title: Adipose stromal cell-derived cancer-associated fibroblasts promote pancreatic adenocarcinoma through SFRP4 signaling

city: New York

first: Lingyi

last: Cai

state: New York

address: 2960 Broadway

institute: Columbia University

summary: Progression of pancreatic ductal adenocarcinoma (PDAC) and other carcinomas relies on cancer-associated fibroblasts (CAFs). A subset of CAFs is derived from adipose stromal cells (ASCs) recruited by tumors and the ASC-CAF conversion has been associated with invasiveness and poor prognosis. To explore the underlying molecular mechanisms, we used a model based on primary ASC derived from human visceral adipose tissue co-cultured with human PDAC cell line Capan-1. To investigate cancer progression in vivo, we also used mice orthotopically grafted with mouse KPC cells. Genomic analysis revealed that Capan-1 co-culture induces Wnt and TGFβ signaling and extracellular matrix (ECM) gene expression in ASC. We investigated the function of two markers of the fibroblastic transition highly induced by cancer cells: a long non-coding RNA LINC01614 and a Wnt signaling modulator SFRP4. By using ASC with either SFRP4 or LINC01614 knocked out (ko), we showed that both genes are required for Wnt / TGFβ signaling and ECM induction in ASCs by Capan1. Analysis of changes in Capan-1 genes that rely on LINC01614 and SFRP4 expression in ASC also identified the Wnt and TGF pathways. SFRP4 ko in ASCs suppressed both migration and invasion of Capan-1 cells. We show that tumors in SFRP4 ko mice have less desmoplasia, less epithelial dedifferentiation, reduced growth rate, and reduced progression to metastasis. We conclude that SFRP4 promotes cancer progression in pancreatic cancer and is a promising therapeutic target.

overall_design: Visceral adipose tissue biopsies from a single patient were digested and the stromal vascular fraction was isolated and given the nomenclature vASC. These cells were then engineered to express red fluorescent protein (RFP) via transduction of a lentiviral contruct that also contained a puromycin resistance gene to allow for targeted selection of RFP+ cells. Capan-1 cells were engineered to express green fluorescent protein (GFP) via transduction of a lentiviral contruct that also contained a puromycin resistance gene to select for GFP+ cells. Seperate cohorts of the vASC_RFP cells were further engineered for knockdown of the LINC01614 and SFRP4 genes using CRISPR/Cas9 targeted mutagenesis via lentiviral transduction. The CRISPR/Cas9 construct targeting these genes also contained a blasticidin resistance gene to allow for selection of positively transduced cells. vASC_RFP, vASC_LINC01614_RFP, and vASC_SFRP4_RFP cells were cultured alone or in coculture with Capan-1_GFP cells in replicates for seven days. Cells were then trypsinized, made into single cell suspensions, and sorted (RFP vs GFP) using FACS. Total RNA-sequencing was performed on sorted cells to analyze changes in gene expressions.

first: Mikhail

last: Kolonin

first: Dimitris

last: Anastassiou

first: Joseph

last: Rupert


title: Myofibroblasts induce neuroplasticity to promote pancreatic inflammation and cancer progression

status: Public on Jan 12 2026

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

country: USA

institute: Cold Spring Harbor Laboratory

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Epigenome-wide DNA Methylation Profiling in the Investigation of Treatment and Life-Course Exposures and Adverse Health Outcomes in Survivors of Childhood Cancer from the St. Jude Lifetime Cohort

status: Public on Jan 13 2026

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary:
Long-term survivors of childhood cancer experience treatment-related cardiotoxicity among a broad spectrum of chronic health conditions, which may be further aggrevated by suboptimal life-course social/behavioral/environmental exposures. Epigenetic mechanisms, particularly DNA methylation (DNAm), provide a potential link through which these exposures become biologically embedded and subsequently influence long-term health outcomes.
Epigenome-wide association studies (EWAS) identified DNAm signatures associated with both treatment effects as well as life-course exposures. In parallel, DNAm variations were also evaluated in relation to cardiometabolic risk factors, cardiovascular diseases, and other chronic health conditions, revealing individual CpG sites or genes/geomic regions where these CpGs reside linked to clinically relevant phenotypes. Together, these findings support DNAm as a molecular interface connecting diverse exposures to adverse health outcomes.
In addition, epigenetic age acceleration, assessed using DNAm-based aging biomarkers, was observed among survivors exposed to cancer treatments. Epigenetic age acceleration mediated a substantial proportion of the associations between cancer treatment exposures and cardiometabolic risk factors or cardiovascular diseases, supporting accelerated biological aging as a key pathway linking cancer treatment to long-term morbidity. Lifestyle and health behaviors, as well as social vulnerability and psychosocial stress, were also associated with variations in epigenetic age acceleration, highlighting the potential modifiability of aging-related pathways in ameliorating late-effects among childhood cancer survivors.
In conclusion, these findings establish DNAm—captured through EWAS signatures and epigenetic age acceleration—as central molecular mechanisms linking treatment effects and life-course exposures to cardiotoxicity along with other chronic health conditions in childhood cancer survivors. This integrative epigenetic framework supports the use of DNAm-based biomarkers for risk stratification and nominates modifiable pathways as potential intervention targets  to improve long-term survivorship outcomes.

overall_design:
We included childhood cancer survivors and community controls from the St. Jude Lifetime Cohort Study, a retrospective hospital-based cohort with prospective clinical follow-up. DNA methylation profiles were generated using the Illumina Infinium MethylationEPIC BeadChip from blood- or saliva-derived DNA. A subset of participants contributed DNAm profiles at more than one time point.

The data generation was supported by grant awards from the National Cancer Institute at the National Institutes of Health (R01 CA290112 and R01 CA279520 to Dr Wang, U01 CA195547 to Drs Hudson and Ness) and by grant the V-Foundation grant (DT2020-014 to Dr. Wang).


title: Strongly regulated “super-target” transcription factors exert an outsized influence in microRNA-regulated networks

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

summary: To elucidate the role of microRNAs (miRNAs), it is essential to identify their direct post-transcriptional targets. However, identifying the most functionally significant targets is challenging due to factors such as the inherent limitations of predictive algorithms, the abundance of RNA interactions detected in co-precipitation studies, and the prevalence of non-productive targeting caused by weak interactions or unfavorable stoichiometries. We introduce the concept of 'super-targets'—genes whose regulation disproportionately drives miRNA functionality by virtue of both strong targeting and the critical role of the gene itself, such as a transcription factor whose disruption has broad downstream effects. A prime example is the reciprocal regulation between the miR-200 family and ZEB transcription factors, which governs the epithelial-mesenchymal status of cells. To assess the impact of such 'super-targeting,' we developed a system that isolates ZEB regulation from all other miR-200 activities. This approach reveals a complex network of transcriptional and post-transcriptional regulation, where miR-200’s ability to maintain an epithelial phenotype and suppress cell migration is fully dependent on the repression of ZEB1 and ZEB2, though other effects are ZEB-independent. Our findings suggest that a significant portion of miRNA regulatory impact may result from the potent targeting of a few key genes, highlighting that indirect transcriptional effects are a fundamental mechanism of miRNA function and likely more impactful than numerous modestly-regulated direct targets that otherwise dominate the publication landscape.

overall_design: RNA-seq profiling of wild-type MDA-MB-231 cells and their derivatives with DOX-inducible ZEB1 and ZEB2 expression constructs (lacking 3'UTRs and thus, insensitive to miR-200 mediated repression).  miR-200c or control miRNAs were co-transfected.

middle: A

first: Julie

middle: M

last: Bracken

first: Laura

last: Sourdin

first: Gregory

middle: J

last: Goodall

first: Cameron

middle: P


title: Transposon sequencing reveals Burkholderia gene fitness in a spaceflight-relevant plant-pathogen interaction

city: Kennedy Space Center

first: Aubrie

middle: E.

last: O'Rourke

state: Florida

address: Kennedy Space Center

institute: National Aeronautics and Space

summary: The spaceflight environment imparts unique selective pressures on the plants and microbes of plant growth chambers on the International Space Station (ISS), which generally manifests through genetic signatures associated with a heightened response to stress. Terrestrially, a baseline understanding of the gene fitness response for any plant growth promoting microbe when in a tripartite relationship with host and pathogen is currently unknown and is important to characterize before closed-environment spaceflight implementation. To that end, this study evaluated the behavior of an ISS plant habitat isolate of Burkholderia contaminans as tomato seeds transition to seedlings and assessed gene fitness during challenge with Fusarium oxysporum f. sp. lycopersici (FOL), the causal agent of Fusarium wilt. To probe mechanisms underlying the bacterial-fungal interaction between B. contaminans and FOL in the tomato root zone, a genome-wide transposon mutant library was developed of the B. contaminans isolate.  Using a seed film delivery method vetted for spaceflight, a Tn-Seq library of B. contaminans was applied to Solanum lycopersicum cv. Red Robin seeds. Transposon sequencing (Tn-Seq) analysis revealed that the type II secretion system (T2SS) was critical for root zone establishment, whereas a Nudix hydrolase was specifically important for responding to FOL infection, and provided further confirmation that antifungal and siderophore-producing gene clusters were not.

overall_design: In each plant growth vessel (magenta jar) two seed films were placed in one corner of each for the following scenarios: a) “NoSeed”-a control where only the B. contaminans Tn-Seq library (108 CFU/mL) is applied, b) “Root” or “Shoot”-a treatment where B. contaminans Tn-Seq library (108 CFU/mL) plus seed is applied and c) “FOLRoot” or “FOLShoot”-a treatment of B. contaminans Tn-Seq library (108 CFU/mL) plus seed for additional FOL challenge. The final 108 CFU/mL count was obtained by adding 10 µL droplets of the bacterial cultures at 1010 CFU/mL to the seed film. The B. contaminans Tn-Seq library was revived by slightly thawing the freezer stock and pipetting 100 mL of Tn-Seq library into 3 mL of TSB containing 50 mg/mL kanamycin and incubated at 35°C with shaking at 200 rpm for 16 hours. Three separate Tn-Seq starter cultures were prepared to serve as timepoint 0 (T0) and to inoculate the seed films as the three biological replicates (TnA, TnB, and TnC) of the experiment. Cells which were not used for the experiment were retained as T0 for Tn-Seq sequencing. Magenta vessels were placed into a controlled-environment chamber set to 50% RH and ambient CO2. At seven days after initiation, vessels were thinned to one plant per vessel and 10 µL of 103 CFU/mL FOL culture was applied to the corner opposite to the established plant in the fungal control and experimental treatment vessels. Plants were grown for 28 days total before they were photographed and harvested. At harvest, shoot and root tissues were separated and placed into 50 mL Falcon tubes with 10 mL of 50 mg/mL kanamycin in TSB media and allowed to grow for 16 hours at 35°C with shaking at 200 rpm to select for the transposed B. contaminans Tn-Seq library. Plant material was removed from the Falcon tube, the bacterial culture was pelleted by centrifugation at 3000 rpm for 5 min, and media decanted. Three cell pellets were obtained for scenarios a, b roots, b shoots, c roots, c shoots, and timepoint 0 for a total of 18 cell pellets for DNA extraction. A total of 19 Tn-Seq libraries were prepared including the input library that made the freezer stock.

