishment of Capsule-based multi-step processing of single-cell and cultures. Data includes inC-seq barcoding of GFP and RFP gDNA amplicon derived from a 1:1 mix of K562 and L1210 single-cells processed in CAGES. Washed cells were encapsulated into CAGEs, lyzed, washed, followed by mRNA capture via oligo-dT RT. gDNA targeted with CMV and RFP or GFP loci primers was amplified in CAGEs and barcoded using split-pool CAGE aproach. Barcoded gDNA amplicon were indexed and sequenced using Illumina
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - gDNA amplicon; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1 and CMV gDNA loci.

PBMCs: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of cryopreserved PBMCs processed in CAGES. Thawed and washed cells were encapsulated into CAGEs, lyzed, washed, followed by mRNA capture via oligo-dT RT. cDNA was amplified in CAGEs and barcoded using inC-seq split-and-pool implementation. Barcoded cDNA was used for 3? end RNA-seq library preparation using NEBNext® Ultra? II DNA Library Prep Kit for Illumina.
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT and UMI.

Cell_Culturing: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of K562, L929 and induced pluripotent stems cells cultured in CAGES. After culturing, cells were lyzed followed by mRNA capture via oligo-dT RT. cDNA was purified, amplified and was used for 3? end RNA-seq library preparation using NEBNext® Ultra? II DNA Library Prep Kit for Illumina.
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read4 - UMI [no barcodes were used]

CAGE_Colonies: RNA-seq data for the establishment of Capsule-based multi-step processing of single-cells and live cultures. Data includes inC-RNAseq of mixed K562 and L1210 cells expanded into clones from single cells inside CAGEs in the presence of Decitabine, 5-Azacytidine or Vorinostat.  Cells were pretreated with drugs and encapsulated into CAGEs, followed culturing. Cells were lysed after 0, 2, 4, 6 days followed by oligo dT mRNA capture. cDNA was barcoded using split-pool inC-seq approach and Barcoded DNA was used for scRNA-seq library construction
Raw sequencing data are available via SRA. Fastq were demultiplexed to a sample resolution and contain all 4 reads. Read1 - transcript; read2 - PCR barcode, read3 - index; read - ligation barcode2, ligation barcode1, RT/ATAC/PCR barcode and UMI [for RNAseq].

[UPDATE] Please note that new .h5ad files have been added for GSM9228947 and GSM9228948 samples on Mar 26, 2026.

first: Haoxiang

last: sun

first: Arpita

last: Kulkarni

first: Theresa

last: Torre

first: Allon

last: Klein


title: Deciphering the cis-regulatory code of alternative splicing in human cell lines

status: Public on Sep 08 2025

city: seattle

first: Samantha

last: Koplik

email: skoplik@uw.edu, kopliksam@gmail.com

state: Washington

address: 185 Stevens Way

department: Electrical and Computer Engineering

institute: University of Washington

summary: Alternative splicing (AS) is a key mechanism of gene expression diversity, and dysregulation of AS is implicated in many human diseases. Identifying variants that disrupt splicing and characterizing their impact on isoform abundance across different cell types remains challenging. Here, we perform massively parallel reporter assays (MPRAs) to measure splicing phenotypes of over 87,000 sequence variants in five cell lines of different tissue origin. The MPRA encompasses 2,096 short human exons from 1,733 genes and tens of thousands of single and double variants. Our measurements identify variants that strongly modulate splicing but are currently classified as variants of unknown significance or have not yet been described. We systematically identify putative RNA-binding protein (RBP) binding motifs and quantify effect sizes associated with the disruption of these motifs, suggesting possible mechanisms for variant impact.  A comparison across cell lines enables the identification of variants that differentially modulate splicing.

overall_design: Massively parallel splicing reporter assay (MPRA) testing ~87,000 exon and variant sequences cloned into a Citrine–SMN2 minigene backbone. Constructs were transfected into five human cell lines (HEK293, HeLa, K562, MCF7, HMC3) with biological replicates. Sequencing was used to quantify exon inclusion (PSI) across replicates, and processed PSI values are reported.

first: Angela

last: Yu

first: Georg

last: Seelig


title: Identification of cells exhibiting elevated ERBB network activity in KRas/ Myc-driven lung tumours

status: Public on Sep 15 2025

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland Institute

summary: Our lab has identified a completely unexpected requirement for ERBB signalling in KRAS‐driven Lung Adenocarcinoma (LuAd). We have shown that this requirement is present from the very outset of lung tumour initiation, and, crucially, we have found a pronounced increase in ERBB signalling during progression from low grade adenocarcinoma to locally invasive disease. We hypothesize that this increased activity, which manifests as strongly elevated expression of multiple EGF/ERBB-family ligands, such as Amphiregulin (AREG), and paracrine activation of ERBB2 on infiltrating macrophages, may be exploited for early detection of KRAS‐ driven malignancy. Alongside a more general increase in AREG expression as tumours progress to higher grade disease, we find individual cells that express extremely high levels of AREG mRNA. We refer to these cells as AREG super-expressers and their lineage identity is unknown. Cell morphology suggests they maybe epithelial, however, unlike the bulk of tumours, these cells fail to express the lung epithelial marker SPC and staining for cytokeratins is inconclusive. Their detection at and adjacent to the tumour:normal interface suggests that they maybe disseminating tumour cells undergoing EMT. Alternatively, they may belong to another lung-resident or infiltrating population, induced to express AREG through direct contact with tumour cells. Immediately adjacent to progressing tumours we find large numbers of F4/80-positive macrophages that stain strongly for tyrosine phosphorylated ERBB2 (p-Tyr-ERBB2), suggesting paracrine activation in response to local production of ERBB ligands. The aim of this part of the work is to identify the cell lineage of the AREG superexpressers and to investigate the effect of ERBB-inhibition using the multi-ERBB inhibitor Neratinib.

overall_design: scRNA-seq was performed on whole-tumour cell suspensions from lungs of SPC-Cre+ KrasG12D+/-;MYC+/+ (KM) genetically engineered mice 8-9 weeks after transgene induction. Three days prior to culling, mice received daily (3 doses total) intraperitoneal injections of neratinib in peanut oil (80mg/kg), peanut oil, or were left untreated (n=3 per group).

first: Bjorn

last: Kruspig

first: Sarah

last: Laing

first: Ximena L.

last: Raffo-Iraolagoitia

first: Ann

last: Hedley

first: Ya-Ching

last: Hsieh

first: Kristina

last: Kirschner

first: Crispin

last: Miller

first: Daniel J.

last: Murphy


title: Erythropoietin Exposure Impairs B Cell Development and Promotes Myeloid-Imprinted Biphenotypic Progenitors

status: Public on Sep 01 2025

city: Nouzilly

first: Pascal

last: Froment

address: INRAE Nouzilly

department: UMR 7247 INRAE/CNRS/Université de Tours/IFCE

institute: INRAE

summary: Erythropoietin (EPO) is the major regulator of erythropoiesis, with levels increasing in response to anemia or hypoxia. Recombinant human EPO (rhEPO) is commonly used to treat anemia in patients with chronic kidney disease or cancer. Beyond its role in erythropoiesis, EPO exerts immunomodulatory effects. Emerging evidence suggests that EPO modulates other hematopoietic lineages, such as megakaryocytes while negatively impacting B-cell development. However, its influence on lympho-hematopoiesis remains insufficiently explored. We investigated the effects of EPO on B lymphopoiesis in the context of hyper-EPOemia-induced stress hematopoiesis. Using an EPO supplementation model in C57BL/6 mice, we demonstrate that EPO impairs B lymphopoiesis during Pre-Pro-B to Pro-B transition, by downregulating essential receptor like IL-7 receptor. Conversely, EPO promotes early B-cell development at the common lymphoid progenitor (CLP) and Pre-Pro-B stages. Remarkably, EPO induces the emergence of atypical B-cell precursors with a myeloid imprint, including CSF1R/CD115-expressing CLPs and CD11b and CD16/32-expressing Pre-Pro-B cells. Gene expression profiling revealed that EPO reprograms early B-cell precursors, upregulating a myeloid transcriptional signature while downregulating B-lymphoid identity genes as for instance genes targeted by key transcription factors IRF4, FOXO1, ERG and IRF8. Additionally, EPO exposure impairs hematopoietic stem and progenitor cell proliferation, induces oxidative stress and disrupts iron homeostasis. We additionally observed lymphoid over myeloid progenitor imbalance in the bone marrow and increased extramedullary hematopoiesis in the spleen. In conclusion, hyper-EPOemia reprograms B lymphopoiesis and promotes the emergence of mixed-lineage myeloid-like B cells. Future studies will explore EPO’s effects on lymphoid progenitor fate under hypoxic and infectious conditions.

