title: RNA-seq of Ixodes scapularis salivary glands [bulkRNA-dissociated-SG]

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

summary: Applications of transcriptomics have significantly advanced the identification of numerous tick salivary molecules involved in feeding and the transmission of tick-borne pathogens. In this study, we analyze the salivary gland transcriptome of Ixodes scapularis, the main vector of Borrelia burgdorferi in the U.S. We use next-generation sequencing to provide a more detailed view.

overall_design: The Ixodes scapularis ticks used in this study were obtained from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Prior to infestation, unfed ticks were maintained at 21°C and 85% relative humidity. One day before feeding, female ticks were paired with males to allow mating. Adult ticks were placed on the outer ear of four naïve female New Zealand rabbits, restricted by orthopedic stockinets that were glued in place. A total of 20 female and 20 male ticks (40 ticks per ear, 80 ticks per rabbit) were allowed to attach. To classify ticks by blood-feeding index, partially fed ticks were collected from the host based on engorgement size, sorted by weight, and divided into biological triplicates: an unfed group (UF) (15 females per replicate, weighing 1.6 mg in average), group G2 (5 females per replicate, weighing 7.2 mg in average), and group G5 (4 females per replicate, weighting 41.5 mg in average). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, 70% ethanol, and a final rinse with nuclease-free water. Ticks were dissected within two hours of removal. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization. Total RNA was isolated using the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's instructions. RNA integrity and quantity were assessed using a 4200 TapeStation system (Agilent Technologies). Illumina libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection, and sequencing was performed on an Illumina NovaSeq 6000 DNA sequencer. Raw sequencing data were trimmed and aligned to the Ixodes scapularis reference genome (ASM1692078v2). We used the RNA-seek workflow  https://github.com/skchronicles/RNA-seek), which performs multiple steps including quality assessment with FastQC, FQScreen, Kraken, and BBTools; adaptor removal and quality trimming with Cutadapt; read alignments using STAR in 2-pass mode; and read quantification with RSEM.


title: Development and Application of G4-Flame as a Visual Biosensor for G4-DNA

status: Public on Feb 20 2026

city: hefei

first: sun

last: xuedan

address: daoxiangcun

country: China

institute: ustc

type: Genome binding/occupancy profiling by high throughput sequencing

summary: G4-DNA, a non-canonical tetrahelical nucleic acid structure stabilized by stacked G-quartets via Hoogsteen hydrogen bonding, plays critical roles in genomic regulation and disease pathogenesis. Current methodologies for detecting these structures face limitations in specificity, spatiotemporal resolution, and live-cell applicability. To address these challenges, we engineered G4-Flame, a genetically encoded fluorescent biosensor utilizing Circularly Permuted Fluorescent Protein (CPFP) technology. By strategically positioning a G4-specific binding domain proximal to the fluorophore of circularly permuted YFP (cpYFP), G4-Flame achieves real-time, high-resolution visualization of G4-DNA dynamics in living systems, with specificity across diverse G4 conformations. Experimental validation revealed distinct spatiotemporal patterns of G4-DNA during the cell cycle: nuclear G4-DNA levels peaked during the S phase, while mitochondrial G4-DNA was found to suppress the expression of mitochondrial-encoded genes. Clinically, serum analysis revealed significantly elevated G4-DNA levels in cancer patients compared to healthy controls. This work establishes G4-Flame as a transformative tool for investigating G4-DNA spatiotemporal regulation and advances its potential as a biomarker for early cancer detection, bridging fundamental research with clinical translation.

overall_design: The experimental design of this study systematically investigates genome-wide G4-DNA recognition and its cell cycle dynamics by combining genomic mapping and cellular imaging approaches. The core of the methodology employs CUT&Tag to perform a genome-wide consistency analysis, comparing the occupancy profiles obtained using the engineered probe G4-Flame (detected via an anti-HA antibody) with those from the endogenous G4-specific BG4 antibody. To study cell cycle-dependent changes, HEK293T cells expressing an NLS-tagged G4-Flame probe were synchronized at the G1/S boundary using a thymidine double-block protocol. The dynamics of nuclear G4-DNA were then directly visualized and compared between G1 and S phases through fluorescence microscopy imaging, thus integrating genome-wide comparative data with single-cell observational analysis.

first: Xuedan

last: Sun

first: Ruyi

last: Liu


title: RNA-seq of Ixodes scapularis salivary glands [bulkRNA-intact-SG]

country: USA

type: Expression profiling by high throughput sequencing

overall_design: Ixodes scapularis ticks were purchased from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Unfed ticks were maintained at 21°C and 85% relative humidity before infestation on rabbits. One day prior to feeding, female ticks were paired with males to mate. Adult ticks were restricted to feed on the outer part of the ear of four naïve female New Zealand rabbits, using orthopedic stockinets glued in place. A total of 20 adult females and 20 males (40 ticks per ear, 80 ticks per animal) were placed into the tick containment apparatus and allowed to attach. To group ticks by blood-feeding index, partially fed ticks were collected from the host during feeding, selected by engorgement size, sorted by weight, and divided into biological triplicates: unfed group (UF) (20 females per replicate, weight 1.6 ± 0.2 mg), group G1 (5 females per replicate, weight 2.8 ± 0.6 mg), group G2 (5 females per replicate, weight 7.3 ± 0.8 mg), group G3 (3 females per replicate, weight 15.9 ± 1.7 mg), group G4 (3 females per replicate, weight 24.6 ± 2.9 mg), group G5 (3 females, weight 44.5 ± 5.8 mg), and group G6 (2 females, weight 105.6 ± 15.9 mg). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, and 70% ethanol, followed by a final rinse with nuclease-free water. Ticks were dissected within two hours after removal from the host. Tick salivary glands (SGs) were dissected in fresh, ice-cold, nuclease-free phosphate-buffered saline (PBS), pH 7.4 (Invitrogen, Carlsbad, CA, USA). After dissection, the salivary glands were gently washed in fresh, ice-cold, nuclease-free PBS, pH 7.4, and then immediately stored in RNAlater (Invitrogen, Carlsbad, CA, USA) prior to RNA extraction. After removal from RNAlater, SGs were gently washed in nuclease-free PBS, pH 7.4. Total RNA was isolated using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer's instructions. RNA integrity and quantity were assessed using a 4200 TapeStation system (Agilent Technologies). Illumina libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with polyA selection, and sequencing was performed on an Illumina NovaSeq 6000 DNA sequencer. Raw sequencing data were trimmed and aligned to the Ixodes scapularis reference genome (ASM1692078v2). We used the RNA-seek workflow (https://github.com/skchronicles/RNA-seek), which performs multiple steps including quality assessment with FastQC, FQScreen, Kraken, and BBTools; adaptor removal and quality trimming with Cutadapt; read alignments using STAR in 2-pass mode; and read quantification with RSEM.


title: The transcriptome of Dermacentor andersoni salivary glands at single cell resolution

summary: Applications of transcriptomics have significantly advanced the identification of numerous tick salivary molecules involved in feeding and the transmission of tick-borne pathogens. In this study, we analyze the salivary gland transcriptome of Dermacentor andertsoni, the vector of Rickettsia rickettsii in the U.S., at single cell resolution.

overall_design: Dermacentor andersoni adult ticks were collected in May 2023 from vegetation near Lake Como, Montana, USA. Ticks were sampled using the flagging method, where a white flannel cloth was swept over low-lying vegetation and bushes. After collection, ticks were transported to the laboratory and maintained in an environmental incubator at 21°C and 85% relative humidity, with a 12h/12h light/dark cycle. Ticks were removed from incubator and salivary glands were dissected. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization. The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the library was sequenced by the Illumina NovaSeq 6000 System. The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Raw sequencing data were aligned to the D. andersoni (GCF_023375885.1) reference genome and quantified using Cell Ranger tool (v7.0.1). Low-quality cells (4,405 cells) were excluded using a threshold of three median absolute deviations (MAD) from the median of the overall cell population for both unique molecular identifier (UMI) or feature counts and mitochondrial content. Putative doublets were identified and removed using scDblFinder R package (v 1.18.0), yielding 14,400 high-quality cells for downstream analyses. Cell clustering was performed following routine steps provided in the Seurat (v4.3) pipeline. Counts were natural log (log1p)-transformed, followed by scaling and dimensionality reduction (1:10), with visualization using PCA and UMAP. Cells were clustered using the shared nearest-neighbor approach based on the Louvain algorithm (resolution = 0.15), and the results were projected onto UMAP. Differential gene expression analysis (min.pct = 0.25, logfc.threshold = 0.25, q < 0.05) across cell clusters were conducted using the Wilcoxon rank-sum test via the ‘FindMarkers’ and ‘FindAllMarkers’ functions, respectively.


title: Comprehensive molecular profiling of regenerated retinal neurons in the adult zebrafish

status: Public on Feb 23 2026

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

summary: Unlike mammals, zebrafish possess a remarkable capacity to regenerate ablated retinal neurons. In response to cellular injury and death, Müller glia dedifferentiate into a stem cell state, and each gives rise to a single Müller glia-derived progenitor. Progenitors then proliferate and differentiate into to replace the ablated retinal neurons. This study aimed to determine if the injury context influences the quantity of regenerated neurons and to comprehensively identify the cellular and molecular characteristics and diversity of newly born regenerated neurons during regenerative neurogenesis. To definitely label Muller glia-derived regenerated neurons, we utilized a genetic lineage tracing line, Tg(mmp9:creERt2;Ola.actb2:loxp-dsRed-loxp-eGFP). By integrating this approach with scRNAseq and morphological profiling, we characterize quantity, molecular and morphological identity, and diversity of regenerated neurons across two distinct injury models, an intense light photolytic lesion or an intraocular injection of the excitotoxin, NMDA which procedures selective damage to photoreceptors or inner retinal neurons, respectively. Our data show that while regenerated neurons are biased toward the cell type originally ablated, both lesion modes consistently generate other cell types. This suggests a robust intrinsic neurogenic program present among Muller glia-derived progenitors. Transcriptome analysis demonstrates a high degree of similarity between regenerated and endogenous populations, indicating successful restoration of homeostatic molecular signitures. Finally, subtype analysis of amacrine cells show generation of diverse subtype and successful reestablishment of their neurochemical and morphological identities equivalent to their original counterparts. These findings demonstrate that regenerative neurogenesis in the zebrafish retina can faithfully reconstitute the specialized cellular diversity and molecular and structural complexity of the mature retina.