first: Anya

last: Volter

first: Jessica

last: Atkin

first: Aaron

last: Curry

first: Anirudha

last: Dixit


title: Functional characterisation of tumour suppressor PDCD4 reveals a previously undisclosed role in the control of cell adhesion

city: Cambridge

first: Veronica

last: Dezi

address: Tennis Ct Rd

department: MRC Toxicology Unit

country: United Kingdom

institute: University of Cambridge

summary: PDCD4 is a multifunctional RNA binding protein which has tumour suppressor function. To more fully understand how dysregulation of this protein contributes to carcinogenesis we have carried out a comprehensive analysis of the role of PDCD4 in RNA metabolism in untransformed epithelial cells. We show that PDCD4 predominantly localises in the nucleus, where it interacts with proteins involved in a range of different RNA metabolic processes. We find that PDCD4 knockdown is associated with significant changes in either the expression or splicing of a number of transcripts, although it appears to have an indirect role in splicing. We identified the RNA targets of PDCD4 using iCLIP and observed an enrichment in binding to transcripts encoding cell adhesion and structural proteins. Consistent with these data, we show that PDCD4 acts as a general regulator of cell adhesion, which in a tumour setting would increase the metastatic potential of cells, and demonstrate that the nuclear localisation of PDCD4 is crucial in this process. Overall, the information obtained in untransformed cells provides new perspective for the role of PDCD4 as a tumour suppressor.

overall_design: We knocked down PDCD4 with 10nM siRNAs for 48 hours (siPDCD4) and compared the effects on gene expression to control cells (siCT)


title: Dual Mechanisms of Supporting Cell Regeneration in the Neonatal Mouse Cochlea

city: Stanford

first: Alan

last: Cheng

state: CA

address: 240 Pasteur Drive

institute: Stanford University

summary: Cochlear supporting cells are critical for proper hearing function and regeneration of hair cells, which are responsible for perceiving sound in the inner ear. In the neonatal mouse cochlea, when supporting cells are ablated, they can regenerate through progenitor cells in the cochlea. Here, we show through single cell RNA sequencing and in vivo fate mapping, that upon supporting cell ablation in the neonatal cochlea, inner phalangeal cells regenerate through two independent mechanisms; one which requires proliferation and the other by which transdifferentiation (i.e. regeneration without mitotic division) of cochlear progenitor cells occurs. These dual mechanisms are spatially distinct where transdifferentiation occurs in all three turns of the cochlea, while proliferation-induced regeneration occurs exclusively in the apical and middle turns. Inhibiting proliferation using aphidicolin, slightly decreased the number of regenerated IPhCs in the apex middle turns, but not the base, after damage. We also observed a medial to lateral transition in the compartmentalization of the GER after supporting cell damage, suggesting de-differentiation of these domains. Overall, our study reveals GER cells as supporting cell progenitors that undergo dual mechanisms of regeneration (mitotic and non-mitotic). Additionally, we uncover transcriptomic changes after supporting cell damage in the neonatal mouse cochlea that could be used as gene targets in therapies for hearing loss.

overall_design: Whole cochlea from postnatal days (P) 4, P5, P6 and P7 Ki67CreERT/+;Lgr5DTR/+;Rosa26RtdTomato/+ (damage) and Ki67CreERT/+;Rosa26RtdTomato/+ (control) mice were dissociated in biological duplicate for single cell RNA-sequencing. Cells were processed using 10X Genomics Chromium Single Cell 3' Reagents v3.1. After sequencing, Cell Ranger was used for read mapping and quantification, followed by further analysis using Seurat.

first: Julia

last: Abitbol

first: Maggie

middle: S

last: Matern

middle: G


title: Uridine Diphosphate Drives Myeloid Differentiation and Functional Reprogramming Through Dynamic Transcriptional Networks

status: Public on Jan 11 2026

city: Catanzaro

first: Giuseppe

last: Fiume

address: Viale Europa, Campus "S. Venuta", Ed. Bioscienze,Germaneto

department: Department of Experimental and Clinical Medicine

country: Italy

institute: University of Catanzaro "Magna Graecia"

summary:
PBMC were stimulated with UDP (100 micromolar) or left untreated (NT) for the indicated points. RNA was extracted and subjected to Nanostring nCounter Immunology Panel
The expression of around 500 genes of immunological relevance was analyzed in the different samples.

overall_design: Gene expression profiling by Nanostring Immunological Panel was performed on PBMC  stimulated with UDP (100 micromolar) or left untreated (NT) for the indicated points.

first: Caterina

last: Giordano

first: Emilio

last: Straface

first: Debora

last: Gentile


title: ComBO: A combined human bone and lympho-myeloid bone marrow organoid for pre-clinical modelling of haematopoietic disorders

city: Oxford

first: Yuqi

last: Shen

state: Oxfordshiore

address: MRC WIMM, University of Oxford

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: We developed a new combined human bone and lympho-myeloid bone marrow organoid (comBO) model using human induced pluripotent stem cells (hiPSCs). To characterise this model, we employed 10x single-cell RNA sequencing (scRNA-seq) to analyze cell composition and cell-cell interactions. Additionally, we engrafted the comBOs with cells derived from healthy donors or multiple myeloma patients and performed scRNA-seq to explore its potential for disease modeling.

overall_design: Two approaches were used to generate the comBO model: bulk hydrogel and granular gel. scRNA-seq was applied to both versions for comparative analysis. Subsequently, the fragmented gel method was used to generate comBO organoids engrafted with cells from one healthy donor and three multiple myeloma patients. scRNA-seq was then performed to identify differences in cell composition and interactions across these conditions.

first: Antonio

last: Rodriguez-Romera

first: Kristian

last: Gurashi

first: Samuel

last: Kemble

first: Charlotte

last: Smith

first: Abdullah

middle: O

last: Khan


summary:
PDCD4 is a multifunctional RNA binding protein which has tumour suppressor function. To more fully understand how dysregulation of this protein contributes to carcinogenesis we have carried out a comprehensive analysis of the role of PDCD4 in RNA metabolism in
untransformed epithelial cells. We show that PDCD4 predominantly localises in the nucleus, where it interacts with proteins involved in a range of different RNA metabolic processes. We find that PDCD4 knockdown is associated with significant changes in either the expression or splicing of a number of transcripts, although it appears to have an indirect role in splicing. We identified the RNA targets of PDCD4 using iCLIP and observed an enrichment in binding to transcripts encoding cell adhesion and structural proteins. Consistent with these data, we show that PDCD4 acts as a general regulator of cell adhesion, which in a tumour setting would increase the metastatic potential of cells, and demonstrate that the nuclear localisation of PDCD4 is crucial in this process. Overall, the information obtained in untransformed cells provides new perspective for the role of PDCD4 as a tumour suppressor.

overall_design: We performed iCLIP and compared the RNAs bound to PDCD4 to those attached to the IgG control


title: Single-cell gene expression profiles of GM-CSF cultured bone marrow cells treated with HCQ or cGAMP.

status: Public on Jan 10 2026

city: Tokyo

first: Hideo

last: Negishi

address: 4-6-1 Shirokanedai, Minato-ku

department: Vaccine Science

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

summary: We performed single-cell RNA sequencing (scRNA-seq) of granulocyte-macrophage colony-stimulating factor (GM-CSF) cultured bone marrow cells (GM-BMCs) treated with hydroxychloroquine (HCQ) or cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) to reveal a divergence of the gene expression pattern in interferon β (IFNβ)-expressing cells between HCQ and cGAMP treatments.

overall_design: Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. GM-BMCs were treated with HCQ (100 μM) or cGAMP (5 μg/ml) for 6 h and subjected to scRNA-seq analysis.

first: Yusuke

last: Wada

first: Tatsuma

last: Ban

first: Ken

last: Ishii


title: The role of hippocampal niche exosomes in rat hippocampal neurogenesis after fimbria-fornix transection

city: nantong

first: wen

last: li

address: qixiu road 19

country: China

institute: Nantong University

summary: Exosomes transfer signaling molecules such as proteins, lipids, and RNAs to facilitate cell–cell communication and play an important role in the stem cell microenvironment. In previous work, we demonstrated that rat fimbria–fornix transection (FFT) enhances neurogenesis from neural stem cells (NSCs) in the subgranular zone (SGZ). However, how neurogenesis is modulated after denervation remains unknown. Here, we investigated whether exosomes in a denervated hippocampal niche may affect neurogenesis.  Using the FFT rat model, we extracted hippocampal exosomes and used RNA sequencing to identify noncoding RNA expression profiles.

overall_design: The rat hippocampal tissue (denervated and untreated) was quickly harvested on ice. It was then digested with 0.125% trypsin at 37 °C for 30 min and the serum without exosomes was added to stop digestion. The Total Exosome Isolation Kit (from plasma) (Invitrogen, USA) was added to the supernatant after 4 °C, 3000g, 30 min centrifugation for an overnight stand. Then, after 4 °C, 10,000g, 1 h centrifugation, the precipitation was resuspended with 50 μl DPBS, and exosomes were harvested for the following experiments. high-throughput sequencing ofexosomes from hippocampal niche.

first: Guohua

last: Jin

first: Xiang

last: Cheng

first: Wen

last: Li


title: Gene expression profiles of GM-CSF cultured bone marrow cells treated with HCQ or cGAMP.

summary: We performed RNA sequencing (RNA-seq) of granulocyte-macrophage colony-stimulating factor (GM-CSF) cultured bone marrow cells (GM-BMCs) treated with hydroxychloroquine (HCQ) or cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) to compare the gene expression profiles between HCQ and cGAMP treatments in GM-BMCs.

overall_design: Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. GM-BMCs were treated with HCQ (100 μM) or cGAMP (5 μg/ml) for the indicated time periods and subjected to RNA-seq analysis.