overall_design: For each cell population, batches of 100 cells (4–5 replicates) were sorted by FACS in 96-well V-bottom plate wells containing 2 mL of lysis buffer (Ultra-pure Water, 10% Triton X-100, RNasinPlus 40Uµ/l; Promega). After evaporation of the lysis buffer at 95ºC for 3 min, first strand cDNA synthesis was performed using the Maxima H Minus Reverse Transcriptase (Thermo Fisher), E3V6NEXT primers (specifiµc primer for each well) and Template Switching Primer: E5V6NEXT. Resulting cDNAs were pooled and purified by the DNA Clean and Concentrator TM-5 kit (Zymo research) and treated with Exonuclease I (New England Biolabs) before amplification using the Advantage 2 PCR kit (Clontech) and the SINGV6 primer (95°C for 1 min, 15 cycles at 95°C for 15 s, 65°C for 30 s, 68°C for 6 min and 72°C for 10 min). PCR products were purified by Agencourt AMPure XP (Beckman Coulter). Libraries were prepared using the Illumina DNA Prep kit (Illumina) according to the manufacturer’s guidelines and sequenced on a NextSeq 2000 (Illumina) at the Genome East Platform of the IGBMC (Strasbourg, France). Image analysis and base calling were performed using RTA 2.7.7 and Bcl-2fastq 2.17.1.14 software and adapter dimer reads were removed using Dimer Remover (https://sourceforge.net/projects/dimerremover/).

first: Andrada

last: Chiron

first: Stéphanie

last: Bessoles

first: Guillaume

last: Sarrabayrouse

first: Kutaiba

last: Alhaj-Hussen

first: Corentin

last: Joulain

first: Thomas

last: Darde

first: Pierre

last: De La Grange

first: Amine

last: Abina

first: Bruno

last: Canque

first: Roman

last: Krzysiek

first: Salima

last: Hacein-Bey-Abina


title: Discovery of antimicrobial peptides targeting Acinetobacter baumannii via a pre-trained and fine-tuned few-shot learning-based pipeline

city: Hangzhou

first: Junjie

last: Huang

state: Zhejiang

address: 150 Dongfang Street Xiasha, Qiantang District

department: Center for AI and Intelligent Medicine

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

summary: Acinetobacter baumannii, a robust Gram-negative bacterium known for inducing nosocomial infections and displaying multidrug resistance, remains a formidable challenge to combat. The limited arsenal of antimicrobial peptides targeting this pathogen underscores the need for innovative strategies. Here, we report a pioneering few-shot learning-based pipeline to identify potent antimicrobial peptides targeting A. baumannii. This pipeline effectively scans through the entire libraries of hexapeptides, heptapeptides, and octapeptides, encompassing tens of billions of candidates, despite the extreme scarcity of available training data. Comprising classification, ranking, and regression modules as an integration, each module is trained using a few-shot learning strategy involving pre-training and multiple fine-tuning steps while incorporating similar and true data fine-tuning. This methodology mitigates the potential overfitting concerns due to the small size of the training samples and then enhances the predictive capability of the pipeline. The results highlight the robustness and versatility of the methodology, demonstrating its effectiveness in discovering AMPs against A. baumannii and C. albicans, while demonstrating low off-target toxicity and negligible susceptibility to drug resistance. Additionally, the EME7(7) exhibits efficacy in controlling A. baumannii infections within a mouse pneumonia model, notably without inducing kidney injury — a contrast to the observed effects of polymyxin B. This work provides a paradigm for addressing the challenges posed by limited data availability.

overall_design: Bacteria suspensions (10^8 c.f.u. mL-1, dispersed in PBS) were incubated with PBS and EME7(7) at concentrations of 2×MIC for 2 h. They were pelleted in centrifuge tubes by centrifugation at 12000 rpm/min for 15 min at 4 °C and washed in PBS thrice (10^9 c.f.u. mL-1) and immediately frozen in liquid nitrogen. Thereafter, RNAs of samples were extracted and analyzed by a Real-Time PCR Detection System (CFX384, Bio-Rad, USA) for measuring concentrations.

first: Wentao

last: Zhang

first: Aowen

last: Wang

first: Yunzhi

last: Jiang

first: Yuxian

last: Lai

first: Yanchao

last: Xu

first: Cong

first: Junbo

last: Zhao

first: Peng


title: Transcriptional reprogramming in mantle cell lymphoma promotes BTK inhibitor resistance

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary: Resistance to Bruton’s tyrosine kinase inhibitors (BTKi) remains a major therapeutic challenge in B-cell malignancies, limiting treatment durability. We demonstrate BRG1-mediated chromatin remodeling as a major driver of BTKi resistance. We show that cancer-associated BRG1 ATPase domain mutations protect cells from BTKi-induced ferroptosis by limiting reactive oxygen species (ROS) production and labile iron. Mechanistically, the BRG1T910M mutation activates the unfolded protein response (UPR) via ATF4, leading to upregulation of MEF2B, a key suppressor of ferroptosis. MEF2B further inhibits mitochondrial respiration and thus prevent BTKi-induced mitophagy and ferroptosis. Pharmacological inhibition of BRG1 promotes ferroptosis by suppressing pro-survival B cell receptor (BCR) signaling and the ATF4-MEF2B axis. We show that a clinical stage BRG1 inhibitor restores ferroptosis in BTKi-resistant cells and synergizes with BTKi across various MCL models. Together we propose  for co-targeting BRG1 and BTK in treatment of B-cell malignancies.

overall_design:
MINO cells expressing wildtype or mutant BRG1 or treated with FHD-286 were analyzed by RNA-seq. JEKO cells ectopically expressing MEF2B were analyzed by RNA-seq. Primary MCL cells were analyzed by RNA-seq.
MINO cells expressing wildtype or mutant SMARCA4 or treated with FHD-286 were analyzed by ATAC-seq or BRG1/H2K27Ac Cut&Run. CCMCL1 cells expressing cas9-sgROSA or cas9-sgBRG1 were analyzed by ATAC-seq. JEKO cells ectopically expressing MEF2B were analyzed by Cut&Run.

first: Hwang

last: Sooyeon

first: Nikolli

last: Helgi

first: Paik

last: Jihye


title: Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary: This dataset belongs to a study in which we functionally dissect the transcriptional co-regulation by grainyhead-like 2 (GRHL2) and progesterone receptor (PR, also referred to as PGR) in human breast cancer cells. As part of these efforts, we performed CUT&RUN in T47DS for endogenous GRHL2 and PR.  Gene expression is controlled by complex transcriptional networks in which transcription factors and their cognate enhancer elements integrate developmental and environmental cues. The progesterone receptor (PR), a hormone-activated transcription factor, is essential for breast development and physiology, yet how it engages with the chromatin and lineage-specific cofactors remains unclear. Using an unbiased approach, we identify the epithelial transcription factor grainyhead-like 2 (GRHL2) as a key co-regulator of PR activity in hormone responsive breast cancer cells. We show that GRHL2 interacts with PR in a progesterone-independent manner. Upon progesterone stimulation, GRHL2 and PR are both recruited to distal enhancer elements. Furthermore, GRHL2- and PR-bound elements connect spatially through chromatin looping to regulate shared targets. These findings uncover a previously unrecognized mechanism by which GRHL2 and PR coordinate gene regulation through both chromatin binding and 3D genome architecture modification, positioning GRHL2 as a crucial modulator of steroid hormone receptor function.

overall_design: CUT&RUN for PR, GRHL2 and IgG in T47DS cells either non-treated or 1nM R5020 treated for 4 hours.