overall_design: The transgenic line, Tg(mmp9:creERt2;Ola.actb2:loxp-dsRed-loxp-eGFP), was utilized to perform lineage tracing of Müller glia-derived, regenerated neurons. Animals were subjected either to an intense light photolytic lesion or an intraocular injection of the excitotoxin, NMDA. Regenerated, eGFP+ retinal neurons at 14 days post lesion were collected via FACS. eGFP+ cells were loaded into the 10x Genomics Chromium Single Cell System and libraries were generated using V4 chemistry following the manufacturer’s instructions. Libraries were sequenced on the Illumina NovaSeq platform.

first: Hoang

last: Thanh

first: Nagashima

last: Mikiko

first: Awad

last: Sherine


title: Aberrant alternative splicing of AARS2 in congenital cardiomyopathy is regulated by PCBP1

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Erk3 deletion drives oxidative adaptations in skeletal muscle

city: Warsaw

first: Grzegorz

last: Sumara

address: L Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology PAS

summary: Skeletal muscle plays a central role in whole-body energy expenditure and metabolic homeostasis, and improving its mitochondrial function and oxidative fiber profile is considered an effective strategy to counteract diet-induced metabolic impairments, although the molecular regulators of these adaptations are not yet fully understood. Erk3 has been implicated in myotube differentiation and in skeletal muscle adaptations to aerobic exercise; however, its potential role in skeletal muscle during diet-induced metabolic dysfunction remains to be determined.

overall_design: In this study, we used mice with striated muscle-specific Erk3 deletion alongside in vitro cultured C2C12

first: Angel

last: Loza Valdes

first: Carlos

last: Acosta-Gallo

first: Toufic

last: Kassouf

first: Andrei

last: Belykh

first: Dominika

last: Malińska

first: Katia

last: El Ghoz

first: Rabih

last: El-Merahbi

first: Filip

last: Dziaczkowski

first: Kasia

last: Kolczyńska-Matysiak


title: Enhanced cross-linked immunoprecipitation follow by sequencing (eCLIP-seq) of PCBP1 in embryonic mouse heart

summary: PCBP1 is an RNA-binding protein abundantly expressed in the embryonic heart. We sought to determine the RNA interaction of Pcbp1 in embryonic heart.

overall_design: Embryonic day (E) 16.5 C57BL/6N hearts ventricles were snap-frozen follow by cryogrinded, UV crosslinking, and sonication. 20 x E16.5 hearts were pool per biological replicate (40 hearts total, n=2). Immunoprecipiation was performed by a pre-validated PCBP1 antibody (Abcam cat #ab168377). 2% of the sample was taken as the paired input sample. IP and input samples were cut from the membrane at the relative band size of 40kDa to 75kDA above that band size. RNA adapter ligation, reverse transcription, DNA adapater ligation and PCR amplification were performed.

first: Da-Zhi

last: Wang


title: CBP-IDRs regulate acetylation and gene expression [ChIP-Seq]

city: Sheffield

first: Daniel

middle: Arun

last: Bose

state: South Yorkshire

address: University of Sheffield, Firth Court, Western Bank

department: Biosciences

country: United Kingdom

institute: The University of Sheffield

summary: Intrinsically disordered regions (IDRs) have emerged as crucial regulators of protein function, allowing proteins to sense and respond to their environment. Creb binding protein (CBP) and EP300 (p300) are transcription coactivators that regulate gene expression in multicellular organisms, following their recruitment to cis-regulatory elements. CBP and p300 contain large IDRs, however little is known about how these different IDRs work together to regulate CBP function. Here, we show that CBP-IDRs cooperate to control different aspects of CBP behaviour in the nucleus, by regulating the properties of fluid-like condensates formed by endogenous CBP. We show how IDRs with different sequence properties make unique contributions to CBP behaviour by establishing a balance between positive and negative regulation of CBP condensates. These conflicting interactions are functionally important, shaping CBPs response to factors such as lysine acetylation, that influence condensate formation. When disrupted, regulatory CBP-IDRs change how CBP interacts with chromatin, alter patterns of CBP-dependent histone acetylation and change gene expression. Together, our work highlights how IDRs with different sequences, spatially segregated in the same protein, can cooperate to shape protein function.

overall_design:
Chromatin immunoprecipitation sequencing (ChIP-seq) for doxycycline inducible GFP epitope-tagged Crebbp binding protein (CBP) in HEK293T cells. Doxycycline was added to induce GFP expression while not altering overall levels of tagged and untagged CBP. Control  ChIP-seq for endogenous CBP was done in parental HEK293T cells stably expressing Tet3G transactivator protein.
The same system was used to generate datasets for H3K27ac CUT&RUN and total RNAseq, following induction of CBP-GFP expression. Please note that the processed data files generated from both replicates are linked to the corresponding Rep1 sample records.

first: Katie

middle: L

last: Gelder

first: Nicola

middle: A

last: Carruthers

first: Grace

last: Gilbert

first: Laura

middle: J

last: Harrison

first: Thomas

last: Evans

first: Sophie

middle: S

last: Ball

first: Mark

last: Dunning

first: Timothy

middle: D

last: Craggs

first: Alison

middle: E

last: Twelvetrees


title: CBP-IDRs regulate acetylation and gene expression [CUT&Run]

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for doxycycline inducible GFP epitope-tagged Crebbp binding protein (CBP) in HEK293T cells. Doxycycline was added to induce GFP expression while not altering overall levels of tagged and untagged CBP. Control ChIP-seq for endogenous CBP was done in parental HEK293T cells stably expressing Tet3G transactivator protein. The same system was used to generate datasets for H3K27ac CUT&RUN and total RNAseq, following induction of CBP-GFP expression. Please note that the processed data files generated from both replicates are linked to the corresponding Rep1 sample records.


title: CBP-IDRs regulate acetylation and gene expression [RNA-Seq]

overall_design: RNA-seq for doxycycline inducible GFP epitope-tagged Crebbp binding protein (CBP) in HEK293T cells. Doxycycline was added to induce GFP expression while not altering overall levels of tagged and untagged CBP. Control ChIP-seq for endogenous CBP was done in parental HEK293T cells stably expressing Tet3G transactivator protein. The same system was used to generate datasets for H3K27ac CUT&RUN and total RNAseq, following induction of CBP-GFP expression. Please note that the processed data files generated from both replicates are linked to the corresponding Rep1 sample records.


title: Effect of heme on the gene expression of differentiating mouse B cells [RNA-seq]

status: Public on Feb 21 2026

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The effect of heme on the gene expression of differentiating mouse B cells was assessed by isolating splenic CD43- B cells and culturing with LPS, IL2, and IL5.  After 24 hours heme or vehicle control was added to the cultures.  At 72 hours activated B cells and plasmablasts were FACS isolated and RNA-seq performed.

overall_design: RNA-seq was performed on activated B cells and plasmablasts differentiating in the presence or absence of heme in triplicate.

first: Christopher


title: Integrated in vivo and multiparameter in vitro screen uncovers NFIL3 as driver of T cell dysfunction

status: Public on Feb 19 2026

city: New York

first: Sneha

last: Mitra

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: CAR therapy has transformed the treatment landscape for hematological malignancies but its efficacy in solid tumors is limited, owing in part to insufficient functional persistence of the engineered T cells. To elucidate the basis for their functional decline, we conducted a multi- parameter in vivo discovery screen of 400 transcription factors, which revealed NFIL3 as a driver of CAR T cell dysfunction. Genetic disruption of NFIL3 in CAR T cells sustained their expansion, increased cytokine production, overall restraining terminal differentiation. Loss of NFIL3 enhances CAR T cell efficacy, improving tumor control and prolonging survival in xenograft and syngeneic mouse tumor models across different CAR designs. Under chronic stimulation, disruption of NFIL3 establishes a transcriptional state predictive of favorable clinical outcomes. Our findings underscore the power of comprehensive multi-parameter genetic screens conducted in vivo and reveal NFIL3 as a novel therapeutic target to enhance cancer immunotherapy.

overall_design: CAR T cells from two donors at the pre-stimulation, after two rounds and four rounds of tumor stimulation were counted and assessed for scRNA-seq analysis

first: Nayan

last: Jain

first: Yuzhe

last: Shi

first: Celina

last: May

first: Philip

last: Bucher

first: Anton

last: Dobrin

first: Zeguo

last: Zhao

last: Hanina

first: Vinagolu

last: Rajasekhar

first: Christina

last: Leslie

first: Franciso

last: Sánchez-Rivera

first: Judith

last: Feucht

first: Michel

last: Sadelain


title: LMO2 regulates epithelial-mesenchymal plasticity of mammary epithelial cells

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz

summary: Cellular plasticity in mammary epithelial cells enables dynamic cell state changes essential for normal developmental but can be hijacked by breast cancer cells to drive tumor progression. However, the molecular factors that maintain cellular plasticity through the regulation of a hybrid cell state (epithelial/mesenchymal) are not fully defined. As LMO2 has been previously shown to regulate metastasis, here we determined  the role of LMO2 in the normal mammary epithelial cells . Using lineage tracing and knockout mouse models we find that Lmo2 lineage-traced cells persist long-term in the mammary gland, both in the luminal and basal layer but have limited proliferative potential. Lmo2 loss does not impact mammary gland development, but acute deletion decreases in vivo reconstitution. Moreover, LMO2 knockdown in mouse and human mammary epithelial cells (MECs) reduces organoid formation. We find that LMO2 maintains a hybrid cell state and LMO2 knockdown promotes mesenchymal differentiation. Transcriptional profiling of LMO2 knockdown cells reveals significant enrichment in the epithelial-mesenchymal transition (EMT) pathway and upregulation of MCAM, a negative regulator of regenerative capacity in the mammary gland . Altogether, we show that LMO2 plays a role in maintaining cellular plasticity in normal mammary epithelial cells, adding insight into the normal differentiation programs hijacked by cancer cells to drive tumor progression.

overall_design: Bulk RNA sequencing was performed on MCF10A lines derived from human mammary epithelium

first: Shaheen

last: Sikandar

first: Veronica

last: Haro-Acosta


title: Loss of miR-29a/b1 cluster reprograms the tumor microenvironment and contributes to immunosuppression in lung cancer