first: Tomoya

last: Hayashi


title: SOX4 regulates STAT6 to modulate MTHFD2 Expression and Impacts Drug Resistance in Hepatocellular Carcinoma

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

type: Methylation profiling by high throughput sequencing

summary: SOX4 overexpression in hepatocellular carcinoma (HCC) is linked to poor prognosis, modulating gene expression via epigenetic mechanisms. This study reveals SOX4 interacts with DNA demethylases to reduce STAT6 promoter methylation, enhancing STAT6 transcripts. SOX4-STAT6 regulates MTHFD2, critical for NADPH and purine synthesis. Elevated SOX4, STAT6, and MTHFD2 levels correlate with immunotherapy resistance and poor outcomes in HCC. Targeting STAT6 and MTHFD2 in TKI-resistant HCC tumors suppressed growth, highlighting the therapeutic potential of disrupting the SOX4/STAT6/MTHFD2 axis in HCC progression and drug resistance.

overall_design: Analyze the DNA methylation sequence of Hep3B and Hep3B SOX4 knockout cells to understand how SOX4 regulates gene expression through DNA methylation.

first: Chia-Lung

last: Tsai

first: Ming-Chin

last: Yu

first: Chi-Neu


title: Degradation of G-quadruplex-binding proteins in chromatin using G4-ligand-based proteolysis-targeting chimeras

status: Public on Jan 09 2026

first: Xuan

last: He

address: Lensfield Road

department: Chemistry

summary: Targeted protein degradation is a cutting-edge approach in drug discovery, especially for addressing disease-related proteins that have been difficult to target with traditional methods. Here, we present a conceptually distinct strategy utilizing G-quadruplex (G4) ligand-based PROTACs (G4L-PROTACs) to selectively degrade proteins associated with DNA and RNA G-quadruplexes. Our method leverages G4 ligands that bind endogenous G4s and recruit E3 ubiquitin ligases to promote the degradation of cellular G4-binding proteins. We demonstrate degradation of a range of G4-specific binding proteins, including transcription factors and chromatin remodelers such as FUS, SMARCA4, and ATRX. These proteins play crucial roles in diverse cellular processes like transcription regulation and DNA repair, making them important therapeutic targets. Our results highlight the potential of G4L-PROTACs as a versatile tool for selectively degrading G4-binding proteins, offering new possibilities for therapeutic protein degraders, especially in diseases characterized by aberrant G4 activity, such as cancer.

overall_design: Genome binding/occupancy profiling by CUT&Tag experiments and high throughput sequencing for U2OS cells treated with PDS as control and PROTACs.

first: Zixuan

last: Wang

first: Xiaoyun

last: Zhang

first: Jochen

last: Spiegel

first: Sean

last: Flynn

first: Shankar

last: Balasubramanian


title: Nanobody-tethered transposition for dual profiling of chromatin accessibility and DNA methylation

city: guagnzhou

first: tang

last: guorun

address: xingang

institute: Sun Yat-sen University

summary: DNA methylation and histone modifications are critical epigenetic regulators that orchestrate gene expression and modulate various physiological and pathological processes. However, existing methodologies for simultaneous profiling of these epigenetic marks often require high cell input and suffer from data loss due to bisulfite conversion. In this study, we present advanced multimodal chromatin profiling methods, MethylTag and Multi-MethylTag, that address these challenges by integrating Tn5 transposase with methylated adaptors and optimizing post-bisulfite library preparation. These methods enable high-resolution, multi-dimensional chromatin profiling with reduced cell input and improved data integrity. We validated these techniques in various human and mouse cell lines, revealing complex interactions between DNA methylation and histone modifications. Our findings highlight the utility of these approaches in enhancing epigenetic research and deepening our understanding of the regulatory mechanisms underlying gene expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In the 5mC-CUT&Tag method, Tn5 transposase is coupled with protein A/G (pA/G-Tn5) and preloaded with methylated P5 adaptors30. This pA/G-Tn5 complex is directed to specific histone modifications via primary and secondary antibodies, facilitating the incorporation of methylated P5 adaptors at the 5’ ends of nearby DNA fragments. During the subsequent bisulfite treatment, unmethylated cytosines (C) are converted to uracils (read as thymine (T) during sequencing), while 5-methylcytosines (5mC) and the methylated adaptors remain unchanged. Post-bisulfite treatment, the ligation of the 3’ adaptor ensures that the library can be efficiently amplified by PCR, which reduces the high duplication rates and information loss often caused by DNA template breakage during bisulfite conversion. Additionally, fragmented λDNA with methylated adaptors is included as a spike-in control before bisulfite treatment to monitor the C-to-T conversion rate without affecting the amplification and sequencing.

first: Jizhou

last: Liu

first: Guorun

last: Tang

first: Ziang

last: Lu

first: Zhiying

first: Yelin

last: Lan

first: Guanzheng

last: Luo

first: Xiaocheng

last: Weng

first: Yafen

last: Zhou

first: Jindi


title: Single-cell gene expression profiles of lung cells from HCQ-treated mice.

first: Hideo

last: Negishi

summary: We performed single-cell RNA sequencing (scRNA-seq) of lung cells from hydroxychloroquine (HCQ)-treated mice to examine HCQ-induced IFN-I response in the lung.

overall_design: Mice were treated with 50 mg/kg of HCQ (TCI) on days 0, 1, and 2. Lungs were harvested on day 3, lung cells were isolated using the gentleMACS Dissociator (Miltenyi Biotec) according to the manufacturer’s standard protocol, and the cells were subjected to scRNA-seq analysis.

first: Yusuke

last: Wada

first: Tatsuma

last: Ban

first: Ken

last: Ishii


title: EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Polycomb repressive complex 2 (PRC2) establishes transcriptionally silent chromatin by catalyzing histone H3 lysine 27 trimethylation (H3K27me3). Although cofactors such as MTF2 and JARID2 are known to direct PRC2 to nucleation sites and stimulate its catalytic activity, the role of the PRC2-associated factor EPOP has remained unclear and even controversial. Here, we combine biochemical reconstitution and a cellular EED-rescue system to define EPOP’s contribution to initial PRC2 recruitment and de novo H3K27me3 deposition. We show that EPOP, like MTF2, directly stimulates PRC2 histone methyltransferase activity in vitro. In vivo, EPOP is dispensable for initial PRC2 recruitment but promotes de novo H3K27me3 deposition in cooperation with MTF2 and JARID2. Mechanistically, electrophoretic mobility shift assays and reconstituted chromatin substrates reveal that EPOP and MTF2 enhance PRC2–nucleosome binding in a sequence- and chromatin-dependent manner: EPOP preferentially potentiates activity on GA-rich dinucleosomes, whereas MTF2 favors GCN-rich substrates. Together, these findings position EPOP as a positive regulator of PRC2 function during the establishment of H3K27me3 domains, and reveal a paradigm in which distinct cofactors confer DNA-sequence-specific control of de novo H3K27me3 deposition.

overall_design: To dissect the contribution of PRC2 accessory factors to initial PRC2 recruitment and de novo H3K27me3 deposition, we used a mouse embryonic stem cell (mESC) system in which the core PRC2 subunit EED is knocked out, eliminating PRC2 chromatin binding and H3K27me3 after passaging. Re‑expression of HA‑tagged EED (EED‑rescue) was induced and profiled at 0 h (pre‑rescue baseline) and 24 h (early de novo phase). We performed ChIP‑seq for HA‑EED (proxy for PRC2 chromatin recruitment) and ChIP‑seq for H3K27me3 (histone mark deposition) across a factorial panel of genotypes: wild‑type accessory factor background and targeted knockouts of MTF2, JARID2, EPOP, as single KOs and double KOs (MTF2/JARID2, EPOP/MTF2, EPOP/JARID2).This design enables direct comparison of initial PRC2 recruitment (HA‑EED ChIP‑seq) and de novo H3K27me3 deposition (H3K27me3 ChIP‑seq) kinetics in the presence or absence of individual cofactors during the onset of Polycomb domain formation.

first: Jeffrey

last: Granat

first: Sanxiong

first: Danny

last: Reinberg


title: A Prevalent Disease-Associated SNP in the Human ID3 Gene Regulates E-Protein Activity and Cellular Proliferation [HEK293T RNA-Seq]

city: Charlottesville

first: Brett

last: Ransegnola

state: VA

address: 755 Walker Square, Apt 2D

institute: UVA SOM

summary: The helix-loop-helix transcription factor ID3 is a critical regulator of tissue development and homeostasis. Aberrations in ID3 are strongly associated with numerous human disease processes including Burkitt’s lymphoma. We previously identified that a single nucleotide polymorphism (SNP) in ID3 at rs11574 is associated with increased vascular disease burden in three independent cohorts; however, the mechanisms by which this SNP alters ID3 function and impacts vascular cells are unknown. Here, we show that the minor allele of rs11574 specifically disrupts ID3’s ability to bind the E-protein E12. Computational analysis and confirmatory biochemical experiments revealed that rs11574’s effects on ID3:E12 dimerization are dependent upon a key residue within E12’s unique loop domain. Functionally, the disruption of ID3:E12 binding promotes E12 binding to and activation of the p21 promoter. Isogenic human cell lines harboring the rs11574 minor allele exhibited decreased cell proliferation and altered expression of genes involved in proliferation. RNAseq revealed distinct roles for E12 and E47 in transcriptional regulation of vascular smooth muscle cells (VSMCs). Primary human VSMCs from subjects with the rs11574 minor allele exhibited reduced mitogen-stimulated proliferation. Taken together, these results provide the first characterization of altered molecular and cellular functions of this disease-associated SNP in ID3 at rs11574.

overall_design: Bulk mRNAseq of HEK293T cell lines either homozygous for the major allele of rs11574 (maj/maj), homozygous for the minor allele/risk allele (min/min) or heterozygous (HET) 48hr after release from 24hr serum starvation.

first: Christopher

last: Henderson

first: James

last: Garmey

first: Ali

last: Khan

first: Rédouane

last: Aherrahrou

first: Michael

last: Purdy

first: Shijie

last: Wu

first: Andrea

first: Jennifer

middle: L

last: Kirby

last: Lipinski

first: Vicki

last: Gordon

first: Mark

last: Yeager

first: Mete

last: Civelek

first: Coleen

last: McNamara


title: A Prevalent Disease-Associated SNP in the Human ID3 Gene Regulates E-Protein Activity and Cellular Proliferation [VMSC RNA-Seq]

overall_design: Bulk mRNAseq of primary murine vascular smooth muscle cells WT/KO for E12 and WT/KO for E47. n=2 independent extractions. Cells were revived from cryorecovery and lysed for RNAseq in Trizol.