first: Marleen

last: Aarts

first: Anna

last: Nordin

first: Claudio

last: Cantù

first: Antonius

middle: L

last: van Boxtel

first: Renée


title: Systems biology mapping of rBCG-LTAK63-induced protection against tuberculosis reveals the significance of autophagy and circadian rhythm regulation by cAMP

city: São Paulo

first: Luciana

middle: Cezar de Cerqueira

last: Leite

state: SP

address: Avenida Vital Brasil, 1500

department: Desenvolvimento de Vacinas

country: Brazil

institute: Instituto Butantan

summary: Using systems biology and RNA sequencing data from lung cells, we investigated the immune mechanisms of protection induced by this vaccine in mice, both after immunization and following challenge. The RNA-seq data were analyzed using IPA (Ingenuity Pathways Analysis), CEMiTools (modular co-expression analysis). The RNA-seq derived results were analysed through correlation with immune response and disease outcomes, such as bacillary load, pathology score (infiltrated cell number, inflammatory area, and functional area).

overall_design:
Bulk RNA-seq applyed to comprehensively study the impact of rBCG-LTAK63 vaccination in mice at various time points before and after Mtb exposure, aiming to understand how these alterations influence lung immune response and contribute to TB protection.
Babl/c mice were immunized and lungs and lymph nodes were collected, for RNA-seq, at 7, 90 after immunization.  At 90 days after immunization, animals that left were challenged with 500 CFU of Mycobacterium tuberculosis H37Rv, via intranasal instilation.At 97 and 120 days post immunization (7 days and 30 days post challenge), the lungs were collected, RNA sequencing. Eight samples were sequenced in each timepoints. Two saline controls were included (one in 7 dpi and other in 90 dpi). The infection control group, were included at 7dpc and 30 dpc.

first: Lázaro

last: Marques-Neto

first: Monalisa

last: Trentini

first: Ana Carolina

middle: R

last: Moreno

first: Silas

middle: F

last: Eto

last: Carvalho

first: Murilo

middle: S

last: Amaral

first: André

middle: G

last: Martins

last: Gonçalves

first: Ana Marisa

last: Chudzinki-Tavassi

first: Alex

middle: I

last: Kanno

first: Aldo

last: Tagliabue

first: Diana

last: Boraschi

first: Sergio

last: Verjovski-Almeida

first: Helder

last: Nakaya

first: Leonardo

middle: P

last: Farias

first: Pablo

last: Ramos


title: Endothelins influence the proliferation-migration balance of IDH1-mutant glioma cells and promote proneural to mesenchymal transition

city: Montpellier

first: Donovan

last: PINEAU

address: 141 Rue de la Cardonille

institute: IGF

summary: Adult diffuse gliomas are the deadliest brain tumours including IDH-wildtype glioblastomas of worst prognosis and diffuse low grade IDH-mutant astrocytomas and oligodendrogliomas. These glial tumours display distinct tumoral cell population defeating current therapies. Our group has unveiled the role of NOTCH signalling in glioblastoma cell plasticity and in the conversion of oligodendrocytic-like to astrocytic-like tumoral cells in IDH-mutant low-grade gliomas which escalate inevitably to higher grade malignant gliomas. To gain insight into signalling pathways regulating glioma cell plasticity and malignancy, we focused our work on endothelin signalling including endothelin peptide ligands (ET-1, ET-2, ET-3) binding to G-protein coupled endothelin receptors A and B (EDNRA, EDNRB). Here, using glioma patient samples and glioma patient-derived cell lines, we showed that endothelin reduces glioma cell proliferation while increasing migration initiating a proneural to mesenchymal transition. Mechanistically, EDNRB activation led to IP3-dependent calcium mobilization, apamin-sensitive KCNN2/KCNN3 potassium currents and phosphorylation of ERK1/2 and STAT3 in glioma cells. Finally, we studied endothelin receptor regulation by tumoral microenvironment stimuli highlighting a role for EDNRA induced by NOTCH and hypoxia in perivascular hypoxic area in glioblastoma. Altogether, this study demonstrates endothelin signalling as a key player in mesenchymal transformation of diffuse IDH-mutant gliomas and glioblastomas.

overall_design: For RNA sequencing experiments upon endothelin, LGG275, LGG336, BT237, Gb4, Gb7, Gb21 were seeded at 260,000 cells/wells in 3.5 mL of +GFs medium in 6-well plates (#140685, ThermoFisher Nunclon). Cells were treated either with endothelin dilution buffer (PBS with BSA 0.1%) for control condition or with ET-1 at 10 nM final once a day for 5 days before proceeding to RNA extraction 8 hours after the last treatment.

first: Jean-Philippe

last: HUGNOT


title: Endothelins influences the proliferation-migration balance of IDH1-mutant glioma cells and promotes proneural to mesenchymal transition [RNAseq-Gb7-HUVEC]

summary: Adult diffuse gliomas are the deadliest brain tumours including IDH-wildtype glioblastomas of worst prognosis and diffuse low grade IDH-mutant astrocytomas and oligodendrogliomas. These glial tumours display distinct tumoral cell population defeating current therapies. Our group has unveiled the role of NOTCH signalling in glioblastoma cell plasticity and in the conversion of oligodendrocytic-like to astrocytic-like tumoral cells in IDH-mutant low-grade gliomas which escalate inevitably to higher grade malignant gliomas. To gain insight into signalling pathways regulating glioma cell plasticity and malignancy, we focused our work on endothelin signalling including endothelin peptide ligands (ET-1, ET-2, ET-3) binding to G-protein coupled endothelin receptors A and B (EDNRA, EDNRB).  Here, using glioma patient samples and glioma patient-derived cell lines, we showed that endothelin reduces glioma cell proliferation while increasing migration initiating a proneural to mesenchymal transition. Mechanistically, EDNRB activation led to IP3-dependent calcium mobilization, apamin-sensitive KCNN2/KCNN3 potassium currents and phosphorylation of ERK1/2 and STAT3 in glioma cells. Finally, we studied endothelin receptor regulation by tumoral microenvironment stimuli highlighting a role for EDNRA induced by NOTCH and hypoxia in perivascular hypoxic area in glioblastoma. Altogether, this study demonstrates endothelin signalling as a key player in mesenchymal transformation of diffuse IDH-mutant gliomas and glioblastomas.

overall_design: RNAseq analyses of Gb7 glioblastoma stem cell line cells upon coculture with HUVEC endothelial cells (Human Umbilical Vein Endothelial Cells)

first: Hugo

last: ARNOLD


title: RNAseq analysis of Neuro-2a cells after infection with HSV-1

status: Public on Aug 31 2025

first: Xiang

last: Yuhang

address: Yuhang Tang street

summary: We used HSV-1 to infect Neuro-2a cells (MOI=10) for 5h, and set the mock group without infection as a control. Host genes that were significantly changed between HSV-1 infected and control groups were compared.

overall_design: We focused on genes that were significantly up-regulated or down-regulated in the infected group compared to the control group. Three replicates were set for each group, named MOCK1, MOCK2, MOCK3, HSV1, HSV2, and HSV3.

first: Dongli

last: Pan

first: Yuhang

last: Xiang


title: RNAseq analysis of LGG275, a diffuse IDH-mutant low-grade astrocytoma cell line treated with different molecules (cytokines, compounds and coatings) plus Gb4, IDH-wildtype glioblastoma stem cell line treated with ET1

summary: The goal of the present study was to identify regulators of diffuse low-grade glioma cell behaviour (proliferation, differentiation and cell death) based on candidates anti- and pro-proliferative molecules identified by an in vitro custom drug screening assay using absolute cell number as a readout

overall_design: RNA-seq profiling of LGG275, a diffuse IDH-mutant low-grade glioma cell line upon different compounds and RNA-seq profiling of Gb4, a diffuse IDH-wildtype glioblastoma stem cell line upon ET1 after 5 days of treatment once a day before proceeding to RNA extraction 8 hours after the last treatment.

last: Pineau

first: Stefan

last: Nicolescu

last: Hugnot


title: On the way to elucidate the effects of cannabidiol (CBD) on living organisms - assessment of changes in the global transcription profile of the hippocampus in a mouse model

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

institute: University of Agriculture in Krakow

summary:
Cannabidiol (CBD) is a phytocannabinoid that has anti-inflammatory, immunomodulatory, antioxidant, anxiolytic, antipsychotic, and anticonvulsant effects. This study aims to examine the effects of CBD on behavior, immune system activity, and stress levels, and to determine its impact on transcriptomic alterations in selected mouse organs.