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

summary: Immune checkpoint inhibitors (ICI), like those that block PD-1/PD-L1, have revolutionized oncological therapy for patients with non-small cell lung cancer (NSCLC). However, most patients demonstrate no clinical benefit or acquire resistance, even in PD-L1+ populations, highlighting the critical need to dissect tumor survival dependencies to overcome resistance. Using our unique Kras/p53-driven lung cancer models which demonstrate acquired or intrinsic resistance to ICI, we performed single cell RNA-sequencing and focused on predicted upstream regulators of differentially expressed genes (DEGs) in the malignant cell cluster of resistant tumors. We found that the micro-RNA, miR-29, was downregulated in tumors with anti-PD-1 resistance, leading to significant upregulation of a multitude of miR-29 targets. Interestingly, we found that the immunosuppressive molecule Enpp2/ATX was one of these genes modulated due to miR-29 loss, and re-expression of miR-29 in anti-PD-1 resistant models diminished ATX tumor expression, diminished the fibrotic microenvironment, and increased CD8 infiltration. Additionally, analysis of lung adenocarcinoma patients revealed miR-29-high patients had increased CD8A expression and enrichment in immunoregulatory pathways. Together, these data provide evidence that the miR-29 family broadly regulates the tumor microenvironment, including anti-tumor immune-related pathways in lung cancer, through control of ATX among many other target genes, with implications in ICI response.

overall_design: Kras/p53 mutant murine lung cancer cells were implanted in vivo. The 344SQ are the parental line and the 140P (PD1R1) samples were derived from the 344SQ cells after in vivo treatment and resistance to anti-PD-1 therapy. The 344SQ and PD1R1 tumors were collected after 4 and 6 weeks of in vivo growth (T1 and T2) and analyzed by scRNA-seq for differentially expressed genes between the two models specifically in the malignant compartment.

first: Jessica

last: Konen

first: Yanhua

last: Tian

first: Yuanxin

last: Xi


title: Transcriptome of embryonic hearts with cardiomyocyte-specific deficiency of Pcbp1

first: Yao Wei

last: Lu

summary: We generated cardiomyocyte-specific Pcbp1 knockout mice, and observed ventricular non-compaction defects and abnormal cardiac morphogenesis at E12.5 and E16.5. Majority of homozygous mutant mice died shortly after birth. We sought to identify the transcriptome changes at E16.5 by Pcbp1-deficiency in cardiomyocytes.

overall_design: We cross Pcbp1-Flox mice with Ctnt-Cre to generate cardiomyocyte-specific deletion of Pcbp1. On embryonic day (E) 16.5, cardiac ventricles from mutant mice and littermate controls were dissected, snap frozen and processed for RNA isolation. Genotype of individual embryos were confirmed by PCR from DNA isolated from yolk-sacs or tail tips. E16.5 heart RNA were processed for rRNA-depleted library construction and RNA-sequencing.

first: Da-Zhi

last: Wang


title: Patient-derived cell lines unveil COL1A2 as a predictor of docetaxel resistance in breast cancer

status: Public on Feb 18 2026

city: Guiyang

first: jianjun

last: huang

state: Guizhou

address: 9, Beijing Road

department: School of Clinical Medicine

institute: Guizhou Medical University

summary: Breast cancer is the most common type of malignant tumour among women globally, with a major cause of cancer-related mortality worldwide. Chemoresistance presents a significant challenge in breast cancer therapy and serves as the primary factor contributing to tumour recurrence and metastasis. At present, there is a paucity of effective predictive strategies in this field. In this study, we successfully established patient-derived primary cancer cell lines (PCCL) from four patients with HR+/HER2- breast cancer (Luminal B, HER2 non-amplified) using primary cell culture technology. The retention of the original tumour's pathological characteristics and drug response heterogeneity was confirmed. The aim was to delve into the mechanisms and predictive models underlying chemotherapy resistance in HR+/HER2- breast cancer. Our investigation revealed varying sensitivities of PCCL to taxanes, including docetaxel. Through RNA sequencing and protein-protein interaction (PPI) network analysis, we discovered that the COL1A2 gene is significantly overexpressed in HR+/HER2- breast cancer patients exhibiting docetaxel resistance. Notably, this overexpression shows a negative correlation with the patients' pathological complete response rate (pCR) and recurrence-free survival (RFS). In functional assays, higher COL1A2 expression correlated with diminished docetaxel sensitivity in HR+/HER2-negative breast cancer cells. These findings are consistent with the imaging assessments and postoperative pathological outcomes of patients who underwent neoadjuvant therapy (AC-T regimen). These findings suggest that COL1A2 is associated with reduced chemotherapy sensitivity in HR+/HER2- breast cancer and may serve as a candidate biomarker to guide neoadjuvant taxane selection. Overall, this study provides a novel theoretical foundation for selecting neoadjuvant chemotherapy drugs for advanced breast cancer patients.

overall_design: RNA-seq of human Breast cancer: docetaxel-resistant group and docetaxel-sensitive group


title: Effect of heme on the chromatin accessibility of differentiating mouse B cells

first: Chris

last: Scharer

summary: The effect of heme on the chromatin accessibility of differentiating mouse B cells was assessed by isolating splenic CD43- B cells and culturing with LPS, IL2, and IL5.  After 24 hours heme or vehicle control was added to the cultures.  At 72 hours activated B cells and plasmablasts were FACS isolated and ATAC-seq performed.

overall_design: ATAC-seq was performed on activated B cells and plasmablasts differentiating in the presence or absence of heme in triplicate.

first: Christopher


title: Transcriptome of embryonic hearts with cardiomyocyte-specific deficiency of Aars2

summary: We generated cardiomyocyte-specific Aars2 knockout mice, and observed ventricular non-compaction defects and abnormal cardiac morphogenesis at E16.5. All homozygous mutant mice died before birth. We sought to identify the transcriptome changes at E16.5 by Aars2-deficiency in cardiomyocytes.

overall_design: We cross Aars2-Flox mice with Ctnt-Cre to generate cardiomyocyte-specific deletion of Aars2. On embryonic day (E) 16.5, cardiac ventricles from mutant mice and littermate controls were dissected, snap frozen and processed for RNA isolation. Genotype of individual embryos were confirmed by PCR from DNA isolated from yolk-sacs or tail tips. E16.5 heart RNA were processed for rRNA-depleted library construction and RNA-sequencing.


title: Transcriptome of adult hearts with cardiomyocyte-specific deficiency of Aars2

summary: We generated cardiomyocyte-specific Aars2 knockout mice using Myh6-Cre, and observed progressive cardiac function decline starting at postnatal day (P) 28, with severe chamber dilation, and  phenotypes reminance of mitochondrial cardiomyopathy. All homozygous mutant mice died before reaching P70. We sought to identify the transcriptome changes by Aars2-deficiency at P14 and P21 in adult, prior to the onset of the cardiomyopathy.

overall_design: We cross Aars2-Flox mice with Myh6-Cre to generate cardiomyocyte-specific deletion of Aars2. At P14 or P21, heart apex from mutant mice, heterozygous and cre-negative controls were dissected, snap frozen and processed for RNA isolation. Genotype of individual embryos were confirmed by PCR from DNA isolated from tail tips. RNA were processed for rRNA-depleted library construction and RNA-sequencing.


title: Single-nucleus and Spatial Transcriptomics Reveal Intestinal Cellular Heterogeneity, Differentiation, and Cell Communication Mechanisms in SAP-induced Intestinal Injury

city: Jinan

first: Shulei

last: Zhao

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology


title: Biosacetalin 1,1-Diethoxyethane enhances aerobic respiration via activation of AMP-activated protein kinase

city: Jeollanam-do

first: Seung-Rock

last: Lee

address: Seoyang-ro, Hwasun-eup, Hwasun-gun

department: Biochemistry

country: South Korea

institute: Chonnam National University Medical school

summary: The enzyme 5ʹ-adenosine monophosphate (AMP)-activated protein kinase (AMPK) is a key regulator of cellular energy metabolism, playing a protective role in cardiovascular remodeling and diseases. Here, 1,1-Diethoxyethane (1,1-DEE), a compound traditionally known as a flavoring agent in wine and distilled spirits, was identified as an AMPK activator. By analyzing AC16 cardiomyocytes with the Seahorse Mito Stress Test, we found that 1,1-DEE induced a transient inhibition of both mitochondrial respiration and glycolysis, resulting in reduced ATP production. This metabolic disturbance triggered AMPK activation in a time- and concentration-dependent manner, leading to adaptive increases in the phosphorylation of acetyl-CoA carboxylase and 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2, which promotes fatty acid oxidation and glycolysis. AMPK activation also enhanced mitochondrial biogenesis by upregulating peroxisome proliferator-activated receptor gamma coactivator 1-alpha and mitochondrial transcription factor A. These alterations led to a sustained increase in both mitochondrial respiration and glycolysis. Overall, our findings unravel the important physiological role of 1,1-DEE in energy homeostasis through AMPK activation and aerobic respiration. This mechanism may hold therapeutic potential for the prevention and treatment of metabolic and cardiovascular diseases.

overall_design: RNA-seq of profiling of heart tissues of C57BL/6J mice (normal diet (ND) group and 1,1-DEE-treated group) after 8 weeks of treatment.

first: Thang

last: Nguyen Huu


title: The transcriptome of Ixodes scapularis salivary glands at single cell resolution

first: Lucas

last: Tirloni

summary: Applications of transcriptomics have significantly advanced the identification of numerous tick salivary molecules involved in feeding and the transmission of tick-borne pathogens. In this study, we analyze the salivary gland transcriptome of Ixodes scapularis, the main vector of Borrelia burgdorferi in the U.S., at single cell resolution.

overall_design: The Ixodes scapularis ticks used in this study were obtained from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Prior to infestation, unfed ticks were maintained at 21°C and 85% relative humidity. One day before feeding, female ticks were paired with males to allow mating. Adult ticks were placed on the outer ear of four naïve female New Zealand rabbits, restricted by orthopedic stockinets that were glued in place. A total of 20 female and 20 male ticks (40 ticks per ear, 80 ticks per rabbit) were allowed to attach. To classify ticks by blood-feeding index, partially fed ticks were collected from the host based on engorgement size, sorted by weight, and divided into biological triplicates: an unfed group (UF) (15 females per replicate, weighing 1.6 mg in average), group G2 (5 females per replicate, weighing 7.2 mg in average), and group G5 (4 females per replicate, weighting 41.5 mg in average). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, 70% ethanol, and a final rinse with nuclease-free water. Ticks were dissected within two hours of removal. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization. The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation in triplicate for three groups and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the libraries were sequenced by the Illumina NovaSeq 6000 System. The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Cell Ranger was used to perform sample demultiplexing, barcode processing, and single-cell gene counting. The 'cellranger count' function was applied for alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting. The genome of I. scapularis published in 2021 (University of Maryland) was used as the reference genome for the alignment.  Following generation of gene-cell matrices from Cell Ranger, further analysis was performed using Seurat v3, an R package for analysis of single cell RNAseq data. Quality control was not applied to exclude cells with high mitochondrial gene content, because mitochondrial genes were expected to be upregulated in feeding groups.  The gene expression matrix was then normalized and scaled. Variable features were identified using the 'vst' method in the 'FindVariableFeatures' function. Dimensionality reduction was performed using principal component analysis (PCA). The most significant principal components were selected for downstream analyses. Based on these components, shared nearest neighbor (SNN) graph-based clustering was performed. Clusters were visualized using Uniform Manifold Approximation and Projection (UMAP). For each cluster, differential gene expression was performed to identify cluster-specific marker genes. These markers were used to annotate cell clusters based on known marker genes for cell types.