last: Zhou


title: Single Cell Transcriptome of Highly Heterogenous Hepato-Hematopoietic Lineages in Fetal Liver Organoids from Human Pluripotent Stem Cells

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate the differentiation of hematopoietic fetal liver organoids (hFLOs) from induced pluripotent stem cell, we performed single cell RNA-Sequencing on different culture days.

overall_design: FLO cultures on day 10 (prior to hematopoietic growth cocktail) and hFLO cultures on days 13, 16 and 20 (after hematopoietic growth cocktai, total n=4 samples) were singularized prior single cell-RNA sequencing

first: Milad

last: Rezvani

first: Kyle

last: Lewis

first: Konrad

last: Thorner

first: Norikazu

last: Saiki

first: Takanori

last: Takebe


title: Characterization of mouse melanocytes reveals ultrastructural and immunological insights into the inner ear function [RNA-Seq]

status: Public on Jan 08 2026

city: Jinan

first: Jing

last: Cai

state: Shandong

address: 4 Duanxing West Road

department: Shandong Provincial ENT Hospital

institute: Shandong University

summary: Melanocytes are important components of the inner ear’s cellular architecture. However, limited morphological research has hindered a complete understanding of inner ear function. This study characterized the morphology of inner ear melanocytes and cells often misidentified as melanocytes. Immunofluorescence, Smart-seq, transmission/field emission scanning electron microscopy, and immunoelectron microscopy were used. Cells with a “black ball” appearance in the vestibule were identified as macrophages. We examined variation in melanocytes or macrophages with age, strain, and cisplatin injury. Kir4.1 expression and the greater noise resistance observed in pigmented mice suggest potential melanocyte functions. Based on melanin distribution in Pou3f4y/- mice, we hypothesize that melanocytes migrate from the modiolus along Reissner's membrane to the stria vascularis, following a base to apex gradient. These findings provide novel ultrastructural and immunological insights into inner ear function.

overall_design: By comparing the results of two sets of sequencing, the possible mechanism of inner ear pigmentation in Pou3f4y/- mice was determined.

first: Lei

last: Xu

first: Yongdong

last: Song

first: Aizhen

last: Zhang

first: Zheng

last: Li

first: Boqin

first: Haibo

last: Wang


title: NKG2D Upregulation Enhances T and NK Cell Cytotoxicity, Sensitizes Tumors to Combined αPD1 and αVEGF Therapy, and Contributes to Hearing Loss Prevention in Vestibular Schwannoma Model

city: Columbus

first: Long-Sheng

last: Chang

address: 575 Children's Crossroad

institute: Abigail Wexner Institute at Nationwide Children's Hospital

summary: Background: NF2-related schwannomatosis (NF2-SWN) is a debilitating condition that calls for robust treatment options. NF2-SWN is characterized by bilateral vestibular schwannomas (VSs), which grow over time and can result in irreversible sensorineural hearing loss, significantly affecting the quality of life for those affected. At present, there are no FDA-approved medications specifically for treating VS or related hearing loss. VS management involves radiotherapy or surgical resection, while bevacizumab, an anti-vascular endothelial growth factor monoclonal antibody (αVEGF), has been used off-label in NF2-SWN to shrink the tumor. However, not all patients respond and the effect is not always durable. There is a critical need for effective medications that can stop VS growth and associated hearing loss. While immune checkpoint inhibitors have transformed cancer therapy, their potential has not been thoroughly explored in non-malignant tumors such as VS. Methods: We characterize the effects of combined anti-programmed cell death protein-1 (αPD1) and αVEGF treatment on tumor growth and hearing function in two syngeneic, immune-competent VS models. Results: Combining αVEGF with αPD1 treatment significantly enhances the antitumor efficacy of each monotherapy. Specifically, i) αVEGF augments αPD1 efficacy by normalizing tumor vasculature to improve drug delivery and immune cell infiltration, and by activating the antitumor cytotoxicity of T and NK cells via NKG2D upregulation; and ii) combined αPD1 with αVEGF treatment effectively controls the growth of tumors that progressed despite αVEGF treatment. Conclusion: These findings provide a strong foundation for the αPD1 with αVEGF combination therapies to treat patients with NF2-SWN.

overall_design: Single cells were extracted from 3 NF2-mutated treatment-naïve schwannomas and 1 bevacizumab-treated schwannoma from an NF2 patient that was on bevacizumab for almost 10 years scRNA libraries were prepared using the 10x Genomics platform.

first: Natalie

last: Wu


title: Single-cell gene expression analysis using lung derived cells from SARS-CoV-2-infected mice in aged and adult mice

city: Kumamoto-city

first: Takushi

last: Nomura

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Joint Research Center for Human Retrovirus Infection

institute: Kumamoto University

summary: We conducted single-cell gene expression analysis to elucidate the molecular basis of immune cells in the mouse lung associated with age-dependent severity of COVID-19 infection. In aged infected mice, genes associated with inflammation were more highly expressed in several cell populations compared to adult infected mice.

overall_design: We isolated live CD45-positive cells from the lungs of representative mice from aged and adult SARS-CoV-2-infected groups, as well as their uninfected control groups, and subjected them to 10x single-cell gene expression, TCR, and BCR analysis.

first: Rise

last: Kurokawa

first: Chatherine

last: Mtali

first: Innocent

last: Daniel

first: Thorbjorg

last: Einarsdottir

first: Omnia

last: Reda

first: Nobuko

last: Irie

first: Sakhor

middle: W

last: Binti

first: Koki

last: Niimura

first: Mitsuyoshi

last: Takatori

first: Kenji

last: Sugata

first: Chanidapa

last: Tye

first: Yorifumi

last: Satou

first: Masahiro

last: Ono


title: DNA Replication Dynamics within the Centromeres of Chromosome Y and Chromosome 21 in Human Neural Progenitor Cells Overexpressing Tau Proteins

city: Bethesda

first: Mirit

middle: I

last: Aladjem

state: MD

address: 37 Convent Dr. Building 37, Room 5068D

department: DNA Replication Group

institute: National Cancer Institute

summary: Aging somatic cells are characterized by specific chromosome aneuploidy. This work examines the role of DNA replication within the centromeres of chromosomes Y (ChrY) and 21 (Chr21). The aneuploidy of these two chromosomes is associated with Alzheimer's Disease (AD) pathology. Using human neural progenitor cells engineered to overexpress wild-type (wt) and pseudo-hyper-phosphorylated (php) Tau proteins, we developed a novel method to analyze replication dynamics in centromeric regions. Our findings reveal overexpression reduces the replication initiation events that are active within alpha satellite sequences in control condition. Mass spectrometry analysis on immunoprecipitated Tau identified nuclear interactors of Tau, particularly in its php form, which might directly influence chromatin architecture and gene expression. This research provides critical insights into the molecular mechanisms of aneuploidy in tauopathies.

overall_design: Nascent strands were purified with the lambda exonuclease methods from CIMH cells

first: Bhushan

last: Thakur

first: Carl

last: Schildkraut

first: Elisa

last: Balzano


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [scRNA-seq]

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

address: Building 560

summary: Alternative splicing is a pervasive gene regulatory mechanism critical for diversifying the human proteome. To systematically investigate its role in cell fate determination, we developed scCHyMErA-Seq, a scalable CRISPR-based exon deletion screening platform integrated with 10x Genomics single-cell transcriptomic readouts. This tool enables efficient exon deletion while simultaneously capturing Cas9/Cas12a guides and polyadenylated transcripts at single-cell resolution. Applying scCHyMErA-Seq to high-throughput profiling of alternative cassette exons, we identified numerous exons with strong regulatory effects on gene expression. Analysis of NRF1 alternative exon-7 revealed that this exon modulates NRF1 transcriptional activity by regulating its recruitment to the promoters of target genes. Importantly, gene expression profiles generated using scCHyMErA-Seq accurately recapitulate findings from traditional, labor-intensive orthogonal methods, while offering enhanced scalability and efficiency. Overall, scCHyMErA-Seq represents a robust and versatile platform for systematically unraveling the functional impact of alternative splicing by directly linking specific splicing variants to transcriptional phenotypes.

overall_design: HAP1 cells co-expressing spCas9 and opCas12a were transduced with a hybrid guide RNA (hgRNA) library designed to induce deletions in 224 exons and knockouts in 161 genes at a low multiplicity of infection (MOI = 0.1). Transduced cells underwent selection with puromycin for two days. Four days post-transduction, a total of 413,190 cells were processed using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index), with protocol modifications to enable the specific amplification of Cas12a gRNA libraries. For sequencing, libraries corresponding to 1) gene expression, 2) CRISPR perturbations (Cas9 & Cas12a gRNAs using conventional 10x Genomics CRISPR libraries), and 3) Cas12a-specific sequencing (using a custom Cas12 gRNA-specific amplification protocol) were pooled at a 4:1:1 molar ratio. Sequencing was performed on an Illumina NovaSeq platform using a 100-cycle kit, following the standard 10x Genomics protocol: Read 1: 28 bp, Index i7: 10 bp, Index i5: 10 bp, Read 2: 90 bp.

first: Bandana

last: Kumari

first: Arun

last: Damodaran

first: Wilfried

last: Guiblet

first: Mei-Sheng

last: Xiao

first: Amit

middle: K

last: Behera

first: Tyler

last: On

last: Mcintosh

first: Maxwell

last: Teszler

first: Chelsee

last: Holloway

first: Sandra

last: Le

first: Nikhil

last: Parab

first: Yongmei

last: Zhao

first: Michael

last: Aregger


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [RNA-seq_Rescue_exp]

overall_design: RNA-Sequencing was performed in HEK293 Flp-in cells depleted from endogenous NRF1 with RNAi (non-targeting siRNAs were used as control) while expressing either full-length NRF1 (NRF1-FL) or the NRF1 isoform lacking exon-7(NRF1-∆E7) at endogenous levels using dox-inducible HEK293 Flp-In cell lines to systematically explore if NRF1 exon-7 regulates gene expression.