(Study funded by the National Science Centre, Poland; project no. 2020/39/O/NZ9/00821)

overall_design: Male mice of the standard C57BL/6J strain were used. The animals were classified into two groups - (I) short-term CBD administration (2 days) and (II) long-term CBD administration (28 days). In each of the main groups, there were three subgroups receiving different doses of CBD - from low, commonly used in supplementation (0.2 mg/kg bw), through medium (10 mg/kg bw), to high, used in some clinical trials (20 mg/kg bw). Additionally, a control group (placebo/vehicle) was maintained in each of the main groups. Chemically pure Cannabidiol (CBD) was administered intraperitoneally (in the research group) to ensure that the substances reached the blood vessels of the digestive system. CBD was administered in a single daily dose. The mice were housed under standard conditions and with standard feeding and watering ad libitum. They were also tested daily (group I) or every third day (group II) to determine well-being and health. After the period of CBD administration, the mice were immediately euthanized and organs such as the brain (various brain structures including hippocampus), spleen, and liver were collected. In this part of the experiment, hippocampus samples were used to isolate total RNA. The recovered RNA was quality assessed and used to prepare directional libraries for high throughput transcriptome sequencing using CORALL mRNA-Seq V2 kit (Lexogen).  The libraries were sequenced commercially in a 2x150bp paired-end run. The obtained sequence data were used to analyze the differential expression between the different CBD dosages and the control group. Differentially expressed genes were classified into particular processes or functions and were subjected to statistical testing for overrepresentation. The synthesis of the obtained data will allow the proposal of potential mechanisms of CBD action and create an atlas of changes taking place in the transcriptome of the main target organs.

first: Jakub

last: Żurowski

first: Sebastian

last: Sawicki

first: Ewa

last: Ocłoń

first: Tomasz

last: Szmatoła

first: Igor

last: Jasielczuk

first: Karolina

last: Mizera-Szpilka


title: Serum Amyloid A (SAA) induces transcription affecting inflammation

city: Baltimore

first: George

middle: Henry

last: Sack

state: Maryland

address: 725 N. Wolfe Street

department: Department of Physiology, Pharmacology and Therapeutics

institute: Johns Hopkins University School of Medicine

summary: The 104 aa protein Serum Amyloid A (SAA) is a prominent member of the acute phase response (APR) a remarkably conserved and stereotyped set of serum protein changes associated with inflammation and other stimuli. N-terminal fragments of SAA can form fibrils that can accumulate in organs (“amyloidosis”). No specific biologic function has been identified for SAA; it has been considered an inert “biomarker.” In contrast to this perception of passivity, we report that exposure to both N-terminal decapeptides and intact SAA monomers can induce multiple transcripts in both enteroids and HEK293 cells. The spectrum of transcripts prominently includes proteins related to inflammation and NF-κB control, specifically NFKB1A, TNFA1P3 and IER3. SAA thus can act directly through specific transcription to alter cellular physiology with direct effects on inflammation, likely helping explain its remarkable evolutionary conservation as part of primordial defense.

overall_design: RNA-seq profiling of HEK293 cells treated with full-length SAA protein, with corresponding vehicle controls (HOH + 0.05% BSA). Samples were harvested at specific time points to capture transcriptional changes.

middle: H

last: Sack Jr

first: Joseph

last: Yun

first: Conover

last: Talbot Jr


title: DNAPKCs as a therapeutic target in small cell lung cancer

status: Public on Aug 27 2025

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

summary: Small cell lung cancer is the most aggressive form of lung cancer. Current frontline treatment of anti-PD-L1 with chemotherapy only results in a modest increase in overall survival and progression-free survival due to the poor immunogenic nature of SCLC. In this investigation, we report DNAPKcs inhibition sensitizes SCLC by inducing apoptosis and DNA damage leading to micro-nuclei formation. These aberrant cytosolic DNA activates cGAS-STING pathway resulting in induction of type-I/II interferon and MHC class-I. This study provides evidence of proteasomal degradation of cMYC in a GSK3B dependent manner in response to DNAPKcs inhibition further enhancing pro-inflammatory immune pathways. Using two unique immune-competent SCLC GEM models, we show STING mediated modulation of tumor immune microenvironment by increasing CD8+ T cells, MHC-I+ cells, and M1 macrophages in response to DNAPKcs inhibition with anti-PD-L1 therapy. We further provide strong evidence of significant tumor regression in immune-competent GEMMs by treatment with DNAPKcs inhibitor alone and in combination DNAPKcsi and anti-PD-L1. Taken together this study reports induction of DNAPKcs inhibitor increases the efficacy of immune checkpoint blockade therapy remarkably by activating immune microenvironment in a STING-MYC dependent manner which is of significant translational value.

overall_design: RNA.seq analysis data of small cell lung cancer cells, DMS114, H146, H196, H446, H720 and H1341  comparing only DMSO treated (control) and NU7441 treated cells.

first: Triparna

last: Sen

first: Dan

last: Hasson

first: Subhamoy

last: Chakraborty

first: Charles

last: Coleman


title: Distinct immunometabolic signatures of type 1 versus type 2 diabetes in a murine model of myocardial infarction

status: Public on Aug 26 2025

city: Jackson

first: Alan

last: Mouton

state: Mississippi

address: 2500 North State Street

department: Physiology and Biophysics

institute: University of Mississippi Medical Center

summary: Background: Diabetes mellitus (DM), which consists of type I and type 2 diabetes (T1D and T2D), is a known risk factor for myocardial infarction (MI) and negatively impacts post-MI outcomes. However, the mechanisms by which DM exacerbates cardiac remodeling in T1D versus T2D have not been well defined. Here, we assessed acute and chronic post-MI outcomes in T1D and T2D mice, focusing on immune and metabolic pathways. Methods: T1D was induced in adult male mice by a single high dose of streptozotocin (STZ), and T2D induced by high fat/fructose feeding and multiple low STZ doses. Two weeks following STZ administration, MI was induced by permanent coronary artery ligation, and mice were studied at days (D) 3, 7, and 28 post-MI. Cardiac function was assessed by echocardiography. Results: Compared to non-diabetic mice, T1D and T2D mice had worse cardiac dysfunction after MI, including increased wall thinning and decreased ejection fraction, despite similar infarct sizes. T1D mice also displayed acute pulmonary congestion. By RNA-sequencing analysis, T1D and T2D mice displayed upregulation of genes associated with canonical chemokine/monocyte-mediated inflammatory pathways, and downregulation of genes associated with extracellular matrix remodeling. T1D and T2D delayed activation of M2-like (CD206+) macrophages in the heart, and impaired normal collagen and elastin deposition after MI. T2D also increased expression of genes associated with T cell activation, and increased CD8+ T cells in the infarct. T1D and T2D hearts showed signs of impaired glucose and ketone oxidation, and T1D hearts had increased markers of fatty acid oxidation. Extracted D3 cardiac macrophages from T1D and T2D mice exhibited higher basal oxygen consumption, and increased M1 markers and chemokine expression. Plasma from T1D and T2D mice increased chemokine expression (Ccl2, Ccl7, Cxcl1) in cultured bone marrow macrophages, and T2D plasma impaired mitochondrial function. Conclusions: DM promotes adverse cardiac remodeling, which is associated with activation of overlapping and unique inflammatory pathways, impaired ECM remodeling, remote metabolic remodeling, and alterations in macrophage metabolism. Our results provide novel insights into potential therapeutic pathways for DM patients suffering from MI.