title: Netrin-1 blockade alleviates resistance to first line chemotherapy in locally advanced pancreatic cancer

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary: Netrin-1, a developmental cue, is a master regulator of tumor Epithelial-to-mesenchymal transition (EMT). Pancreatic cancer is a challenging indication where netrin-1 and its receptor neogenin have been shown to promote tumor progression and metastasis in animal models. Here we report the results of a single arm phase 1b study assessing the combination of an anti-netrin-1 antibody (NP137) with standard chemotherapy (mFOLFIRINOX) in first-line patients with locally advanced pancreatic cancer. Fourty-three patients were included in this trial and received mFOLFIRINOX plus NP137 once every two weeks for up to 12 cycles (6 months). NP137 was well tolerated. Median PFS was 10.85 months (95% CI, 10.03 – 15.61) and median OS was 16.43 months (95% CI, 12.75 – NR) with 21 patients still alive at time of the data cut-off. Laser capture microdissection followed by microbulk RNA sequencing was  performed on 22 pre-therapeutic and 6 surgery samples and revealed that the main pathway downregulated with the combination mFOLFIRINOX+NP137 is EMT, strengthening the mechanism of action of NP137. Moreover, analysis of pre-therapeutic samples revealed extended survival outcomes of patients with tumor cells expressing high levels of the netrin-1 receptor Neogenin, an observation validated by Neogenin immunostaining. Our results support netrin-1 blockade alleviates resistance to standard of care chemotherapy by inducing tumor re-epithelialization, particularly in neogenin-high pancreatic cancer.

overall_design:
Single arm phase 1b study assessing the combination of an anti-netrin-1 antibody (NP137) with standard chemotherapy (mFOLFIRINOX) in first-line patients with locally advanced pancreatic cancer.
---------
Phenotype variables:
# ID_paired= subject ID
# timepoint
Pre = sample obtained before therapy
Post = sample obtained after therapy
# response (RECIST)
PR= Partial Response
SD= Stable Disease
# survival
PFS_time= Progression free survival (days)
PFS_status: 0= no progressed, 1= progressed
OS_time= Overall survival (days)
OS_status: 0=alive, 1=dead


title: Effect of cardiomyocyte-specific activation of nuclear receptor subfamily 4 group A member 2 (NR4A2) on poly(A) RNA expression profile in the mouse heart [RNA-seq]

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

summary: Nuclear receptor subfamily 4 group A member 2 (NR4A2) is a widely expressed immediate early gene induced by a host of physiological signals such as growth factors, cytokines, and neurotransmitters. In the adult mammalian heart, including in cardiomyocytes, NR4A2 mRNAs increase more than 60-fold in response to beta-adrenergic stimulation. However, the nature of the transcriptional remodeling induced by NR4A2 in the stressed heart has remained poorly investigated. We show here that NR4A2 activation in mouse cardiomyocytes profoundly alters the sub-transcriptomes controlling metabolic pathways and calcium transients in the heart. At the metabolic level, NR4A2 induced the expression of glycolytic enzymes while simultaneously down-regulating fatty acid oxidation. Increased NR4A2 expression was also associated with the repression of several genes critical for t-tubules formation, dyads organization, and calcium flux. The findings shed light on a novel regulatory mechanism controlling cardiac homeostasis, and establish a framework to investigate further the roles played by NR4A2 in fetal reprogramming of the adult mammalian heart under various stress conditions.

overall_design: Cardiac poly(A) RNA-seq profiling of mice with cardiomyocyte-specific, tamoxifen-inducible expression of the nuclear receptor NR4A2 and of their Cre recombinase expression control littermates before (Day 0) and at 3 days, 6 days, and 12 days  after tamoxifen treatment.

first: Harmancey

last: Romain

first: Ashraf

last: Sadia


title: FGF8 induces bone and joint regeneration at middle phalanx amputation wounds in neonate mice

city: Bryan

first: Andreea

last: Trache

address: 402 John Sharp Pkwy

department: Medical Physiology

institute: Texas A&M University

summary: Mice and humans have limited regenerative capacity following limb amputation, with regenerative responses restricted to amputations transecting the distal digit tip, (P3). Unlike P3, amputations of the adjacent skeletal segment, the middle phalanx, P2, are non-regenerative. Here, we report that FGF8 drives synovial joint regeneration at P2 amputation wounds in neonate mice. This response is characterized by the regeneration of a synovial cavity, a skeletal nodule lined with articular-like cartilage, tendon and ligament regeneration, and partial P2 stump regeneration. FGF8-induced joint regeneration is associated with the upregulation of several, but not all, genes that characterize joint development, and is morphologically distinct from digit joint development. Lineage tracing studies demonstrate that cells at the amputation wound contribute to the regenerated joint structures. These studies provide evidence that the otherwise non-regenerative P2 amputation wound possesses tremendous regenerative capacity that is not activated under normal circumstances.

overall_design: scRNA-seq analysis of middle phalanx amputations in neonate mice (8 days postnatal, PN8).

first: Ling

last: Yu

first: Mingquan

last: Yan

first: Sarah

middle: M

last: Wolff

first: Joseph

last: Knue

first: Hannah

last: Smith

first: Connor

middle: P

last: Dolan

first: Ken

last: Muneoka

first: Selim

last: Romero

first: James

last: Cai

first: Carissa

last: Yun

first: Devon

last: Boland

first: Regina

last: Brunauer

first: Lindsay

last: Dawson


title: Maternal gut microbial legacy shapes intestinal health and colitis susceptibility of offspring

city: Daegu

first: Ji-Min

last: Lee

address: 680, Gukchaebosang-ro

department: Cell & Matrix Research Institute

institute: Kyungpook National University

summary: Offspring born to mothers with colitis exhibited gut microbial dysbiosis, impaired barrier function, low-grade intestinal inflammation, compromised Wnt signaling and reduced crypt cell proliferation, which collectively increased their susceptibility to colitis in adulthood.

overall_design: 1.5% dextral sulfate sodium (DSS) was treated to induce colitis for 5 days at 2nd trimester of pregnant mice.  We examined their offspring's intestinal conditions and collected fecal samples at 3-week after birth.

first: Hoyul

first: Eun Soo

last: Kim


title: Effect of HIF-1alpha and HIF-2alpha on hypoxic response in Panc1 cells

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: The hypoxic response is influence by both the tissue of origin and local environmental influences, and mediated in large part by the hypoxia-inducible transcription factors HIF-1 and HIF-2. We looked at Panc1 cells, a pancreatic adenocarcinoma cell line, and compared the response to hypoxia in both regular tissue culture media and in pancreatic TIFM (tumor interstitial fluid media), and assessed the degree to which HIF-1 and HIF-2 knockout mediates  changes in the hypoxia response.

overall_design: RNA-sequencing of Panc1 control cells, HIF-1a knockout cells, and two independently derived clones of HIF-2a knockout cells, generated by CRISPR-Cas 9 technology. Samples are exposed to normoxia (20% O2)/regular media (DMEM + 10% FBS + 1% P/S), hypoxia (1% O2)/regular media, or hypoxia/pancreatic TIFM (described by Muir A et al., eLife 2023), for 48 hours.

first: Maimon

last: Hubbi

first: Chi

middle: V

last: Dang


title: Post-replicative chromatin accessibility predicts cell fate change.

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: It has long been hypothesized that DNA replication is important in reconfiguring the chromatin landscape during cell identity changes in development, disease, and reprogramming contexts. There is now a large body of work showing that DNA replication indeed alters chromatin structure and composition, but a function for these changes has remained elusive. Using replication-coupled ATAC-seq in differentiating embryonic stem cells and reprogramming mouse embryonic fibroblasts, we profiled replicated and unreplicated chromatin within the same cells and observed de novo chromatin opening specifically in the replicated fraction. These opening events created an accessibility landscape similar to that seen in the unreplicated fraction from later timepoints, especially in reprogramming. By parsing reprogramming fibroblasts based on proliferative history, we confirmed that reprogramming potential can be predicted by proliferation rate. This work bridges the gap between replication-induced structural chromatin changes and functional consequences by demonstrating that replication facilitates a “window of opportunity” that advances the chromatin landscape during cell identity change.

overall_design: repli-ATAC-seq time series in differentiating mouse embryonic stem cells and reprogramming mouse fibroblasts, and ATAC-seq in reprogramming mouse fibroblasts sorted based on CellViolet proliferation staining.

first: Teresa

last: Knudsen

first: Nazaret

last: Reveron-Gomez

first: Alva

last: Biran

first: Nicolas

last: Alcaraz

first: Sihem

last: Cheloufi

first: Konrad

last: Hochedlinger

first: Joshua

last: Brickman

first: Kathleen

middle: R

last: Stewart-Morgan


title: Effect of cardiomyocyte-specific activation of nuclear receptor subfamily 4 group A member 2 (NR4A2) on the regulation of gene expression in the mouse heart [ChIP-Seq]

first: Romain

last: Harmancey

summary: Nuclear receptor subfamily 4 group A member 2 (NR4A2) is a widely expressed immediate early gene induced by a host of physiological signals such as growth factors, cytokines, and neurotransmitters. In the adult mammalian heart, including in cardiomyocytes, NR4A2 mRNAs increase more than 60-fold in response to beta-adrenergic stimulation. However, the identity of the genes directly regulated by NR4A2 in the stressed heart has remained poorly investigated. Using quantitative ChIP-seq data, we show here that activation of glycolysis in the mouse heart upon NR4A2 induction is directly linked to increased binding of the nuclear receptor to the promoter and enhancers of genes encoding glycolytic enzymes. Increased binding of NR4A2 to enhancers located within the imprinted Dlk1-Dio3 locus was also associated with the up-regulation of several dozen non-coding RNAs (lncRNAs and miRNAs) known for coordinating critical steps of cardiac development and for inhibiting mitochondrial function in myocytes. The findings shed light on a novel regulatory mechanism controlling cardiac homeostasis, and establish a framework to investigate further the roles played by NR4A2 in cardiac metabolic remodeling in the face of various acute and pathological stress conditions.