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [ChIP-Seq]

overall_design: ChIP-sequencing was conducted in HEK293 Flp-In cells stably expressing FLAG-tagged full-length (FL) and ∆Exon-7 NRF1 isoforms. Immunoprecipitation was performed using FLAG antibodies, with HEK293 cells expressing FLAG-EGFP serving as a negative control.


title: Single-Cell Exon Deletion Profiling Reveals Splicing Events That Shape Gene Expression and Cell State Dynamics [RNA-seq_BaseEditor]

overall_design: RNA sequencing was performed in HEK293T cells transfected with base-editing vectors designed to introduce mutations at the splice sites of endogenous NRF1 exon 7, effectively promoting exon skipping.


title: Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila

city: Bunkyo-ku

first: Raku

last: Saito

state: Tokyo-to

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: The zinc finger-associated domain (ZAD)-containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.

overall_design: ChIP-seq and Micro-C of Drosophila nc14 early embryo, and RNA-seq of Drosophila adult ovaries. All samples include 2 replicates.

first: Yusuke

last: Umemura

first: Shiho

last: Makino

first: Takashi

last: Fukaya


title: HDI-STARR-seq library profiling of differential accessible chromatin regions (DARs) in livers of male, female and male treated with continuous growth hormone (cGH) mice.

status: Public on Jan 07 2026

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models, which are confounded by vector-induced innate immune responses and lack the physiologically relevant cellular and endogenous hormonal context and chromatin environment of complex mammalian tissues. Here, we combine hydrodynamic injection (HDI) with a modified STARR-seq-based MPRA, designated HDI-STARR-seq (PMID:39716078)  to determine condition-specific enhancer activity in mouse liver at scale. Analysis of a synthetic STARR-seq library, comprised of 23,912 reporters regions spanning 1839 ATAC regions enabled functional assessment of mouse liver enhancer activity in vivo across three distinct biological conditions: male iver, feamle liver and continuous growth hormone (GH)-infused male liver, which is substantially feminized with regards to gene expression. HDI-STARR-seq reporters representing 305 ATAC regions showed sex-biased and GH-responsive enhancer activity that mirrored the regulation of their chromatin accessibility in hepatocytes, validating these sites as functional, physiologically regulated enhancers. These enhancers were enriched for activating histone marks (H3K4me1, H3K27ac) and for binding sites for GH-activated transcriptional regulator STAT5 and for the STAT5-dependent, sex-specific repressors BCL6 and CUX2, consistent with a cohesive regulatory network controlling hepatocyte lipid and xenobiotic metabolism. Further, de novo motif analysis identified binding sites for HNF4A and for several novel factors specifically enriched at the regulated enhancers. Importantly, sex-biased and GH-regulated functional enhancers were linked to both MASLD (metabolic dysfunction-associated steatotic liver disease)-enabling and MASLD-protective genes, indicating that GH-dependent chromatin remodeling at these loci is a key determinant of sex-differential liver metabolic disease susceptibility. This integrated in vivo approach defines a validated set of GH-regulated hepatocyte enhancers through which chromatin accessibility and transcription factor binding drive sexual dimorphism in hepatic metabolism and sex-specific MASLD risk.

overall_design: We implemented the synthetic STARR-seq library in control male liver, control female liver and cGH-treated male liver to quantitatively measure intrinsic transcription activity in the corresponding group. A pool of chemically-synthetic DNA fragments in 210 nt length were amplified and delivered to untreated adult male CD-1 mice, untreated adult female CD-1 mice,and 10d cGH-treated male male using osmotic pump. A pooled plasmid library was delivered into mice using hydrodynamic tail vein injection (HDI) for in vivo transfection, preferentially for livers. For a STARR-seq library, three types of sequencing libraries incorporated in this submission (i.e., STARR-seq  plasmid libraries, STARR-seq DNA libraries and STARR-seq RNA libraries) are generated by PCR amplification using  the same PCR condition. The STARR-seq plasmid library, which is the same material injected in HDI livers, represents the abundance of each reporter assaying  DNaseI digested regions in response to sex-specific open chromatin regions or TCPOBOP-responsive open chromatin regions. DNA plasmids extracted from a small piece of  HDI livers  were amplified using DNA reporter-specific primers, and  represented the intake plasmids in livers. The read counts of each reporter were used as denominator to calculate STARR-seq enhancer activity. Poly-adenylated RNA plasmids extracted from HDI livers were reverse-transcribed followed by DNase treatment, and amplified using RNA reporter-specific primers, and represented the self-transcribing activity of the DHS. The read counts of each reporter were used as numerator to calculate STARR-seq enhancer activity.

first: Ting-Ya

last: Chang


title: Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

summary: Genome folding is not static, but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here we show that extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and for the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

overall_design: Hi-C using in various mouse embryonic stem cell lines with auxin- or dTAG-inducible degrons inserted on endogenous NIPBL, RAD21, WAPL, PDS5A and PDS5B.

first: Shah

last: Rini


title: The cellular balance of NIPBL and PDS5 tunes the rate of cohesin loop extrusion and shapes chromosome organization across scales

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

overall_design: Refer to individual Series


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [RNAseq]

city: Cambridge

first: Ally

last: Nicolella

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

summary: NMDA (N-methyl-d-aspartate) receptor dysfunction is widely implicated in pathophysiology of autism spectrum disorder (ASD), a neurodevelopmental condition with a strong genetic basis. Here we investigated heterozygous mouse mutants carrying the ASD-linked C456Y mutation of Grin2b, a high-confidence ASD risk gene encoding the GluN2B subunit of the NMDA receptors. Comprehensive transcriptomic analyses across multiple brain regions and postnatal ages revealed large-scale gene expression changes, particularly in pathways related to oxidative phosphorylation and ribosome/translation, suggesting brain-wide alteration of energy metabolism and protein synthesis in Grin2b+/C456Y mice. Starting from transcriptomic evidence, we additionally discovered widespread splicing abnormalities, and impaired hippocampal neurogenesis in Grin2b mutants. Interestingly, the underlying genes and the spatial and temporal patterns of transcriptomic changes in Grin2b+/C456Y mice differed substantially from those observed in mutant mice lacking Grin2a, which encodes the GluN2A subunit of the NMDA receptor but is a schizophrenia risk gene. These findings underscore the distinct role of Grin2b in brain development and function and reveal potential mechanisms by which Grin2b loss of function may lead to neurodevelopmental disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from substantia nigra (SN) at 2, 4, 12 and 20 weeks of age in Grin2a mutant mice.

first: Farsi

last: Zohreh

first: Nicolella

last: Ally


title: Efficient processing of widespread R-loops through an endo- and exo-cleavage coupling mode prevents genome instability

city: Beijing

first: weibin

last: wang

address: No. 38 Academy Road

institute: Peking University Health Science Center

summary: Excessive accumulation of R-loops is thought to be one of the major causes of genome instability. Endonuclease RNaseH1 acts as a classic, common R-loop resolvase to prevent R-loop accumulation genome-widely, whether there is any exonuclease complementing and teaming up with RNaseH1 to more efficiently resolve genome-wide R-loops is worth investigation. Here we identify an exonuclease REXO4, which collaborates with RNaseH1 endonuclease to more efficiently degrade R-loops in an “endo- and exo-cleavage coupling” manner. Specifically, among many members of DEDDh exonuclease family, REXO4 has the most significant effect on R-loop suppression. REXO4 directly degrades RNA strand in R-loop from the end or internal nick through its 3’-5’ exonuclease activity, and also stimulates RNaseH1 endonuclease activity. The genome-wide R-loop regions regulated by REXO4 highly overlap with those regulated by RNaseH1, and REXO4 overexpression counteracts genome-wide R-loop accumulation caused by RNaseH1 deficiency. Furthermore, REXO4-deficient tumors display elevated R-loop mutation burden, and tumor patient-derived mutations in REXO4 enzymatic region all impair R-loop cleavage activity. Interfering with REXO4 increases the sensitivity of tumor cells to alkylating and G4 stabilizing drugs. Therefore, our study proposes a model for highly efficient processing of genome-wide R-loops by endo- and exo-cleavage, which provides additional insights into understanding the link between R-loop associated genome instability and tumors.

overall_design: To investigate whether REXO4 and RNaseH1 bind to R-loops , we performed ChIP-seq using tet-on stable expression cell lines of nuclease-dead mutant REXO4-D386A or RNaseH1-D210N.

first: Han

last: Yang

first: Chen

last: Nie

first: Jiadong

last: Wang

first: Weibin


title: DRIP-seq reveals REXO4 and RNaseH1 work together to process R-loops in the same genomic region across the genome.

summary: Endonuclease RNaseH1 acts as a common R-loop resolvase to prevent R-loop accumulation genome-widely, whether there is any exonuclease complementing RNaseH1 to more efficiently resolve R-loops is worth investigation. Here we identify an exonuclease REXO4, which collaborates with RNaseH1 to efficiently degrade R-loops in an “endo- and exo-cleavage coupling” manner.DNA-RNA immunoprecipitation followed by sequencing (DRIP-seq) shows that R-loop regions regulated by REXO4 highly overlap with those regulated by RNaseH1.

overall_design: To investigate whether REXO4 and RNaseH1 work together to process R-loops in the same genomic region, we performed DRIP-seq after knocking down REXO4 and RNaseH1 using siRNA in U2OS cells.


title: Evolutionarily divergent transcriptomic programs in ovarian folliculogenesis across mice, monkeys and humans [Mouse]

status: Public on Jan 19 2026

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Understanding the mechanisms for human ovarian folliculogenesis is fundamental to reproductive biology and medicine. Here, we investigated transcriptomic dynamics in individual oocytes and their associated granulosa cells (GCs) during folliculogenesis in mice, monkeys and humans. Unlike mouse oocytes, which exhibited stage-specific, stepwise transcriptomic maturation, monkey and human oocytes showed minimal transcriptomic changes until the secondary follicle stage and could be broadly categorized as either immature or mature. In all three species, most highly variable genes (HVGs) during oocyte growth displayed monotonic up- or downregulation, with limited overlap in HVGs across species. GCs exhibited similarly species-specific transcriptomic trajectories. Correspondingly, intercellular communication pathways, including ligand–receptor signaling, gap junctions, and metabolic coupling between oocytes and GCs, demonstrated substantial species-specific differences. Nonetheless, X-chromosome dosage compensation and repression of evolutionarily young transposons were conserved across species. We established in vitro culture systems supporting preantral to antral follicle development in monkeys and humans, revealing relatively normal oocyte transcriptome maturation but aberrant GC profiles. By delineating interspecies differences in folliculogenesis, this study provides a framework for understanding human ovarian development and advancing its in vitro reconstruction.