overall_design: Mouse left ventricular infarct tissue collected at day 7 after myocardial infarction induced by permanent ligation of the coronary artery

first: A


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [CLIP-seq]

city: San Francisco

first: Hani

last: Goodarzi

institute: UCSF

summary: Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet post-transcriptional regulation likely influences these patterns as well. However, the quantitative contribution of post-transcriptional mechanisms to cancer transcriptome dynamics remains unclear. Here, we systematically measured mRNA dynamics across diverse breast cancer models, revealing that mRNA stability significantly shapes gene expression variability. To decipher the regulatory grammar underlying these dynamics, we developed GreyHound, an interpretable multimodal deep-learning framework integrating RNA sequence features and RNA-binding protein (RBP) expression. GreyHound identified an extensive network of RBPs and their regulons underlying variations in mRNA stability. Among these, we uncovered a metastasis-suppressive regulatory axis centered on the RNA-binding protein RBMS3 and its post-transcriptional control of the redox regulator TXNIP. Functional and molecular analyses revealed that RBMS3 depletion resulted in targeted transcript destabilization, which was associated with poor clinical outcomes and enhanced metastatic potential in xenograft models. Using in vivo epistasis studies, we confirmed that RBMS3 regulation of TXNIP mRNA stability drives this metastasis-suppressive program. These findings position the RBMS3-TXNIP regulatory axis as a key post-transcriptional mechanism in breast cancer and illustrate how interpretable models of RNA dynamics can uncover hidden regulatory programs in disease.

overall_design: To directly uncover the binding sites of RBMS3, we employed CLIP-seq on FLAG-tagged RBMS3 expressing MDA-MB-231 cells.

first: Heather

last: Karner


title: Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen

city: Philadelphia

first: Ricardo

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

summary: The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their importance, the mechanisms governing LAD positioning in human cells remain poorly understood. To this end, we performed a genome-wide imaging-based screen and identified 101 genes critical for perinuclear LAD localization, with a significant enrichment for RNA-binding proteins. Among these, hnRNPK emerged as a key regulator, required for the perinuclear positioning of approximately 70% of LADs genome-wide. Loss of hnRNPK led to their repositioning away from the nuclear periphery without altering global heterochromatin state, yet resulted in misexpression of genes within these domains. Notably, hnRNPK-sensitive LADs are uniquely enriched for H3K27me3, distinguishing them from hnRNPK-insensitive LADs that are predominantly marked by H3K9me3. These findings reveal mechanistically distinct classes of LADs and suggest that specialized pathways underlie their spatial organization. Our results uncover a pivotal role for hnRNPK in regulating chromatin architecture and highlight the broader diversity of LAD tethering mechanisms.

overall_design:
LB1, H3K9me2, H3K9me3, and H3K27me3 ChIP-seq in HCT116 cells in control and HNRNPK knockdown.
Bulk RNA-seq in HCT116 cells in control and HNRNPK knockdown.

first: Patrick

last: Walsh

first: Elizabeth

middle: B

last: Kraeutler

last: Linares-Saldana

first: May

last: Wai

first: Joanatta

last: Shapiro

first: Shuo

last: Zhang

first: Son

middle: C

last: Nguyen

first: Parisha

last: Shah

first: Daniel

last: Park

first: Haris

last: Muzaffar

first: Rajan

last: Jain

first: Eric

last: Joyce


title: Transcriptome of the hindgut of Aedes aegypti wild type females fed on sucrose ad libitum

first: Laura

middle: B.

last: Duvall

address: 1212 Amsterdam Ave

institute: Columbia University

summary: Aedes aegypti mosquitoes are efficient vectors of human disease including Zika, Dengue and Chikungunya. After taking a blood meal, proteins from the blood are broken down into amino acids that are essential for egg development and growth. We have discovered a novel role for a neuropeptide receptor in the hindgut that coordinates blood utilization. The hindgut is not a tissue normally implicated in blood digestion, therefore we conducted RNA-seq profiling of the hindgut in wild type females to obtain a transcriptomic profile of these tissues in non-blood fed conditions.

overall_design: RNA-seq profiling of the hindgut of wild type 5-15 day old Aedes aegypti female mosquitoes fed on sucrose ad libitum

first: Chloe

last: Greppi

first: Kyle

last: Frank

first: Victoria

last: Saltz


title: Transient Ddx61-enriched condensates refine heart regeneration programs

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

summary: Gene regulatory mechanisms that underlie tissue regeneration have been largely studied at the level of transcription. Here, proximity labeling methods identified enhanced presence of Processing body (P-body) marker, Ddx61, in zebrafish heart muscle cells induced to divide by injury or mitogenic stimulation. We found that Ddx61-containing condensates emerge and develop complex, transient structures in cardiomyocytes during cardiogenic settings in adult zebrafish, developing mice, and human stem cell-derived myocardium. Mutations in zebrafish ddx61 disrupted cardiomyocyte cycling and differentiation after cardiac injury or mitogen presence, and DDX61 knockdown in human cardiomyocytes inhibited similar parameters under maturation conditions in vitro. RNA affinity and proteomic profiling implicated mRNAs preferentially associating with Ddx61 during regeneration, and induced transgenic expression of one of these mRNAs, encoding the BMP signaling inhibitor, Chordin, disrupted indicators of heart regeneration after cardiac injury. Our experiments provide evidence that mRNA sorting by specialized context-dependent condensates can modulate gene expression and impact tissue regenerative capacity.

overall_design: Ddx61/Ddx6 pulldown and isolation of associated mRNAs during heart regeneration in zebrafish. For this 120 hearts were used for one sample. Uninjured and 14 days post injury hearts were used. Dublicate samples for each condition.

first: Mira

last: Pronobis


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [BRCA_SLAM-seq]

first: Hani

last: Goodarzi

overall_design: To explore the variations in RNA stability underlying heterogeneity of gene expression in breast cancer, we performed SLAM-seq on six breast cancer cell lines from different subtypes.

first: Heather

last: Karner


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer [shRBMS3_RNAseq]

overall_design: To investigate the mechanisms of RNA regulation through RBMS3 in breast cancer, we knocked down RBMS3 in MDA-MB-231 cells. With differential gene expression analysis we examined RBMS3 target transcripts.

first: Tabea

last: Mittmann


title: Gene expression changes related to immunosuppression in patients with traumatic brain injury (Part 1)

status: Public on Aug 22 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary:
Background : Traumatic brain injury (TBI) can alter various immune functions, including immunosuppression and constitutes a risk factor for nosocomial infections and organ dysfunction. Although TBI can induce a decline in immune cell function, the detailed mechanisms remain unclarified. This study aimed to clarify the mechanism of immunosuppression caused by TBI using a comprehensive transcriptome analysis of immune cells.
Methods : Six patients with traumatic brain injury and acute subdural hematoma were admitted to our hospital. We focused on three major subsets of immune cells responsible for the immune response: CD4+ T cells, CD8+ T cells, and monocytes. We evaluated the changes in immune function after injury using comprehensive transcriptome analysis. Blood samples were collected immediately after admission and one week later, and the data were compared with those of healthy volunteers.
Results : CD4+ T cells and CD8+ T cells decreased over seven days following injury, and a decrease in cell adhesion and endoplasmic reticulum function was observed. It was suggested that the process of protein synthesis from RNA was impaired and that overall cell function was reduced. Monocytes also show a decrease in endoplasmic reticulum function, but classical and nonclassical monocyte subsets show an increase in functions related to platelet activation and tissue repair.
Conclusions : Comprehensive transcriptome analysis confirmed a decrease in endoplasmic reticulum function in CD4+ T cells, CD8+ T cells, and monocytes. This study facilitates further elucidation of the mechanisms of immunosuppression due to trauma and the development of new therapeutic strategies to suppress secondary infections.

overall_design: We performed a retrospective, observational, case-control, single-center study.  Samples from the patients were collected at two timepoints: within 24 h of admission and on the 7th or 8th day of admission. PBMCs were isolated from fresh whole blood. Two panels were used to identify subsets of CD4+ T cells, CD8+ T cells, and monocytes from PBMCs. Total RNA was extracted from the sorted cells. Whole-transcriptome sequencing was performed on an Illumina NovaSeq 6000 platform using a 151-base pair-end sequencing strategy.