overall_design: Comparative analysis of ChIP-seq profiles of NR4A2 obtained in mice with cardiomyocyte-specific, tamoxifen-inducible expression of the nuclear receptor NR4A2 (Nr4a2-icTg) and that of their Cre recombinase expression control littermates at 3 days after tamoxifen treatment. Validation of the NR4A2 antibody for ChIP-seq analyses and generation of normalized ChIP-seq data were carried out by Active Motif’s Epigenetic Services team.

first: Harmancey

last: Romain

first: Ashraf

last: Sadia


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [multiplex_and_CITE_seq]

status: Public on Feb 17 2026

city: Würzburg

first: Stefan

last: Thomann

address: Versbacher Strasse 9

country: Germany

institute: Würzburg Systems Immunology

summary: The liver biliary niche serves as a reservoir of tissue-resident immune cells and supports tissue fibrosis upon damage, yet the role of peribiliary immune cells during cholangitis remains poorly understood. Here, we induce cholestatic liver injury mirroring human biliary diseases with bile acid retention in mice to establish a spatial and multimodal single-cell RNA sequencing atlas of the liver and liver-draining lymph nodes (LN). We characterized a hepatic disease state trajectory from dendritic cell precursors (preDCs) to a mature subset of pro-inflammatory Mgl2+ type 2 conventional dendritic cells (cDC2B) and observed dynamic crosstalk with γδ  T cells inducing an Il17 response (γδ T17). Dissection of the cDC2B-γδ T cell communication node identified the Icosl-Icos pair as an important cell contact-dependent interaction, which was validated in vitro. In vivo, cDC2B depletion attenuated γδ T17 responses in cholestatic liver injury, and liver fibrosis was reduced in a model of inducible γδ T cell depletion and in an Il17-deficient background.  Our work demonstrates dynamic turnover of cDC2 within the biliary niche during cholestasis, and a profibrogenic function of γδ T cells contingent on the induction by peribiliary cDC2B, highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche.

overall_design:
Multimodal mouse and human scRNA seq data. 6 human liver samples to capture pseudonormal liver cells and identify niche interactions. Furthermore a DDC disease atlas consisting of 12 samples covering a control and 5 disease timepoints to analyse immune cell dynamics in the DDC model. Furthermore, scRNA-seq datasets covering inflammatory resolution after long-term DDC diet and a short term DDC diet in combination with a cDC2B depletion. A CITE-seq dataset from liver draining lymph nodes at a control and two disease timepoints for the analysis of cDC2 dynamics. Two  experiments of liver immune cells capturing transcriptome and genomic accessibility data modalities at steady state and early cholestasis (DDC D5). Finally, multiplexed scRNA seq data of liver and lymph node derived γδ T cells undergoing cholestasis/cholestasis resolution and disease after cDC2B cell depletion.

Please note that the feature_*.csv file (linked to each ADT or CSL sample records) describes what antibody derived tags were detected in the respective .mtx file (containing the ADT data reads), which is linked to the corresponding GEX sample records.

first: Dominic

last: Grün


title: Single-nucleus and Spatial Transcriptomics Reveal Intestinal Cellular Heterogeneity, Differentiation, and Cell Communication Mechanisms in SAP-induced Intestinal Injury [snRNA-seq]

first: Shulei

last: Zhao

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Background Acute pancreatitis (AP) is a severe inflammatory disease that frequently causes multi-organ damage, with intestinal injury being a major complication. The mechanisms underlying SAP-induced intestinal injury remain unclear, particularly regarding spatial cellular reorganization and functional interactions. Methods This study constructed a severe acute pancreatitis (SAP) rat model and employed single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptome sequencing (stRNA-seq) technologies to systematically analyze the dynamic changes in intestinal cellular composition, spatial distribution, and function during SAP-induced intestinal injury. Results snRNA-seq identified 18 major ileal cell populations spanning epithelial, immune, stem/TA, and stromal compartments. SAP was associated with compositional remodeling characterized by downward trends in Lgr5⁺/Olfm4⁺ stem cells, TA1, goblet cells, and Paneth cells, with a reciprocal increase in enterocytes, although most proportion changes did not reach statistical significance at the animal level. Spatial transcriptomics independently captured SAP-associated tissue remodeling, including a significant reduction in Paneth cells accompanied by increases in fat cells, macrophages, goblet cells, and TA2 cells. Across epithelial lineages, SAP induced a transcriptional shift toward immune interaction with up-regulation of antigen presentation–related genes (e.g., Cd74, Apoa1) and down-regulation of antimicrobial/barrier effectors (e.g., Defa24, Pla2g2a, Dmbt1), which was corroborated by spatial expression patterns and spatially variable gene programs enriched for host defense responses. Pseudotime analysis suggested a redistribution of epithelial states along the stem/TA-to-enterocyte continuum, with relative depletion of early states and expansion of enterocyte-dominant states in SAP. CellChat analysis revealed globally intensified intercellular communication and nominated FN1 as the pathway with the highest differential information flow, with Lgr5⁺ stem cells predicted as prominent FN1 senders targeting enterocytes and smooth muscle cells. SCENIC identified reduced activity and expression of Hmga2/Myb regulons in stem compartments, and immunofluorescence showed decreasing trends in Hmga2/Myb-positive Olfm4⁺ and Lgr5⁺ stem cells in SAP. Conclusions Integrated single-nucleus and spatial transcriptomics reveal that SAP is accompanied by spatially organized ileal remodeling, epithelial immune-interacting rewiring, and altered neighborhood architecture, together with an ECM-centered FN1 signaling axis and attenuated Hmga2/Myb-associated regulatory programs in stem compartments. These findings provide a spatially informed cellular framework and generate testable hypotheses for mechanisms underlying impaired epithelial regeneration during SAP-associated intestinal injury.

overall_design: Severe acute pancreatitis (SAP) was induced in Sprague–Dawley rats and compared with control (CON) rats. Ileal tissues were collected and profiled using single-nucleus RNA sequencing (snRNA-seq; CON n=3, SAP n=3) and Stereo-seq spatial transcriptomics (CON n=2, SAP n=2) to characterize SAP-associated changes in cellular composition, differentiation trajectories, spatial organization, and cell–cell communication.

first: Lechang

last: Zhang

first: Changqin

last: Xu

first: Tong

last: Su

last: Xiao

first: Xu

last: Yi

first: Yuemin

last: Feng

first: Jing

last: Wang


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis

summary:
The liver biliary niche serves as a reservoir of tissue-resident immune cells and supports tissue fibrosis upon damage, yet the role of peribiliary immune cells during cholangitis remains poorly understood. Here, we induce cholestatic liver injury mirroring human biliary diseases with bile acid retention in mice to establish a spatial and multimodal single-cell RNA sequencing atlas of the liver and liver-draining lymph nodes (LN). We characterized a hepatic disease state trajectory from dendritic cell precursors (preDCs) to a mature subset of pro-inflammatory Mgl2+ type 2 conventional dendritic cells (cDC2B) and observed dynamic crosstalk with γδ  T cells inducing an Il17 response (γδ T17). Dissection of the cDC2B-γδ T cell communication node identified the Icosl-Icos pair as an important cell contact-dependent interaction, which was validated in vitro. In vivo, cDC2B depletion attenuated γδ T17 responses in cholestatic liver injury, and liver fibrosis was reduced in a model of inducible γδ T cell depletion and in an Il17-deficient background.  Our work demonstrates dynamic turnover of cDC2 within the biliary niche during cholestasis, and a profibrogenic function of γδ T cells contingent on the induction by peribiliary cDC2B, highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche.

Spatial Transcriptomics Data (Xenium Platform) of Mouse Liver tissues treated with DDC diet for 5 days.

overall_design: single sample single timepoint


city: Xuzhou

first: Hui

state: Jiangsu

address: 209 Tongshan Road, Kejiao A513

department: Pathogenic Biology and Immunology

institute: XuZhou Medical University

summary: Aging accelerates central nervous system remyelination failure and neurodegeneration. Microglia promote remyelination by phagocytosing myelin debris, but this function is impaired by aging-related CD22 upregulation. However, the molecular mechanisms counteracting premature aging-related microglial dysfunction and remyelination impairment remain unclear. Here, we report that Aurka-Bhlhe41 axis prevents premature aging-like microglial dysfunction and promotes remyelination by restraining progressive CD22 upregulation. We identified that microglia-enriched Bhlhe41 was negatively autoregulated and inhibited by Aurka loss. Bhlhe41- or Aurka-deficient young mice exhibited aging-like microglial morphology, phagocytic deficits, progressive CD22 upregulation, and remyelination impairment in cuprizone-induced demyelination model. Conversely, ectopic Bhlhe41 expression induced hypertrophic microglia, and counteracted phagocytic deficits and CD22 upregulation in Aurka-deficient microglia. CD22 blockade restored phagocytic function and remyelination in Bhlhe41-deficient mice. Notably, a conserved pattern of CD22 upregulation was observed in human PCDH9high microglia subsets with BHLHE41 downregulation. These findings offer insights into potential therapeutic strategies to combat aging-related neurodegeneration and central nervous system functional decline.

overall_design: Microglia from young Bhlhe41 dtomato-Cre/+ mice (control mice, N = 3) and Bhlhe41 dTomato-Cre/dTomato-Cre  mice (Bhlhe41 deficient mice) were enriched by 40% Percoll followed by FACS sorting of CD45low CD11b+ Cx3cr1+ cells. Gene expression microarray analysis was performed using SurePrint G3 Mouse GE v2 8x60K Microarray.

first: Weixin

last: Yan

last: Li


title: Lysosomal Downregulation of the Mu Opioid Receptor is Opposed by the Retromer Complex

city: Portland

first: Braden

last: Lobingier

state: Oregon

address: 3181 SW Sam Jackson Park Road, Mail Code L-334

department: Chemical Physiology and Biochemistry

institute: Oregon Health and Sciences University

summary: The mu opioid receptor (MOR) is protected from opioid-induced trafficking to lysosomes and proteolytic downregulation by its ability to access the endosomal recycling pathway through its C-terminal recycling motif, LENL. MOR sorting towards the lysosome results in downregulation of opioid signaling while recycling of MOR to the plasma membrane preserves signaling function. However, the mechanisms by which LENL promotes MOR recycling are unknown, and this sequence does not match any known consensus recycling motif. Here we took a functional genomics approach with a comparative genome-wide screen design to identify genes which control opioid receptor expression and downregulation. We identified 146 hits including all three subunits of the endosomal Retromer complex. We show that the LENL motif in MOR is a novel Retromer recycling motif and that LENL is a necessary, sufficient, and conserved mechanism to give MOR access to the Retromer recycling pathway and protect MOR from agonist-induced downregulation to multiple clinically relevant opioids including fentanyl and methadone.