first: Baku

last: Nakakita

first: Ken

last: Mizuta

first: Yoshitaka

last: Katou

first: Hidetaka

last: Tasaki

first: Tomonori

last: Nakamura

first: Chizuru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Ikuo

last: Kawamoto

first: Tomoyuki

last: Tsukiyama

first: Xun

last: Chen

first: Guillaume

last: Bourque

first: Junko

last: Otsuki

first: Mikiya

last: Nakatsuka

first: Akihito

last: Horie

first: Masaki

last: Mandai

first: Mitinori

last: Saitou

first: Hiroshi

last: Ohta


title: Neofunctionalization of a P-type ATPase enables fluconazole efflux in Candida auris

status: Public on Jan 06 2026

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: Candida auris is an emerging fungal pathogen known for its high resistance to fluconazole, the most commonly prescribed antifungal. However, the genetic regulators of fluconazole susceptibility remain insufficiently understood in C. auris. Using a pooled screen of piggyBac (PB) transposition mutants, we identify significant enrichment of mitochondrial genes whose inactivation causes reduced fluconazole susceptibility. Genome-wide genetic interaction analysis of a representative mitochondrial gene-deleted mutant, pet309Δ, implicates that mitochondrial dysfunction reduces fluconazole susceptibility by enhancing Cdr1 efflux activity post-transcriptionally and through the vacuolar calcium pump homolog Cdt1. We further demonstrate that Cdt1, beyond its canonical calcium-pumping function, mediates fluconazole efflux, evidenced by its fluconazole-induced, calcineurin-dependent plasma membrane localization and dependence on ATP hydrolysis. Additionally, Cdt1 accelerates the evolution of fluconazole resistance, and its transcript levels correlate with susceptibility across clinical isolates. Our findings define a novel role for Cdt1 in fluconazole efflux in C. auris.

overall_design: mRNA profiles of pet309Δ and WT cells.

first: Jiaxin

last: Gao


title: Identification of a neoplastic Tfh-like cellular subset in a mouse model of angioimmunoblastic T cell lymphoma (AITL)

city: Montreal

first: Saba

last: Mohammaei

address: 110 Pine Ave W

country: Canada

institute: IRCM

summary: Nodal T-follicular helper cell lymphoma, angioimmunoblastic type (nTFHL-AI, or AITL), is an aggressive peripheral T cell lymphoma without effective treatments. It has been shown that genetic and epigenetic changes lead to the expansion of neoplastic CD4+ T cells originating from T follicular helper (Tfh) cells, which subsequently cause B cell expansion and tumor. However, it remains unclear if the Tfh-like cell populations contain a subset that drive tumor progression and, if so, whether such a subset may have druggable targets. Using a mouse model of AITL driven by heterozygous sanroque mutation (Roquinsan/+), we identified a tumor-enriched Tfh cell subset highly expressing CXCR6 and IL-18 receptor, termed “Double-Expressor (DE) Tfh” cells. DE Tfh cells also expressed higher levels of enhancer of zeste homolog 2 (EZH2). In vitro data indicated that IL-18 and EZH2 are required for the proliferation of DE Tfh cells. Furthermore, DE Tfh cells have a potent capacity to expand B cells when adoptively transferred to lymphopenic recipients. On the other hand, depletion of DE Tfh cells via Ezh2 gene deletion, inhibition of EZH2 (using FDA-approved drug, tazemetostat), or anti-CXCR6 mAb led to tumor regression. These findings may be relevant to a subset of AITL cases since we found that ~20-30%  of AITL patient samples have concomittantly elevated expression of CXCR6, IL-18R1, and IFNG. Thus, our study identified a pathogenic Tfh-like subset essential for AITL tumor progression in a mouse model and suggests that identifying and targeting DE Tfh-like subset in AITL patients might be an effective strategy.

overall_design:
Tumor or tumor-free lymph node (control) were isolated from Roquinsan/+ mice and stained to sort live CD4+CXCR5+PD-1+ T follicular helper-like cells (>95% purity), and were analyzed by scRNA-seq.

>>>Submitter states that raw data for this study are no longer available.<<<

first: Antoine

last: Bouchard

first: Woong-Kyung

last: Suh


title: BRD2 bridging TFIID and histone acetylation in transcriptional initiation [RNA-Seq]

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary:
Members of the bromodomain and extraterminal domain (BET) transcription factor family play a central role in the regulation of gene expression. BET domain factors have also been proposed as major targets for multiple diseases, with inhibitors designed to block the binding of BET bromodomains to acetylated histones. However, recent studies demonstrated that the BETdomain of BRD4 is not involved in its transcriptional function and the specific mechanisms by which other individual BET-domain containing proteins distinctly regulate transcription remain poorly understood. Here, we demonstrate that BRD2 promotes transcriptional initiation by RNA Polymerase II (Pol II) at gene promoters and enhancers, predominantly in a bromodomaindependent manner. Our biochemical studies demonstrated that histone H4K16 acetylated histone-bound BET domain of BRD2 facilitates the recruitment of the transcription preinitiation complex TBP/TFIID to chromatin. Loss or inhibition of BRD2 bromodomains prompts the formation of BRD2-specific nuclear foci that sequester TFIID away from chromatin, leading to a genome-wide defect in transcriptional initiation. Our molecular studies demonstrated that the BET domains of BRD2 and BRD4 are not functionally exchangeable, highlighting distinct but cooperative roles for BET-domain family members in transcriptional initiation and elongation control to promote proper regulation of gene expression

TT-seq series available here: https://doi.org/10.5281/zenodo.17554013

overall_design: RNA-seq profiling of wild type DLD-1 cells

first: Bin

last: Zheng

first: Ruxuan

last: Qiu

first: Yuki

last: Aoi

first: Marta

last: Iwanaszko


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [grin2b_snRNAseq]

first: Ally

last: Nicolella

overall_design: snRNA-Seq analysis of hippocampus (HP), striatum (STR), Thalamus (TH) and prefrontal cortex (PFC) at 4 weeks in Grin2b mutant mice.

first: Farsi

last: Zohreh

first: Nicoellla

last: Ally


title: Multifaceted B-cell response to transient HIV viraemia in elite controllers

city: London

first: Laura

middle: E

last: McCoy

address: Pears Building, Rowland Hill Street

institute: University College London

summary: Chronic HIV infection drives B-cell dysfunction associated with the accumulation of tissue-like memory (TLMs) and activated memory B cells (MBCs) but decline in resting memory B cells. TLM origin and the mechanisms driving their expansion in HIV infection remain unclear. To elucidate this, we performed single-cell RNA/BCR sequencing of PMBCs enriched for B cells from an elite HIV controller pre-, during and post-viral blip. This provided a new insight into multifaceted functional B-cell response to transient HIV viraemia as likely happens during the early phase of anti-retroviral therapy cessation, highlighting the TLM heterogeneity and the contribution of innate-like B cells which might have important clinical implications for anti-HIV vaccine and therapy design.

overall_design: scRNA/BCR/CITE-seq profiling of PBMCs enriched for B cells obtained from an elite HIV controller (no anti-viral treatment) at three different timepoints (pre, during and post viral blip).

first: Ondrej

last: Suchanek

first: Luke

last: Muir

first: Peter

last: Thomas


title: Akr1b7 functions as a master regulator in ovarian aging [superSAGE]

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

summary: At the beginning of ovarian aging, the ovulation of immature oocytes is accelerated, finally leading to the arrest of ovulation despite the remaining oocytes. Here RNA expression in ovarian aging of mice is comprehensively analyzed during the estrous cycle after ovulation stimulation, and an aldo-keto reductase Akr1b7 pathway transiently increased in the young ovary is eliminated in the aged mice. Akr1b7-/- mice enhance the ovulation of immature oocytes, and the KITL expression in Akr1b7-expressed stromal is attenuated, accompanied by oocyte Akt essential for the follicular development inactivation in primordial follicles. The estrous cycle is extended due to the prolonged diestrous stage by a sustained progesterone level in Akr1b7-/- mice ovaries, which is caused by the decline of Cyp17a1, a major metabolite enzyme of progesterone in Akr1b7-expressed theca cell layers. Taken together, the decreased Akr1b7 pathway causes the ovulation of immature oocytes and the prolonged estrous cycle, typical symptoms of ovarian aging.

overall_design: Examination of comprehensive RNA analysis by superSAGE  in YNG and OLD ovaries at 24h–96h after hCG administration.

first: Keishiro

last: Isayama

first: Kenji

last: Watanabe

first: Masato

last: Ohtsuka

first: Seisuke

last: Kimura

first: Tomoaki

last: Murata

first: Takeshi

last: Honda

first: Masataka

last: Asagiri

first: Shun

last: Sato

first: Hiroshi

last: Tamura

first: Norihiro

last: Sugino


title: Phenylhydrazone-based Endoplasmic Reticulum Proteostasis Regulator Compounds with Enhanced Biological Activity

status: Public on Jan 05 2026

city: La Jolla

first: Gabriel

last: Kline

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

summary: Pharmacological enhancement of endoplasmic reticulum (ER) proteostasis is an attractive strategy to mitigate pathology linked to etiologically-diverse protein misfolding diseases. However, despite this promise, few compounds have been identified that enhance ER proteostasis through defined mechanisms of action. We previously identified the phenylhydrazone-based compound AA263 as a compound that promotes adaptive ER proteostasis remodeling through mechanisms including activation of the ATF6 signaling arm of the unfolded protein response (UPR). However, the protein target(s) of AA263 and the potential for further development of this class of ER proteostasis regulators had not been previously explored. Here, we employ chemical proteomics to demonstrate that AA263 covalently targets a subset of ER protein disulfide isomerases, revealing a molecular mechanism for the activation of ATF6 afforded by this compound. We then use medicinal chemistry to establish next-generation AA263 analogs showing improved potency and efficacy for ATF6 activation, as compared to the parent compound. Finally, we show that treatment with these AA263 analogs enhances secretory pathway proteostasis to correct the pathologic protein misfolding and trafficking of both a destabilized, disease-associated α1-antitrypsin (A1AT) variant and an epilepsy-associated GABAA receptor variant. These results establish AA263 analogs with enhanced potential for correcting imbalanced ER proteostasis associated with etiologically-diverse protein misfolding disorders

overall_design: Total RNASequencing of AA263 analog treated HEK293T cells to determine transcriptional activity of pharmacologic ATF6 activators. RNA was submitted to BGI Genomics Co., Ltd. for strand-specific mRNA sequencing on their DNBSEQ platform with three biological replicates per condition.