first: Hiroshi

last: Ito

first: Masakazu

last: Ishikawa

first: Hisatake

last: Matsumoto

last: Ogura

last: Okuzaki

first: Jun

last: Oda


title: Molecular Signatures of Resilience to Alzheimer’s Disease in Neocortical Layer 4 Neurons

status: Public on Aug 24 2025

city: Stanford

first: Inma

last: Cobos

state: California

address: 300 Pasteur Drive, Lane Building, L235

institute: STANFORD UNIVERSITY MEDICAL SCHOOL

summary: Single-cell omics is advancing our understanding of selective neuronal vulnerability in Alzheimer’s disease (AD), revealing specific subtypes that are either susceptible or resilient to neurodegeneration. Using single-nucleus and spatial transcriptomics to compare neocortical regions affected early (prefrontal cortex and precuneus) or late (primary visual cortex) in AD, we identified a resilient excitatory population in layer 4 of the primary visual cortex expressing RORB, CUX2, and EYA4. Layer 4 neurons in association neocortex shared overlapping molecular signatures of resilience. Early in the disease, resilient neurons upregulated genes associated with synapse maintenance, synaptic plasticity, calcium homeostasis, and neuroprotective factors, including GRIN2A, RORA, NRXN1, NLGN1, NCAM2, FGF14, NRG3, NEGR1, and CSMD1. We also identified KCNIP4, which encodes a voltage-gated potassium (Kv) channel-interacting protein that interacts with Kv4.2 channels and presenilins, as a key factor linked to resilience. KCNIP4 was consistently upregulated in the early stages of pathology. Furthermore, AAV-mediated overexpression of Kcnip4 in a humanized AD mouse model reduced the expression of the activity-dependent genes Arc and c-Fos, suggesting compensatory mechanisms against neuronal hyperexcitability. Our dataset provides a valuable resource for investigating mechanisms underlying resilience to neurodegeneration.

overall_design: This single-nucleus RNAseq dataset was generated from postmortem fresh frozen human cerebral cortex from patients who died with Alzheimer’s disease (AD) and age-matched healthy controls. It contains ~ 500,000 nuclei, of which ~ 80% are neurons, from the prefrontal (BA9), precuneus (BA7) and primary visual (BA17) cortices from 46 donors, including 18 donors with no or low AD pathology (Braak 0-II), 10 with intermediate AD pathology (Braak IIII-IV), and 18 with high AD pathology (Braak V-VI). The samples were processed as described in our protocol at https://www.protocols.io/view/isolation-of-single-nuclei-from-postmortem-fresh-f-6tuhenw. Each sample was sorted by FANS (fluorescence-activated nucleus sorting) to collect two populations, one consisting of all nuclei and the other enriched for neurons (NeuN+). We annotated 18 excitatory and 19 inhibitory neuronal cell types, as well as glial and vascular cells.

first: S Akila Parvathy

last: Dharshini

first: Marcos

last: Otero-Garcia

first: Weijing

last: Tang


title: Bulk RNA-seq of rat sciatic nerve distal to crush after magnetic nanoparticle–mediated magnetic force stimulation

city: Jilin

first: wang

last: yang

address: Xin-Min Street NO. 1

institute: Orthopaedic Center, The First Hospital of Jilin University

summary: To explore the effect of magnetic mechanical force mediated by magnetic nanoparticles in a gradient magnetic field environment on the repair phenotype of Schwann cells in injured sciatic nerves, we established a rat sciatic nerve crush injury model and locally injected magnetic nanoparticles under the epineurium at the distal end of the crush site.

overall_design:
After modeling, the rats were exposed to a gradient magnetic field environment daily to subject the injured sciatic nerve to magnetic force stimulation. On the 7th day after magnetic force stimulation, the sciatic nerve tissue at the distal end of the crush site was collected for mRNA transcriptome sequencing to observe the effect of magnetic force stimulation mediated by magnetic nanoparticles on the gene expression profile in the sciatic nerve.
B7: magnetic force stimulation, C7: control, ND: sciatic nerve distal.


title: Deciphering Host Stress Responses for Predictable Heterologous Gene Expression in E. coli

status: Public on Aug 21 2025

city: Kgs. Lyngby

first: Christoffer

last: Rode

address: Søltofts Plads, Building 220

country: Denmark

institute: Technical University of Denmark

summary: Predictable expression of heterologous genes remains a key challenge in biotechnology, largely due to cellular stresses imposed on the production host. Here, we systematically dissect stress responses across Escherichia coli strains expressing diverse proteins under varying promoters and translation efficiencies. Using independent component analysis on new and existing large transcriptomic datasets, we identify distinct responses to transcriptional and translational stresses: excessive heterologous mRNA triggers a cold shock response that controls mRNA stability (cspA-I, deaD), while protein production activates a heat shock response involving proteolysis and chaperone functions. We further identify a broad adaptation response, consistently co-activated with the heat shock response during protein production, that provides stationary phase regulation (rspAB) and osmoregulation (betABIT). Targeting these latter functions through strain and media modifications significantly increases eGFP production. Other host stress responses depend on the protein being expressed; for example, we find production of cysteine-rich proteins to uniquely activate functions regulating iron- and redox homeostasis and oxidative stress responses. This work demonstrates a holistic, systems-level view of cellular stresses to heterologous gene expression by considering transcriptional, translational, and product-specific contributions, paving the way toward predictable and optimized expression strategies.

overall_design: RNA-Seq profiling of Escherichia coli hosts containing expression plasmids for different heterologous genes and with variable ribosome binding site strengths.

first: Philip

last: Beulig

first: Mathias

last: Jönsson

first: Morten

last: Nørholm

first: Leonie

middle: J

last: Jahn

first: Daniel

last: Zielinski

first: Bernhard

middle: O

last: Palsson

first: Emre

last: Özdemir

first: Lei

last: Yang


title: JARID2 Inhibition Reprograms Human Hematopoietic Progenitor Cells To Enhance Bone Marrow Transplantation

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

summary: Hematopoietic stem cell transplantation is a common treatment for many blood disorders. Umbilical cord blood (UCB) serves as a valuable source of hematopoietic stem and progenitor cells (HSPCs), particularly for patients lacking a matched donor. However, the limited number of repopulating cells in UCB units restricts its clinical utility. Here, we demonstrate that JARID2 knockdown, distinct from EZH2 loss, increases both the number and functionality of human UCB-derived HSPCs in vitro and in vivo. After ex vivo culture, these functionally enhanced HSPCs were identified as CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻. Mechanistically, JARID2 knockdown promotes a quiescent, long-term self-renewal gene expression program by upregulating STAT1 and MHC class II. Notably, it also confers HSC-like potential to multipotent progenitors (MPPs), enhancing their regenerative capacity. These findings support JARID2 inhibition as a safe and reversible strategy to expand functional HSPCs from UCB ex vivo, potentially increasing access to this life-saving therapy for a broader patient population.

overall_design: To investigate the molecular mechanisms underlying JARID2-KD-mediated expansion and functional enhancement of human HSPCs, enriched umbilical cord blood-derived CD34⁺ cells were transduced with shRenilla, shJARID2, or shEZH2 and cultured ex vivo for 8 days. hCD34⁺ cells were then sorted for CITE-seq analysis. Guided by the CITE-seq findings and complementary functional assays, CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells were further isolated after 8 days of ex vivo culture for bulk RNA-seq, CUT&Tag, and CUT&RUN analyses. For scRNA-seq analysis, shRenilla- or shJARID2-transduced CD34⁺ cells were transplanted into NSG mice, and hCD34⁺ cells were recovered from the bone marrow 20 weeks post-transplantation. For STAT1 CUT&RUN, hCD34⁺ cells were collected either directly from cord blood as naïve controls or after 8 days of ex vivo culture following transduction with shRenilla or shJARID2.

first: Wentao

last: Han

first: Hassan

last: Bjeije

first: Hamza

last: Celik

first: Michael

last: Rettig

first: Nancy

last: Issa

first: Andrew

last: Young

first: Yanan

last: Li

first: Infencia

last: Xavier Raj

first: Christine

last: Zhang

first: Aishwarya

last: Krishnan

first: Tyler

middle: M

last: Parsons

first: Samantha

last: Burkart

first: Jason

last: Arand

first: Wei

first: Jeffrey

last: Magee


title: Engineering a superactivator of smooth muscle gene expression with the Myocardin condensate forming region [ChIP-seq]