overall_design: Single guide RNA (sgRNA) enrichment within sorted cell populations based on fluorogenic reaction readout for opioid receptor abundance after receptor agonist stimulation.

first: Aleksandra

last: Dagunts

first: Hayden

last: Adoff

first: Brandon

last: Novy

first: Lamya

last: Ben Ameur

first: Monica

last: De Maria

first: Arpiar

last: Saunders

first: Braden T


title: Retinoic Acid-Mediated Signaling Regulates Allantoic and Fetoplacental Vascularization

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: The placenta is vital for fetal development, and altered placental vascularization underlies prevalent disorders, including fetal growth restriction, prematurity, and pregnancy complications. Impaired placental vascularization is associated with Vitamin A deficiency, but mechanisms are undefined. To investigate this, we used retinoic acid (RA)-deficient Raldh2⁻/⁻ embryos, and found they exhibit placental endothelial hyperproliferation and impaired arterial-venous remodeling, which were rescued by providing all‑trans‑RA (ATRA) via maternal diet. Single cell RNA sequencing of E9.5 Raldh2+/+, Raldh2⁻/⁻,and Raldh2⁻/⁻+ATRA placental cells, and functional assays, revealed that RA regulates endothelial growth and vascular remodeling via Notch signaling.

overall_design: Placentas from  E9.5 embryos that were WT Raldh2, KO Raldh2, WT Raldh2 (from ATRA fed moms), and KO Raldh2 (from ATRA fed moms) were enzymatically digested into a single cell suspension, depleted of CD45+ cells and enriched for CD31+ cells to increase the number of ECs using microbeads. 5% of all other placental cells were spiked back and analyzed using scRNA-seq.

last: Cwiek

first: Umadevi

first: Karen

last: Hirschi


title: Hh and EGFR-Ras signaling promote distinct steps of tumor progression in the Drosophila follicle epithelium

city: Marburg

first: Katja

last: Rust

address: Emil-Mannkopff-Str. 2

institute: Phillips-University Marburg

summary: Controlled signaling activity is vital for normal tissue homeostasis and oncogenic signaling activation facilitates tumorigenesis. Here we combine single-cell transcriptomics with in-depth genetic and imaging analysis to investigate the role of the EGFR-Ras and Hedgehog signaling pathways in homeostasis of the Drosophila follicle stem cell lineage. We find that Hedgehog signaling simultaneously promotes an undifferentiated state and induces differentiation via activation of the epithelial-mesenchymal-transition associated transcription factor Zfh1. Overactivation of Hedgehog signaling generates a mixed transcriptional state comparable to partial epithelial-mesenchymal-transition. EGFR-Ras overactivation induces cell cycle defects by activating the transcription factors Pointed and E2f1 and impedes differentiation. Overactivation of both pathways blocks differentiation and induces tumor-like growth where follicle cells exhibit a loss of tissue architecture, sustained proliferation and a reduced lifespan of the host. These findings provide new insight into how signaling pathways converge at the transcriptional level to prevent malignant cell behavior.

overall_design: Females of the appropriate genotype were raised at 18°C and shifted to 29°C for 5 days and fed wet yeast daily in the presence of males. Ovaries were dissected and late stages were removed. A single cell suspension was prepared and subjected to single-cell RNA-seqencig using 10x Chromium Next GEM Single-Cell 3´LT Kit v3.1. The resulting libraries were sequenced using NovaSeq 6000 (Illumina).

first: Sari

last: Anschütz

first: Hannah

last: Müller

first: Andrea

last: Schubert

first: Jobelle

last: Peralta

first: Todd

middle: G

last: Nystul


title: Effect of interferon gamma on wild type and SORL1 knockout iPSC-derived microglia

first: Falak

last: Sher

state: New York

address: 630 W 168th street

institute: Columbia University

summary: This study investigates the transcriptomic response of wild-type (WT) and SORL1 knockout (KO) iPSC-derived microglia following treatment. For microglia differentiation protocol please see PMID: 38600587.  Bulk RNA sequencing was performed to assess gene expression changes induced by a 48-hour treatment with 10 ng/ml of IFN-γ. The study aims to explore the role of SORL1 in microglial function and its potential impact on neuroinflammatory or neurodegenerative pathways. Differential gene expression analysis will help identify pathways regulated by SORL1 deficiency in response to external stimuli.

overall_design: Bulk RNA-Seq was performed on wild-type and SORL1 knockout iPSC-derived microglia following a 48-hour treatment with 10 ng/ml IFN-γ, with appropriate untreated controls

first: Imdadul

last: Haq

first: Jason

middle: C

last: Ngo

first: Nainika

last: Roy


title: Hif2α–Lox mediated collagen remodelling is crucial for embryo invasion

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

summary: The mouse uterine gene expressions on pregnancy day 6 were investigated by Visium spatial transcriptome. Contributions of Hif2a-Lox axis was examined by comparing uterine-specific KO mice of Hif2a or Lox with their littermate control.

overall_design: The day when the vaginal plug was detected was considered day 1 of pregnancy. Pregnant mice were euthanized by cervical dislocation on designated days of pregnancy for the evaluation of pregnancy phenotypes and sample collection. Embryo attachment sites were observed as blue bands soon after intravenous injection of 1% solution of Chicago blue dye (Sigma-Aldrich) in saline on day6. Collected tissues were snap-frozen. Frozen sections (10 μm) were mounted on gene expression slides and sent to KOTAI Biotechnologies for subsequent procedures. After reaction with Proteinase K for 30 min, the sections were hybridized with spatial tags on the slides and reverse-transcribed in situ. The synthesized cDNAs were subjected to RNA-sequencing using DNBseq (MGI), producing 300 million reads/sample.

first: Yasushi

last: Hirota


city: San Francisco

address: 513 Parnassus Ave, Box 0412

institute: UCSF

overall_design: Females of the appropriate genotype were raised at 18°C and shifted to 29°C for 14 days and fed wet yeast daily in the presence of males. Ovaries were dissected and late stages were removed. A single cell suspension was prepared and subjected to single-cell RNA-seqencig using 10x Chromium Single-Cell 3’ Reagent Version 2 Kit. The resulting libraries were sequenced using Illumina HiSeq 2500 (Illumina).


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [RNA-seq]

first: Stefan

last: Thomann

overall_design: Multimodal mouse and human scRNA seq data. 6 human liver samples to capture pseudonormal liver cells and identify niche interactions. Furthermore a DDC disease atlas consisting of 12 samples covering a control and 5 disease timepoints to analyse immune cell dynamics in the DDC model. Furthermore, scRNA-seq datasets covering inflammatory resolution after long-term DDC diet and a short term DDC diet in combination with a cDC2B depletion. A CITE-seq dataset from liver draining lymph nodes at a control and two disease timepoints for the analysis of cDC2 dynamics. Two  experiments of liver immune cells capturing transcriptome and genomic accessibility data modalities at steady state and early cholestasis (DDC D5). Finally, multiplexed scRNA seq data of liver and lymph node derived γδ T cells undergoing cholestasis/cholestasis resolution and disease after cDC2B cell depletion.

first: Dominic

last: Grün


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [Multiome]


title: Astrocyte nuclear transcriptome from mouse cortex in Fmr1 KO and Smad4 conditional KO

city: La Jolla

first: James

last: Deng

address: 1 Miramar St, 929133

department: Molecular Neurobiology

institute: Salk Institute

summary: Analysis of astrocyte gene expression at P26-28 in mouse cortex with and without Fmr1 KO as well as with and without astrocyte Smad4 conditional KO.

overall_design: Profiling of astrocyte nuclear RNA from the mouse cortex at P26-28 in the four genotypes (1) Fmr1 WT;Smad4 WT, (2) Fmr1 WT;Smad4 cKO, (3) Fmr1 KO;Smad4 WT, (4) Fmr1 KO;Smad4 cKO, with 4-6 biological replicates per genotype

first: Lara

last: Labarta-Bajo

first: Nicola

last: Allen


title: Gene expression changes in commensal 3D melanoma skin models induced by skin bacteria

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Skin bacteria impact melanoma related pathways

Melanoma represents the most lethal form of skin cancer, with rising numbers of annual incidences worldwide. In an effort to identify new risk factors that promote melanoma development, the contribution of the skin microbiome gained increasing attention. Previous studies already demonstrated an altered composition of the skin microbiome on melanoma sites. Yet, the underlying mechanisms of the interplay between the microbiome and melanoma progression remain elusive. We established a novel co-culture system capable to study host microbiome interactions during melanoma progression in situ. This system consists of a commercial 3D melanoma skin model colonized with skin bacteria obtained from a skin swab of a healthy volunteer. The models showed a stable co-colonization over a period of 12 days, with Streptococcus being the most abundant genus on the last day of cultivation. Transcriptome profiles revealed significant differences in colonized models compared to control. In particular, pathways involved in melanoma progression, like RAF/MAP and PI3K kinase, were upregulated in colonized models. This correlates with the augmented release of the cytokines VEGF, PIGF, and GM-CSF as well as the typical melanoma markers MIA and S100B. Furthermore, the data were supported by an active epithelial-mesenchymal transition in colonized skin models. Taken together, the bacterial community seems to promote the progression of melanoma in our established system, hence we provide an elegant method to elucidate the microbiome’s impact on cancer development in situ.

overall_design: Co-cultures consisting of a commercial 3D melanoma-in-skin model and skin bacteria were analyzed by microarrays. In total the study included 12 samples from 2 conditions and 2 timepoints with 3 biological replicates each: control day 4, colonized day 4, control day 12, colonized day 12.

first: Aline

last: Rosin


title: Loss of meningeal lymphatic endothelial cells results in formation of a novel vascular network with scavenging function.