first: Leonard

last: Yoon

first: Jeffery

last: Kelly

first: Rockland

last: Wiseman


title: Effect of Moderate-Intensity Treadmill Exercise on Bone Quality in Adult Rats and the Underlying Mechanisms

city: beijing

first: Chenchen

last: Li

address: 37 Xueyuan Road

institute: beihang university

summary: While exercise is widely recognized to enhance bone mass, the underlying molecular and cellular mechanisms remain incompletely elucidated. The present study was designed to investigate the effect of moderate-intensity exercise on skeletal quality, morphological characteristics, and metabolic homeostasis in adult Sprague-Dawley (SD) rats. Herein, we aim to investigate the expression profile of mRNAs in rats with exercise and identify promising targets for osteoporosis diagnosis and treatment. RNA sequence were performed in the bones from 3 exercised rats and 3 healthy controls.

overall_design: RNA sequence were performed in the bones from 3 exercised rats and 3 healthy controls. Significantly differentially expressed mRNAs were selectively verified in 6 exercised rats and 6 healthy controls by real-time PCR.

first: Xitong

first: Peipei

last: Shi

first: He

last: Gong


title: Akr1b7 functions as a master regulator in ovarian aging [RNA-seq]

first: Yoichi

last: Mizukami

overall_design: Examination of comprehensive RNA analysis by RNA-seq  in WT and Akr1b7-/- (KO) ovaries at 24h after hCG administration.

first: Keishiro

last: Isayama

first: Kenji


title: A Spatiotemporal Atlas of Cerebrovascular Development in Zebrafish: From Vasculatures to Cells and Molecules

city: Zhan Jiang

first: Xiaoyu

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

summary: The cerebrovascular system plays a pivotal role in brain development and the maintenance of its functions. Although several single-cell transcriptomic studies have delineated the molecular profiles of brain vasculature, integrating these data into a coherent multiscale understanding across molecular, cellular, and vascular network architecture remains a fundamental challenge. Here, we present a comprehensive spatiotemporal atlas of zebrafish cerebrovascular development that bridges these scales by combining in situ sequencing with three-dimensional (3D) vascular network reconstruction. Our quantitative 3D analysis revealed region-specific cerebrovascular growth dynamics at 3, 6, and 11 days post-fertilization. Through single-cell RNA sequencing, we identified endothelial cell (EC) subtypes at these stages and validated their molecular signatures and cross-species conservation during vascular development. Spatial transcriptomics further demonstrated that capillary ECs are the predominant vascular subtype within intracranial vessels, showing progressive enrichment in mesencephalic/metencephalic regions. Importantly, we identified three previously uncharacterized genes (slc16a1a, zgc:158423, and si:ch73-86n18.1) that critically contribute to blood-brain barrier integrity. Our study systematically deciphers the molecular profile of ECs during development, establishing a foundational framework for understanding the dynamic landscape of cerebrovascular development.

overall_design: Endothelial-specific Tg(kdrl:eGFP) transgenic zebrafish line was used to isolate the brain endothelial cells by flow cytometry at 3, 6, and 11 dpf, and then performed  10x Genomics scRNA-seq on the sorted cells with 3' labelling strategy.


title: RNA-seq of HFL-1 Cells Overexpressed GFP, GFP-ERG or GFP-ERG-ΔIDR13

status: Public on Jan 04 2026

city: Chengdu

first: Lu

last: Pu

state: Sichuan

address: #37 Guoxue Alley, Wuhou District

institute: west china hospital

summary: This dataset contains rawRNA-seq data from HFL-1 Cells  Overexpressed GFP, GFP-ERG or GFP-ERG-ΔIDR13. The experiment aims to explore the downstream genes of ERG and its phase separation-deficient mutant to uncover the role of ERG's LLPS activity in regulating gene expression in HFL-1 cells, providing insights into the regulatory networks controlled by ERG in cell senescence.

overall_design: RNA-seq of ERG, its LLPS-deficient mutant ΔIDR13 and GFP control in HFL-1 cells to understand the downstream genes and regulatory activity associated with ERG'S phase separation mechanism.


title: The angiopoietin receptor Tie2 restricts proliferation and sprouting of cardiac endothelial cells

status: Public on Jan 02 2026

city: Helsinki

first: Madeleine

middle: Helena

last: Lackman

state: Uusimaa

address: Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

summary: Tie1 and Tie2 receptors are important in the maintenance of the vascular steady-state. We used scRNAseq to analyze how genetic deletion of Tie1 and Tie2 affects expression of proliferation-related genes in mouse endothelial cells.

overall_design: (1) Stromal-vascular fraction (SVF) of the mouse heart was prepared by enzymatic (mix of collagenases) digestion of the heart tissue. RBC were lyzed by RBC-lysis buffer. (2) EC-enriched fraction of the mouse heart was prepared by enzymatic digestion of the heart tissue. EC fraction was isolated using FACS and antibody staining of the EC markers. (3) EC-enriched fraction of the mouse kidney was prepared by enzymatic digestion of the kidney. EC fraction was isolated using FACS and antibody staining of the EC markers. (4) EC-enriched fraction of the mouse lung was prepared by enzymatic digestion of the lung. EC fraction was isolated using FACS and antibody staining of the EC markers.

first: Andrey

last: Anisimov

middle: H

first: Kari

last: Alitalo

first: Sinem

last: Karaman


title: RNA-seq analysis of rat urethral tissue after tetrahedral DNA nanostructure (TDN) treatment

status: Public on Jan 01 2026

city: Guiyang

first: Jian

address: No. 206, Sixian Street, Baiyun District

department: Department of Sports Medicine

institute: Beijing Jishuitan Hospital Guizhou Hospital

summary: Urethral injury often leads to excessive inflammation and fibrosis, which are major contributors to urethral stricture and impaired tissue repair. Tetrahedral DNA nanostructures (TDN) are emerging nucleic acid nanomaterials with favorable biocompatibility and immunomodulatory properties; however, their transcriptomic effects during urethral injury repair remain poorly understood.  In this study, a rat model of urethral injury was established using a mechanical method, and animals were treated with TDN or vehicle control. Urethral tissues were collected at defined time points after injury and treatment for RNA sequencing (RNA-seq) analysis. Transcriptomic profiling was performed to characterize global gene expression changes associated with urethral injury and to explore the molecular responses to TDN treatment.  This dataset provides a comprehensive resource for investigating gene expression programs involved in urethral injury, inflammation, and fibrosis, and may facilitate further studies on the molecular mechanisms underlying nucleic acid nanomaterial-based therapeutic strategies for urethral repair.

overall_design: Male rats were randomly assigned to different experimental groups, including a control group, a urethral injury model group, and a tetrahedral DNA nanostructure (TDN) treatment group. Urethral injury was induced using a mechanical method, followed by administration of TDN or vehicle control according to the experimental protocol.  Urethral tissues were harvested after treatment, and total RNA was extracted for transcriptome analysis. RNA sequencing (RNA-seq) was performed using an Illumina sequencing platform with paired-end reads. The resulting sequencing data were used to compare global gene expression profiles among experimental groups and to characterize transcriptional changes associated with urethral injury and TDN treatment.


title: MCF-7 cells long-term treated with Fulv plus Abema acquired ESR1 Y537S mutation and exhibited defective RSR and DDR

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

summary: ESR1 mutations are the leading cause of endocrine therapy resistance and progression in ER-positive metastatic breast cancer. ESR1 mutations are detected in ~50% of metastatic breast cancer patients, and identification of effective targeted therapeutics are critically needed. Here, we identified enrichment of dysregulated replication stress and DNA damage responses in multiple ESR1 mutant models. Long-term treatment with endocrine therapy Fulvestrant plus the CDK4/6 inhibitor abemaciclib led to the emergence of a Y537S ESR1 mutation in a cell line, which exhibited dysregulation of replication stress response, enhanced DNA damage response, and synergistic responses to inhibitors of these pathways.

overall_design: RNA-Seq profiling of the MCF-7 parental wild-type ESR1, Abemaciclib resistant MCF-7 with wild-type ESR1, fulvestrant and Abemaciclib reistant MCF-7 treated for 8 months with 3% Y537S ESR1, and fulvestrant and Abemaciclib resistant MCF-7 cells treated for 12 months with 30% Y537S ESR1.

first: Jessica

last: Stevens

first: Sarah

last: Herzog

first: Guowei

last: Gu

first: Sandra

last: Grimm

first: Kloma

last: Cardoza

first: Autumn

last: Hawkins

first: Hangqing

last: Lin

first: Daniela

last: Ramos

first: Amanda

middle: R

last: Beyer

first: David

last: Edwards

first: Derek

last: Dustin

first: Harry

last: Yang

first: Nicole

last: Liang

first: Cristian

last: Coarfa


title: Functionally heterogeneous intratumoral CD4+CD8+ double positive T cells can give rise to single positive T cells [scRNA-seq + scTCR-seq]

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave. N.

department: Immunotherapy Integrated Research Center

institute: Fred Hutchinson Cancer Center

summary: Conventional single positive (SP) CD4+ and CD8+ T cells recognize tumor antigens and help mediate clinical responses with cancer immunotherapy. Double positive CD4+CD8+ (DP) T cells have also been described in human cancers, but their role in the tumor microenvironment (TME) remains unclear. By generating a multi-omic single cell atlas of DP and SP T cells, we find that DP T cells possess phenotypic heterogeneity similar to SP T cells that includes multiple clonally expanded populations of cytotoxic DP T cells in human renal cell carcinoma (RCC). These intratumoral DP T cells can mediate by both MHC class I- and class II-dependent killing of autologous tumor cells. In addition, transcriptional profiling of DP TCR-bearing T cells revealed a gene signature enriched for clinical responders to PD-1 blockade in advanced RCC. We confirm prior observations of SP T cells transitioning into DP T cells and more notably, demonstrate that intratumoral T cells are capable of bidirectional differentiation in which DP T cells serve as precursors to SP T cells in vivo.  In the latter scenario, intratumoral DP T cells are shown to express Rag2, suggesting that the tumor may act as an extrathymic site of T cell development. These findings reveal the multiple roles that DP T cells can possess in anti-tumor immunity.

overall_design: To characterize T-cell heterogeneity in renal cell carcinoma (RCC), we performed single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing (scTCR-seq) using the 10x Genomics platform. Samples were collected from each patient’s tumor tissue, adjacent normal tissue, and peripheral blood mononuclear cells (PBMCs), along with PBMCs from healthy donors. To assign cells to their respective individuals following sequencing, we applied demuxlet, which leverages donor-specific genetic variants derived from bulk RNA-seq to enable genotype-based sample demultiplexing.