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

institute: UTsouthwestern

summary: Differentiation of smooth muscle cells (SMCs) is accompanied by the expression of a battery of genes controlled by serum response factor (SRF), a ubiquitous transcription factor with weak intrinsic transcriptional activity. Myocardin (MYOCD) is a potent transcriptional coactivator that activates smooth muscle differentiation through its association with SRF. MYOCD forms condensates through its highly disordered transcription activation domain (TAD), whereas SRF displays a diffuse distribution within the nucleus. SRF is recruited to nuclear condensates by the TAD of MYOCD (MYOCD-TAD), thereby triggering the smooth muscle gene program. Swapping the weak TAD of SRF with that of MYOCD enables SRF to form condensates and acquire the ability to reprogram fibroblasts to SMCs. SRF-MYOCD-TAD chimeric protein exhibits stronger transcriptional activity on smooth muscle genes than MYOCD. Using protein proximity labelling, quantitative proteomics and super-resolution confocal microscopy, we show that MYOCD-TAD condensates aggregate chromatin remodelers, RNA polymerases, and mRNA processing factors to drive smooth muscle gene expression. These findings provide insights into the mechanisms whereby nuclear condensates promote tissue-specific gene expression and point toward a strategy for engineering superactivators leveraging transcriptional condensates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data and chromatin occupancy and chromatin accessibility (H3K27ac) by ChIP-seq data for 10T1/2 cells reprogrammed by GFP (control), SRF, and SRF chimeric mutants (SRF-MYOCD-TAD, SRF-MYOCD-TAD-FWY/A, SRF-FUSN).

first: Peiheng

last: Gan

first: Akansha

last: Shah

first: Svetlana

last: Bezprozvannaya

first: Kenian

last: Chen

first: Qianqian

last: Ding

first: Hui

first: Xinyi

last: Zhou

first: Ning

last: Liu

first: Eric

middle: N

last: Olson


title: OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization [sciATAC-Seq]

first: Viviana

middle: I.

last: Risca

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

summary: Tagmentation is an efficient approach for sequencing library preparation, which combines DNA fragmentation by transposition of sequencing adapters, using the bacterial cut-and-paste transposase Tn5. Here we present an open-source protocol for the generation of multi-purpose hyperactive Tn5 transposase, including its benchmarking in CUT&Tag, bulk and single-cell ATAC-seq. The OpenTn5 protocol yields multi-milligram quantities of pG-Tn5E54K, L372P protein per liter of E. coli culture, sufficient for thousands of tagmentation reactions and the enzyme retains activity in storage for more than a year.

overall_design: To determine if the performance of in-house pG-Tn5 is comparable to commercial pAG-Tn5 from Epicypher (SKU: 15-1017), we performed CUT&Tag using both enzymes to profile the distribution of H3K27me3 and H3K27ac histone modifications in MCF7 cells. To compare the performance of pG-Tn5 with commercially available Tn5 (Illumina TDE1, CAT: #20034198), we conducted ATAC-seq experiments in MCF7 and K562 human cell lines with matched enzyme volumes. We also performed an in-house pG-Tn5 transposome titration in K562 cells to understand how varying pG-Tn5 enzyme concentration influences ATAC-seq signal globally. We also demonstrated pG-Tn5 can be readily applied to sensitive emerging applications that require custom adapter loading, such as EasySci-ATAC, which was performed in MCF7 cells.

first: Jan

last: Soroczynski

first: Lauren

last: Anderson

first: Joanna

middle: L

last: Yeung

first: Justin

last: Rendleman

first: Deena

last: Oren

first: Hide

last: Konishi


title: Functional investigations of p53 acetylation enabled by heterobifunctional molecules

city: LA JOLLA

first: Christopher

last: Parker

address: 10550 North Torrey Pines Road SR311E

institute: Scripps Research

summary: Post-translational modifications (PTMs) dynamically regulate the critical stress response and tumor suppressive functions of p53. Among these, acetylation events mediated by multiple acetyltransferases lead to differential target gene activation and subsequent cell fate. However, our understanding of these events is incomplete, due to, in part, the inability to selectively and dynamically control p53 acetylation. We recently developed a heterobifunctional small molecule system, AceTAG, to direct the acetyltransferase p300/CBP for targeted protein acetylation in cells. Here, we expand AceTAG to leverage the acetyltransferase PCAF/GCN5 and apply these tools to investigate the functional consequences of targeted p53 acetylation in human cancer cells. We demonstrate that recruitment of p300/CBP or PCAF/GCN5 to p53 results in distinct acetylation events and differentiated transcriptional activities. Further, we show that chemically induced acetylation of multiple hotspot p53 mutants results in increased stabilization and enhancement of transcriptional activity. Collectively, these studies demonstrate the utility of AceTAG for functional investigations of protein acetylation.

overall_design: To investigate transcriptome changes induced by AceTAGp300/CBP-1 and AceTAGPCAF/GCN5-4.

first: Li

middle: Y

first: Soumya

last: Singha Roy

first: Appaso

last: Jadhav

first: Wesley

middle: W

last: Wang

first: Pei

first: Timothy

last: Bishop

first: Michael

last: Erb


title: OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization [ATAC-Seq]


title: A high-resolution temporal transcriptomic dataset of porcine wound healing

status: Public on Aug 20 2025

city: Santa Cruz

first: Ksenia

last: Zlobina

address: 1156 High Street

department: Applied Mathematics

institute: University of California Santa Cruz

summary: The dataset contains observations from an acute wound healing experiment in pigs. Wound samples for RNAseq were taken from both wound edges and wound centers and were collected at multiple time points from day 0 to day 21 post-wound onset.

overall_design: Six domestic pigs (Yorkshire-mix breed, females, 45-50 Kg, pig ID: 1323, 1324, 1325, 1326, 1327, and 1328) were utilized. Twelve full-thickness, circular excision wounds (2 cm in diameter, wound ID: A, B, C, D, E, F, G, H, I, J, K, and L) were created in each animal. Baseline (Day 0) excised skin tissue was collected. During the post-operative period, wound biopsy samples from wound edge and wound center were collected on post-operative days 1, 2, 3, 4, 5, 6, 7, 9, 11, 13, 15, 16, 19, and 21. The biopsy samples were sent for RNA sequencing analysis.

first: Hsin-Ya

last: Yang

first: Manasa

last: Kesapragada

first: Fan

last: Lu

first: Anthony

last: Gallegos

first: Guillermo

last: Villa-Martinez

first: Moyasar

last: Alhamo

first: Kan

last: Zhu

first: Cynthia

last: Recendez

first: Marco

last: Rolandi

first: Athena

last: Soulika

first: Elham

last: Aslankoohi

first: Min

last: Zhao

first: Marcella

last: Gomez

first: Rivkah

last: Isseroff


title: OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization [CUT&Tag]

first: Viviana

last: Risca

first: Jan

last: Soroczynski

first: Lauren

last: Anderson

first: Joanna

last: Yeung

first: Justin

last: Rendleman

first: Deena

last: Oren

first: Hide

last: Konishi


title: LENG8 Functions as a Quality Control Checkpoint for Nuclear Retention and Degradation of Misprocessed RNAs

status: Public on Aug 18 2025

city: Irvine

first: Yongsheng

last: Shi

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

summary: Quality control is essential for maintaining proper gene expression. For example, aberrantly processed RNAs are retained and degraded in the nucleus, and defects in this process have been linked to various diseases, including cancer and neurodegeneration. However, the underlying mechanisms of RNA nuclear retention and degradation remain poorly understood. Through a genome wide CRISPR screen, we identified not only known factors involved in nuclear RNA degradation but also candidate proteins mediating RNA nuclear retention, including the poorly characterized protein LENG8. Our findings reveal that LENG8 is recruited to pre-mRNAs by splicing factors, including components of the U1 snRNP. Once RNA-bound, LENG8 is both necessary and sufficient to sequester RNA in the nucleus. Depletion of LENG8 leads to the leakage of intron containing RNAs and numerous nuclear noncoding RNAs into the cytoplasm, demonstrating its crucial role in RNA retention. Mechanistically, we further discovered that LENG8 lacks a specific region required for forming an intact TREX2 complex, unlike its paralog GANP. As a result, LENG8 retains misprocessed RNAs in the nucleus through a dominant-negative mechanism of TREX2/GANP, despite its ability to recruit TREX and the PCID2-SEM1 complex. Additionally, LENG8 interacts with the ZFC3H1-MTR4-exosome complex to degrade nuclear-retained RNAs, linking it to both RNA retention and degradation pathways. In conclusion, our study uncovers a novel mechanism of gene expression quality control, highlighting LENG8 as a key regulator of RNA nuclear retention and degradation, with potential implications for human disease.

overall_design: Fraction mRNA-seq to study if misprocessed RNAs are exported into cytoplasm after depletion of LENG8; PAS-seq to study if  IPAs are degraded by LENG8 and if IPAs are exported into cytoplasm after depletion of LENG8

first: Lusong

last: Tian


title: JAX Study 10- RNA-seq of male KOLF2.2J hiPSC-derived endoderm and mesoderm homozygous null for three different transcription factors.