status: Public on Feb 16 2026

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: For an extended period of time, the meninges were believed to be devoid of lymphatic vessels. The recent discovery of lymphatic vessels in the dura mater of humans, mice, and zebrafish, and the identification and characterization of scavenging lymphatic endothelial cells in zebrafish leptomeninges have contributed to a better understanding of waste removal routes from the brain. Zebrafish brain lymphatic endothelial cells (BLECs), in particular, have a high propensity for particulate waste removal from the cerebrospinal fluid. To further understand the function of BLECs, we have established a protocol for specifically ablating this cell type during embryonic stages. We show that BLECs do not recover upon complete depletion, even at adult stages. The absence of BLECs results in detrimental effects on the meningeal blood vasculature and on arachnoid mater structure. We further report that, upon BLEC ablation, a novel vessel network forms, which shares characteristics with lymphatic vessels and is able to take up substances injected into the brain parenchyma, thus possibly providing compensatory functions in the absence of BLECs.

overall_design: Single-cell transcriptomes were generated from individual FACS-sorted cells captured from the meninges of adult zebrafish for single-cell RNA-sequencing (Smart-seq3).

first: Katharina

last: Uphoff

first: Andreas

last: van Impel

first: Martin

last: Stehling

first: Christer

last: Betsholtz

last: Schulte-Merker


title: Cell Atlas and Novel Signal Processing Strategy in Primate Insular Cortex [Patch-seq]

city: Guangzhou

first: Ruifeng

last: Liu

state: Guangdong province

address: Jinsui Road, 7#

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and characterized 78 detailed cell types in the macaque AIC, revealing the diversity and specialization of this region in cell type, connectivity profile, signal-processing strategy, and metabolic characteristics. Among these, we identified two transcriptomically and morphoelectrically defined von Economo neuron (VEN) subtypes, DSG2-expressing VEN-L and POC5-expressing VEN-S, transcriptomically relating to extratelencephalic and corticothalamic projection neurons, respectively. We also uncovered a previously underappreciated signal-processing strategy in VENs, whereby the geometry of the dendrite-originating axon initial segment (AIS) reshapes action potential dynamics and enhances somatic responsiveness to deep-layer synaptic inputs. Together, this multimodal atlas establishes a molecular and functional framework for investigating the circuit principles underlying deep-layer projection neurons in the primate AIC.

overall_design: Here we employed a massively parallel 10X genomics single cell RNA-sequencing (scRNA-seq) analysis of the AIC to derive a molecular classification and then related each molecularly distinct cell type to well-established AIC cell types via Patch-seq.

first: Sheng


title: Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion [RNA-seq]

city: New York

first: UkJin

last: Lee

address: 413 E 69th St

department: Sanford I. Weill Department of Medicine

institute: Weill Cornell Medicine

summary: Structural loops are known to collapse in the absence of cohesin, whereas regulatory loops largely persist with only minor transcriptional changes, leaving unresolved questions about cohesin’s role in establishing regulatory interactions during cell state transitions. To investigate this, we degraded RAD21, a core cohesin subunit, in mouse embryonic stem cells (ESCs) transitioning from mitosis to G1 under self-renewal or differentiation conditions. We performed RNA-seq to profile gene expression in ESCs and EpiLCs.

overall_design: RNA-seq to identify transcriptional changes upon RAD21 depletion or CBP/p300 inhibition in ESCs and EpiLCs.

first: Effie

last: Apostolou

first: Alejandra

last: Laguillo-Diego


title: Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion [ChIP-seq]

summary: Structural loops are known to collapse in the absence of cohesin, whereas regulatory loops largely persist with only minor transcriptional changes, leaving unresolved questions about cohesin’s role in establishing regulatory interactions during cell state transitions. To investigate this, we degraded RAD21, a core cohesin subunit, in mouse embryonic stem cells (ESCs) under self-renewal or differentiation conditions. We performed ChIP-seq for H3K4me3, H3K27ac, RAD21 and HA.

overall_design: Characterization of H3K4me3 and H3K27ac marked regions and RAD21 binding regions with ChIP-seq in ESCs and EpiLC


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [scRNA-seq]

first: Stefan

last: Thomann


title: Improved co-transcriptional splicing of readthrough transcripts during chemotherapy treatment [CML_RNA-seq]

status: Public on Feb 15 2026

city: New Haven

first: Paulina

last: Podszywalow-Bartnicka

state: CT

address: 333 Cedar Street

department: Department of Molecular Biophysics and Biochemistry

institute: Yale University

summary: The cellular stress response is an important component of cancer cell response to chemotherapy that can determine cell survival. Herein, we study how the coupling of the RNA processes in leukemia cells is affected in response to stress and therapeutic agents. We used short- and long-read sequencing to follow RNA processing upon treatment.

overall_design: To determine level of gene expression as well as determine changes in alternative splicing we used short-read RNA-seq. We analyzed  polyA selected RNA isolated from whole cells (mRNA) that were CD34+ cell subpopulation enriched from CML patients' samples. Before isolation of total RNA the cells were treated with 1uM Imatinib (im) for 1h  and the cells were collected in paralell with the untreated control cells (untr). Samples were analyzed in a single replicate.

first: Morgan

last: Shine

first: Jing

last: Lin

first: Karla

last: Neugebauer


title: A pH-responsive CS-HA-DAP nanosystem enhances the antitumor activity of deer antler peptides by aggravating DNA damage stress and checkpoint imbalance in triple-negative breast cancer

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

summary: Triple-negative breast cancer (TNBC) frequently exhibits p53 deficiency and increased reliance on DNA damage-checkpoint adaptation, yet effective targeted therapeutic strategies remain limited. Here, we characterized deer antler peptides (DAP) and developed a pH-responsive hyaluronic acid/chitosan nanosystem (CS-HA-DAP) to improve their antitumor activity. DAP consisted mainly of low- to medium-molecular-weight peptides and proteins and inhibited 4T1 cell viability, migration, and invasion, with relatively lower toxicity toward MCF-10A cells. Transcriptomic and molecular analyses indicated that DAP induced persistent DNA damage-associated stress, impaired sustained CHK1 signaling, and disrupted cell-cycle regulation, together with pyroptosis- and ferroptosis-related changes. Molecular docking and inhibitor-combination experiments further supported the involvement of TOP2A- and CHK1-related processes. CS-HA-DAP nanoparticles showed favorable physicochemical properties and acid-responsive release, and enhanced the anti-TNBC effects of free DAP in vitro and in vivo without evident additional toxicity. In orthotopic 4T1 tumor-bearing mice, CS-HA-DAP promoted tumor accumulation, suppressed tumor growth, and showed acceptable preliminary biosafety. Together, these findings identify DAP as a bioactive antitumor peptide mixture and support CS-HA-DAP as a delivery strategy for enhancing its therapeutic potential in TNBC.

overall_design: 4T1 cells were collected from DAP group and the control group. Total RNA pooled was collected from 4T1 cells of three biological replicates  to construct a cDNA library. 4T1 cells transcriptomics were analyzed by Illumina NovaSeq 6000 for high-throughput deep sequencing.

first: Wei

first: Rui

last: Han

first: Chang

first: Xintong


title: Cohesin prevents local mixing of condensed euchromatic domains in living human cells

city: Cleveland

first: Le

last: Xiong

address: 9620 Carnegie Ave N Bldg

institute: Cleveland Clinic

summary: The human genome is folded into chromatin loops by the cohesin complex, forming functional chromatin domains that underlie transcription and DNA replication/repair. However, the physical properties of these domains in living cells, especially in active euchromatin, and how they are regulated by cohesin remain elusive. To address these questions, we combined singlenucleosome imaging/tracking and super-resolution 3D-structured illumination microscopy (3DSIM) with euchromatin-specific labeling of histone H3.3. Using this nanoscopic approach, we revealed that euchromatin is organized into condensed domains constrained by cohesin-mediated loops, challenging the established textbook view of euchromatin as largely open. Transcription machinery appear to be located near the condensed domain surfaces. Cohesin loss increased nucleosome fluidity of these domains without altering their compaction, leading to local mixing of domains and compromising transcriptional insulation. These findings uncover an unexpected physical role of cohesin in maintaining the integrity of condensed euchromatic domains and ensuring proper higher-order regulation of gene expression.

overall_design: ATAC-seq of human colorectal cancer cell line HCT116 with and without 5-Ph IAA treatment

first: Liangqi

last: Xie


title: Regulation of cell identity by 3D super-enhancers

city: Memphis

first: Brian

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Gene regulation and genome structure are intimately linked, but accurate predictions of the elements that form topological regulatory assemblies in mammalian genomes remain elusive. To address this challenge, we developed BOUQUET, a graph theory-derived algorithm that uses multiple facets of genome topology to discern and interrogate communities of cis-regulatory elements (CREs). BOUQUET’s unbiased approach reveals otherwise undetectable CRE communities, including those that cross presumed insulating boundaries and comprise different categories of CRE. Critically, some communities, which we term “3D super-enhancers (3D-SEs)”, accrue exceptional amounts of regulatory apparatus. 3D-SEs are associated with cell identity-defining genes across mammalian tissues. Microscopy analyses show co-localization and co-expression of genes from the same 3D-SE community within transcriptional co-factor puncta, resembling microcompartments. Gene pairs within 3D-SE communities are co-expressed, and CREs within 3D-SEs are co-accessible. Overall, our model more accurately represents the architectural complexity of CRE interactions, the coordination between chromatin conformation and gene regulation, and the connection between super-enhancers and cell identity.

overall_design: genome-wide gene expression profiling of wild type and Mir290 enhancer-deleted mESC v6.5 cell line is conducted by performing RNA-seq

first: Jie

last: Lv

first: Kelsey

last: Maher

first: Alaguraj

last: Veluchamy

first: Yuna

last: Kim

first: Li

last: Dong

first: Bensheng

last: Ju

first: Virginia

last: Valentine

first: Marc

first: Steven

last: Burden

first: John

last: Easton

first: Stanley

middle: B

last: Pounds


title: Transcriptional readthrough and splicing upon chemotherapy treatment [long-read, nascent RNA]

first: Paulina

last: Podszywalow-Bartnicka

summary: The Neugebauer lab has previously shown that splicing occurs co-transcriptionally and is coupled to 3’end cleavage. It is known that stress, such as hyperosmotic shock, affects RNA processing. The cellular stress response is an important component of cancer cell response to chemotherapy that can determine cell survival. Herein, we study how the coupling of the RNA processes in leukemia cells is affected in response to stress and therapeutic agents. We used short- and long-read sequencing to follow RNA processing upon treatment.

overall_design:
To determine changes in RNA processing steps such as transcriptional readthrough and co-transcriptinal splicing we used long-read sequencing. We analyzed nascent RNA isolated from chromatin fraction of cells, that was additionally depleted of polyA-RNA and rRNA.
Before isolation of nascent RNA the cells were  treated with:
- 1uM Imatinib (IM) for 1h and 18h
- 5uM JTE-607 (JTE) for 1h
- 110mM KCl (KCL) for 45min.
All time points ended at the same time and thus the cells were collected in paralell with the untreated control cells (CTRL and CTRLim).
Each experiment was repeated three times (1, 2, 3)

first: Morgan

last: Shine

first: Jing

last: Lin

first: Karla


title: Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion

first: UkJin

last: Lee

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

overall_design: Refer to individual Series


title: Regulation of cell identity by 3D super-enhancers [WGS]

first: Brian

summary: Gene regulation and genome structure are intimately linked, but accurate predictions of the elements that form topological regulatory assemblies in mammalian genomes remain elusive.  To address this challenge, we developed BOUQUET, a graph theory-derived algorithm that uses multiple facets of genome topology to discern and interrogate communities of cis-regulatory elements (CREs). BOUQUET’s unbiased approach reveals otherwise undetectable CRE communities, including those that cross presumed insulating boundaries and comprise different categories of CRE. Critically, some communities, which we term “3D super-enhancers (3D-SEs)”, accrue exceptional amounts of regulatory apparatus. 3D-SEs are associated with cell identity-defining genes across mammalian tissues. Microscopy analyses show co-localization and co-expression of genes from the same 3D-SE community within transcriptional co-factor puncta, resembling microcompartments. Gene pairs within 3D-SE communities are co-expressed, and CREs within 3D-SEs are co-accessible. Overall, our model more accurately represents the architectural complexity of CRE interactions, the coordination between chromatin conformation and gene regulation, and the connection between super-enhancers and cell identity.


title: Estrogen receptor β target gene expression reveals novel repressive functions in aggressive breast cancer [sRNA-Seq]

city: Houston

first: Christoforos

last: Thomas

address: 6670 Bertner Avenue

department: Department of Medicine

institute: Houston Methodist Research Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Inflammatory breast cancer (IBC) is a highly metastatic breast carcinoma with high frequency of estrogen receptor a (ERα) negativity and limited treatment options. We previously explored the second ER subtype, (ERβ) and reported correlation of its tumor expression with reduced metastasis in patients and in preclinical models of the disease. We initially associated the anti-metastatic function of the receptor with the inhibition of actin-based cell migration and the associated Rho GTPase signaling in IBC cells. We have now followed an integrated genomics approach to fully delineate the signaling underlying the anti-metastatic effects of ERβ. Through mapping binding sites in IBC cells that express endogenous and transfected ERβ in the presence of an agonist and interrogating this information with altered expression of protein coding mRNAs and miRNAs we have defined the interaction of a biologically active receptor with the cancer genome that controls metastatic signals. We reveal key  regulatory chromatin binding sites and motifs and identify direct target genes and miRNAs and the associated biological functions. Our new findings implicate the regulation of metabolic pathways and signaling in development and tumor microenvironment in anti-metastatic activity of ERβ. Through a rigorous analysis of target genes in clinical datasets we also associate downstream factors with patient outcomes reporting new molecules with targeting potential and strengthening the relevance of ERβ signaling for the metastatic process in breast cancer. Our findings thus offer an opportunity to validate the tumor repressive role of ERβ through a better understanding of its mechanism of action.

overall_design: Analysis of breast cancer cells with different ERβ levels. KPL4 cells without ERβ (ERβ knockout cells) vs. KPL4 cells with ERβ (ΕRβ knockout cells with transfected ERβ)

first: Spyros

last: Tastsoglou

first: Ilias

last: Karagounis

first: Marios

last: Miliotis

first: Harika

last: Nagandla

first: Kristina

last: Zambo

first: Maria

last: Liousia

first: Naoto

last: Ueno

first: Amit

last: Maity

first: Artemis

last: Hatzigeorgiou


title: Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion [4C-seq]

summary: Structural loops are known to collapse in the absence of cohesin, whereas regulatory loops largely persist with only minor transcriptional changes, leaving unresolved questions about cohesin’s role in establishing regulatory interactions during cell state transitions. To investigate this, we degraded RAD21, a core cohesin subunit, in mouse embryonic stem cells (ESCs) transitioning from mitosis to G1 under self-renewal or differentiation conditions. We performed high-resolution in situ 4C-seq around the promoters of cohesin-sensitive genes (Klf4, Tbx3, Myc, and Fosl2) in ESCs and EpiLCs.

overall_design: 4C-seq for selected genes in ESCs and EpiLCs with or without RAD21 depletion

first: Effie

last: Apostolou

first: Alejandra

last: Laguillo-Diego


title: Estrogen receptor β target gene expression reveals novel repressive functions in aggressive breast cancer [RNA-Seq]

overall_design: Analysis of breast cancer cells with different ERβ levels and after treatment with ERβ agonists. Wild-type KPL4 cells with endogenous ERβ (Control cells) vs. KPL4 cells without ERβ (ERβ knockout cells). KPL4 cells without ERβ (ERβ knockout cells) vs. KPL4 cells with ERβ (ΕRβ knockout cells with transfected ERβ). KPL4 ΕRβ knockout cells with transfected ERβ after treatment with vehicle (DMSO) or the ERβ agonist LY500307 for 24 hours


title: Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion [Micro-C]

summary: Structural loops are known to collapse in the absence of cohesin, whereas regulatory loops largely persist with only minor transcriptional changes, leaving unresolved questions about cohesin’s role in establishing regulatory interactions during cell state transitions. To investigate this, we degraded RAD21, a core cohesin subunit, in mouse embryonic stem cells (ESCs) transitioning from mitosis to G1 under self-renewal or differentiation conditions. We performed Micro-C to map changes in 3D chromatin architecture in ESCs upon RAD21 depletion and p300/CBP inhibition.

overall_design: Micro-C of ESCs in G1 treated with DMSO, dTAG, or A485.


title: Topology-informed regulatory element collections coordinate cell identity gene expression programs[scRNA-Seq]

last: Abraham

summary: Cis-regulatory elements (CREs) contact target genes to regulate their transcription, but CRE interactions are complex and predicting their function is difficult. Contemporary approaches to predict CRE targets generally assume one-to-one associations and linear genomic proximity. These methods fail to account for long-range CRE contacts caused by folding of the genome, or for circumstances in which a single CRE regulates multiple genes or, conversely, a single gene is regulated by multiple CREs. To address these challenges and investigate CRE accumulation, we developed BOUQUET, an integrative, graph-theory-based approach that utilizes multiple aspects of genome topology to probe communities of CREs, their bound apparatus, and their target genes. BOUQUET discovers CRE communities that are undetectable by existing unbiased methods, such as those with interactions that span insulating loop boundaries as well as regulatory communities that are comprised of clustered promoter elements. A subset of these communities, which we term “3D super-enhancers” (3D SEs), is consistent with aspects of the super-enhancer model and accrues exceptional amounts of regulatory apparatus at crucial cell identity-defining genes. In single-cell analyses, pairs of genes found within the same community are co-expressed, and pairs of CREs are co-accessible, suggesting that the regulation of both types of elements within a topologically defined community is tightly coordinated. In confocal microscopy experiments, we regularly observe co-localization and co-expression of in-community genes, an occurrence which frequently takes place within transcriptional co-factor condensates. Our collective approaches more accurately reflect the complexity of CRE interaction networks, underscores the need for incorporating spatial organization in the study of enhancer biology, and provides a framework for the reinterpretation of SEs, their condensates, and their target genes through the lens of 3D chromatin structure.

overall_design: Signle cell gene expression profiling of mESC v6.5 cell line is conducted by performing scRNA-seq

first: Jie

last: Lv

first: Kelsey

last: Maher

first: Alaguraj

last: Veluchamy


title: Transcriptional readthrough and splicing upon chemotherapy treatment

first: Paulina

last: Podszywalow-Bartnicka

overall_design:
To determine level of gene expression and transcriptional readthrough as well as determine changes in alternative splicing we used short-read RNA-seq. We analyzed  polyA selected RNA isolated from whole K562 cells (mRNA) and RNA isolated from the cell nucleuses (nuclear RNA) that was later rRNA-depleted.
Before isolation of total RNA the cells were treated with: - 1uM Imatinib (im) for 1h, 6h and 18h - 5uM JTE-607 (jte) for 1h, 6h and 18h - 110mM KCl (kcl) for 1h and 3h.  Before isolation of nuclear RNA cells were treated with: - im for 1h or 18h - jte for 1h - kcl for 1h  All time points ended at the same time and thus the cells were collected in paralell with the untreated control cells (ctrl).
Each experiment was repeated three times (1, 2, 3)

first: Morgan

last: Shine

first: Jing

last: Lin

first: Karla

last: Neugebauer


title: RNA-seq of TCR-stimulated CD4⁺ T cells from SKG mice treated with the Nr4a1 agonist Cytosporone B

status: Public on Feb 14 2026

city: Kyoto

first: Yoichi

last: Nakayama

state: Kyoto

address: 54, Kawahara-cho, Shogoin

institute: Kyoto University

summary: Rheumatoid arthritis (RA) is a chronic autoimmune disease in which CD4⁺ T cells and T helper 17 (Th17) cells play central roles in driving synovial inflammation. Nr4a1 is an orphan nuclear receptor that acts as a negative regulator of T cell activation. Cytosporone B (CsnB) is a small-molecule Nr4a1 agonist with immunomodulatory properties, but its impact on T cell responses in autoimmune arthritis remains unclear. In this study, we used SKG mice, a T cell–driven model of chronic autoimmune arthritis, to investigate how pharmacologic Nr4a1 activation influences pathogenic T cell responses. CD4⁺ T cells isolated from SKG mice were stimulated through the T cell receptor in vitro in the presence or absence of CsnB, and transcriptomic profiling was performed by RNA sequencing. The resulting dataset provides genome-wide information on CsnB-induced changes in gene expression in activated CD4⁺ T cells, and supports mechanistic analyses of how Nr4a1 activation modulates T cell activation and Th17-related pathways in autoimmune arthritis.

overall_design: Total CD4⁺ T cells were isolated from spleens and lymph nodes of SKG mice using magnetic-activated cell sorting. Purified CD4⁺ T cells were stimulated in vitro on plates coated with anti-CD3 and anti-CD28 antibodies in the presence or absence of the Nr4a1 agonist Cytosporone B (CsnB) for 2 hours.

first: Ryosuke

last: Hiwa


title: Topology-informed regulatory element collections coordinate cell identity gene expression programs[scATAC-Seq]

first: Brian

overall_design: Signle cell chromatin profiling of mESC v6.5 cell line is conducted by performing scATAC-seq