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: This study aims to phenotype iPSC-derived early endoderm and mesoderm that contain homozygous null alleles for the following transcription factors: ISL1, NKX2-1, and EOMES. Null alleles were generated using insertion of a premature termination codon with frameshift (PTC+1) in the case of ISL1 or full protein coding region deletion (KO) for NKX2-1 and EOMES. RNA-seq data was generated after 5 days of initiating differentiation from iPSCs. This analysis allowed the investigation of early embryonic development, cell fate mapping, and lineage analysis.

overall_design: The study involved the generation of RNA-seq on 15 samples. Two of the transcription factors were analyzed in the endoderm differentiation scheme and one in the early mesoderm scheme. Three biological replicates were run for each gene. Additionally, three biological replicates were run of wild-type KOLF2.2J cells (the parental male cell line in which the KOs were generated) under the same differentiation conditions. This comprehensive design allowed the investigation of the effects of transcription factor manipulation during early embryonic development.

first: Juliana

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: RNA seq analysis of MEK inhibitor in combination with 5-azacitidine treated Shp2E76K/+ driven JMML mice

status: Public on Aug 15 2025

city: Indianapolis

first: Santhosh Kumar

last: Pasupuleti

state: Indiana

department: Pediatrics

institute: Indiana University School of Medicine

summary: Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic and myeloproliferative neoplasm of childhood. Excessive proliferation of monocytes into the liver, spleen, lungs, and skin is frequently observed at presentation. Hematopoietic stem cell transplantation (HSCT) is the only curative therapy with a probability of event-free survival at 5-years of approximately 50%. The molecular hallmark of JMML is hyperactivation of the Ras/MAPK signaling pathway with the most common cause being mutations in the gene PTPN11, encoding the protein tyrosine phosphatase SHP2. Current therapeutic strategies in JMML include using MEK inhibitors such as trametinib and PD0325901 (PD-901) or the hypomethylating agent, 5-azactidine, but none of these are curative as monotherapy. In this study, utilizing a gain of function (GOF) Shp2E76K/+ murine model of JMML, we showed that the combination of PD-901 and 5-azacitidine reduced leukocytosis, monocytosis, and splenomegaly and reversed thrombocytopenia. Importantly, this drug combination significantly reduced leukemic hematopoietic stem and progenitor cells (HSC/Ps) in the Shp2E76K/+ mice.

overall_design: To explain the mechanism of action of MEK inhibitor, PD0325901 (PD-901) in combination with hypomethylating agent, 5-azactidine treatment on Shp2E76K/+ driven JMML mice, total RNA was isolated form the BM cells of 4 different drug treatment groups (Group 1: Vehicle, Group 2: PD-901, Group 3: 5-azacitidine, and Group 4: Combo). RNA-sequencing (RNA-seq) was performed on samples from 3 independent mice from each group.

first: Santhosh

middle: K

first: Reuben

last: Kapur

first: Sheng

last: Liu

first: Jun

last: Wan


title: Therapeutic restoration of mitochondria–endoplasmic reticulum crosstalk for osteoarthritis

city: Suzhou

first: Mingzhuang

last: Hou

address: Pinghai Street 899#

institute: Suzhou University

summary: Osteoarthritis is a prevalent joint disease in the aging population. The hallmark of osteoarthritis is the degeneration of the joint cartilage, characterized by changes in chondrocytes including mitochondrial dysfunction. However, the precise mechanisms of how this affects chondrocyte homeostasis and whether such processes can be explored as therapeutic targets for osteoarthritis remain unclear. Here, we show that impaired mitochondrial function and disrupted cartilage matrix metabolism due to loss of mitofusin-2 (MFN2) expression in chondrocytes leads to the development of osteoarthritis. Sirtuin-3 (SIRT3), a key regulator of mitochondrial function, plays a critical role in modulating MFN2 to restore mitochondrial dynamics, reduce fragmentation, and preserve mitochondrial function in chondrocytes. Specifically, SIRT3 directly deacetylates and indirectly deubiquitinates MFN2, preventing its degradation. MFN2-mediated mitochondrial–endoplasmic reticulum (ER) junctions support cellular homeostasis, alleviate ER stress, and maintain mitochondrial calcium ion balance, which collectively mitigate chondrocyte senescence. Extracellular vesicles engineered with MFN2 mRNA effectively prevented cartilage degeneration and restored mobility in osteoarthritic mice. These findings suggest that targeting MFN2 is a promising strategy to prevent cartilage degeneration and alleviate progression of osteoarthritis.

overall_design: We performed gene expression profilling analysis using data obtained from RNA-seq of chondrocytes derived from MFN2wt and MFN2Col2a1-/- mice.

first: Yaoge

last: Deng


title: FOXJ1 regulates microtubule dynamics in nonciliated cells and is a mediator of taxane resistance

city: Boston

first: Steven

last: Balk

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School

summary: Docetaxel is the first-line chemotherapy for metastatic castration-resistant prostate cancer (PC) and taxanes are broadly used in other cancers, but mechanisms of resistance remain to be established. In our study, we generated docetaxel-resistant PC xenografts and found increased expression of genes that drive development of multiciliated cells. These genes included FOXJ1, its upstream activator GMNC, and multiple FOXJ1-regulated genes that are associated with microtubules (MTs). Notably, FOXJ1 gene amplification was more frequent in taxane-exposed PC patients, and its overexpression conferred resistance to docetaxel both in vitro and in vivo. This resistance was associated with a decrease in docetaxel-mediated MT bundling, indicating that FOXJ1-regulated genes act at the level of tubulin to mitigate abnormal MT aggregation. Additionally, overexpression of an MT-associated FOXJ1-regulated gene (TPPP3) had similar effects. Conversely, FOXJ1 knockdown impaired basal MT function, enhanced taxane binding to MTs, and increased docetaxel sensitivity. Finally, analysis of data from the CHAARTED clinical trial showed that higher expression of FOXJ1 was predictive of decreased survival in PC patients treated with docetaxel. Together these findings highlight FOXJ1’s role in regulating MT dynamics in non-ciliated cells and that its increased expression mediates taxane resistance.

overall_design: Mice with LuCaP35CR or LuCaP70CR xenograft tumors were treated with either vehicle or docetaxel (DTX) at 30 mg/kg by i.p. injection every 21 days starting at day 0 as indicated. Docetaxel and vehicle treated xenografts were harvested when they reached ~1500 mm3. The treated tumors were harvested 2 weeks after their final dose of docetaxel. Mice bearing LNCaP FOXJ1_OE and LNCaP EV xenografts were treated with docetaxel (DTX, 30 mg/kg, i.p., 6 mice per each group). The first dose was administered when tumors reached ~250 mm3 (Day 9), and a second dose was given on Day 30. Mice for both groups were  sacrificed 5 days after the second dose, and the tumors were harvested for RNA sequencing.

first: Fang

last: Xie

first: Larysa

last: Poluben

first: Olga

last: Voznesensky