first: Tony

last: Li

first: Arielle

last: Illano

first: Marcel

last: Arias-Badia


title: Epitranscriptomic control of stress adaptations in Escherichia coli

city: Martinsried

first: Kirsten

last: Jung

address: Großhaderner Str. 2-4

country: Germany

institute: LMU

type: Non-coding RNA profiling by high throughput sequencing

summary: Bacterial stress responses have been studied at the phenotypic, transcriptional, and translational levels, demonstrating the presence of an “alarm” phase immediately after stress exposure. However, the contributions of RNA modifications during stress adaptation remain largely unexplored. Here, we map the epitranscriptomic changes of Escherichia coli after exposure to oxidative and acid stress using direct RNA sequencing of mRNA, rRNA, and tRNA, combined with mass spectrometry, deletion mutant phenotyping, and single-nucleotide PCR. We identified widespread, dynamic RNA modifications that include central metabolism transcripts and increased levels of rRNA methylations (m4Cm and m5C) under both stresses, with potential consequences for translation. In uncharged tRNAs, stress-specific modifications via the Mnm and Q pathways accumulated at the wobble position; these modifications proved crucial for survival. Together, these findings reveal a multifaceted layer of post-transcriptional regulation, establishing the first comprehensive view of the bacterial epitranscriptome during the alarm phase of stress adaptation.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA was extracted from two biological replicates each of wild-type E. coli cultured under standard growth conditions (no stress), medium with HCl added (acid stress), or medium with H2O2 added (oxidative stress) to measure RNA modifications throughout the transcriptome (mRNAe samples). Two replicates of in vitro transcribed RNA were synthesized from no-stress RNA samples as unmodified controls. Putative modifications were detected after samples were processed with direct RNA sequencing via Nanopore. A tRNA-specific preparation and sequencing protocol (Nano-tRNAseq) was also employed for the no-stress, acid-stress, and oxidative-stress samples.

first: Sebastián

last: Riquelme-Barrios

first: Siobhan

middle: A

last: Cusack

first: Luis

last: Rivera-Montero

first: Leonardo

last: Vásquez-Camus

first: Maximilian

last: Berg

first: G

last: Nur Yeşiltaç-Tosun

first: Stefanie

last: Kaiser

first: Pascal

last: Giehr

first: Korinna

last: Burdack

first: Brameyer

last: Sophie


title: Broad Profiling of Hepatic and Immunotoxic Effects of Per- and Polyfluoroalkyl Substances (PFASs) Across Sexes and Exposure Durations in C57/BL6 Mice

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Per and Poly-fluorinated alkyl substances (PFAS) are a class of chemicals commonly referred to as “forever chemicals”. Of this class, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) are frequently found in the environment and blood of Canadians. Here, we sought to broadly characterize the effect of PFOS and PFOA on liver toxicity and immunotoxicity in both male and female mice. Experimental mice were exposed to PFOA or PFOS for 28 or 56 days, followed by a comprehensive evaluation that included 6 organ weights, 8 serum biomarkers of liver toxicity, and transcriptomic analysis across 15 treatment conditions. This revealed that both compounds caused hepatomegaly, increased serum liver enzymes, pancreatic atrophy, and reduced serum triglycerides (TGL) regardless of sex or duration of treatment. Transcriptomics identified enrichment of PPAR signaling, lipid metabolism dysfunction, and AGE-RAGE pathways across groups which supports a role for metabolic and oxidative stress in PFAS-induced hepatotoxicity. To characterize immunotoxicity 19 cytokine profiles, and 3 tissue types including the thymus, spleen, and blood were assessed for changes in population dynamics. Immune effects were distinctly sex specific. In males, PFOS led to broad cytokine suppression (IL-4, IL-17α, TNF-α, MCP-1) and a non-significant increase in peripheral T cells following PFOA exposure. In contrast, females exhibited minimal cytokine changes but showed significant alterations in thymocyte development. Together, these findings reveal three key outcomes: (1) both PFASs cause liver and pancreatic toxicity, (2) hepatic effects are largely sex-independent, and (3) immune perturbations are highly sex-dependent. These results underscore the importance of evaluating sex-specific effects in immunotoxicology studies of persistent environmental contaminants.

overall_design: Male and female C57BL/6-Elite mice (6–9 weeks old) were acclimated for two weeks, individually housed (males) or paired (females), with controlled diet and water. Starting at 8–11 weeks old, mice were orally dosed daily via gavage with either PFOA or PFOS at varying doses (0.166 to 1.5 mg/kg/day) for 28 or 56 days. Control groups included vehicle (0.5% Tween 20) and naïve (no gavage) mice. Body weight was recorded daily, and water consumption was measured weekly. After the dosing period, mice were euthanized 24 hours post-final dose for blood and organ collection (liver, pancreas, kidneys, GI tract), which were weighed for analysis.

first: Amelie

last: Blais

first: Allison

last: Loan

first: Eunnara

last: Cho

first: Asia

last: Woodtke

first: Houman

last: Moteshareie

first: Lauren

last: Bradford

first: Zhang

last: Gong

first: Martha

last: Navarro

first: Andy

last: Nong

first: Rocio

last: Aranda-Rodriguez

first: Kristin

last: Eccles

first: David

last: Prescott

first: Azam

last: Tayabali


title: Results of the window-of-opportunity PIONEER trial evaluating addition of the progesterone receptor (PR) agonist megestrol to letrozole for early-stage estrogen receptor (ER) positive breast cancer: exploiting ER-PR interaction

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: The use of progestogens in breast cancer has been controversial. Recent preclinical studies have shown that progestogen-bound PR interacts directly with ER and reprograms ER transcriptional activity. Progestogen co-treatment also enhances the anti-tumor activity of anti-estrogen therapy in mouse xenografts. We report PIONEER (NCT03306472), a 198 patient, 3-arm, randomised phase IIb pre-operative window of opportunity study, which evaluated the anti-estrogen letrozole with or without megestrol at 40mg or 160mg daily. The trial met its primary endpoint, with a greater reduction in proliferation seen when megestrol was added to letrozole.  Mechanistically, this effect was accompanied by reduced ER genomic binding at canonical binding sites, indicating reduced ER transcriptional activity. These results support further evaluation of low dose megestrol, which has two parallel mechanisms for potentially improving breast cancer outcomes in combination with standard anti-estrogen therapy: alleviating. In addition to helping patients experiencing hot flashes as a side effect of treatmentand thereby helping with treatment adherence, megestrol has a and also a direct anti-proliferative effect. in breast cancer patients, when combined with standard anti-estrogen therapy.

overall_design: ChIPseq in core biopsies collected from breast cancer patients enrolled in the PIONEER trial before and after 15 days of treatment

first: Rebecca

last: Burrell

first: Sanjeev

last: Kumar

first: Danya

last: Cheeseman

first: Igor

last: Chernukhin

first: Richard

middle: D

last: Baird


title: MED12 dictates epithelial ovarian cancer cell ferroptosis sensi- 2 tivity via YAP-TEAD1 signaling

city: Guangzhou

first: Xiaolin

last: Luo

address: Dongfeng Road No.651

institute: Sun Yat-sen University Cancer Center

summary: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy, with 11 chemotherapy resistance representing a major therapeutic challenge. Emerging evidence 12 suggests that ferroptosis, an iron-dependent form of regulated cell death, may selectively 13 target chemoresistant cancer cells. Here, we identify MED12 as a critical regulator of fer- 14 roptosis sensitivity in EOC through modulation of the YAP-TEAD1 signaling pathway. 15 Using CRISPR/Cas9-mediated knockout and rescue experiments in EOC cell lines, we 16 demonstrate that MED12 deficiency significantly enhances sensitivity to ferroptosis in- 17 ducers (RSL3 and Erastin), as evidenced by reduced IC50 values. Transcriptomic and 18 chromatin accessibility analyses reveal that MED12 loss activates YAP signaling through 19 TEAD1 upregulation, increasing chromatin accessibility at YAP-TEAD1 target loci and 20 elevating expression of downstream effectors CYR61 and CTGF. Pharmacological inhibi- 21 tion of YAP with verteporfin or siRNA-mediated TEAD1 knockdown reverses ferroptosis 22 sensitivity in MED12-deficient cells, confirming pathway specificity. These findings es- 23 tablish MED12 as a modulator of the YAP-TEAD1-ferroptosis axis and suggest that tar- 24 geting this pathway could overcome chemoresistance in MED12-deficient EOC. Our work 25 provides a mechanistic foundation for exploiting ferroptosis induction as a therapeutic 26 strategy in ovarian cancer.

overall_design: RNAseq assay of HO8910 WT cells,  HO8910 MED12 KO1# cells and HO8910 MED12 KO2#


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice

first: Ally

last: Nicolella

address: 75 Ames St

institute: Broad Institute

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

overall_design: Refer to individual Series


title: Vitamin B12 promotes cefiderocol resistance and small-colony variants in carbapenem-resistant Acinetobacter baumannii.

city: Fullerton

first: M. S.

last: Ramirez

state: CA

address: 800 N. State College Blvd

institute: California State University Fullerton

summary: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a global health threat with few effective treatment options remaining. Cefiderocol, a last-resort siderophore-cephalosporin antibiotic, exploits bacterial iron transport systems via TonB-dependent receptors (TBDRs) to gain cellular entry. However, treatment failures and emerging resistance highlight the complexity of its activity in vivo. In this study, we report an unanticipated cefiderocol resistance mechanism, where vitamin B12, a commonly used micronutrient supplement, modulates cefiderocol susceptibility. Vitamin B12 affect and interact with TBDRs and other metabolic and adaptation processes contributing to increases cefiderocol MIC level and emergence of persistence phenotypes. We show that vitamin B12 supplementations leads to strain-specific transcriptomic responses in the CRAB AB5075 and AMA17 strains, showing downregulation of siderophore transporters, stress responses, metabolic reprogramming, and biofilm-associated genes. Structural modeling and molecular docking reveal overlapping binding sites for vitamin B12 and cefiderocol within key TBDRs such as CirA and PirA, suggesting competitive inhibition. Additionally, vitamin B12 exposure increases cefiderocol MICs across a panel of clinical and reference strains, enhances survival in time-kill assays, and promotes emergence of small colony variants with persistent phenotypes. Notably, this effect is stable, dose-dependent and further seen to be increased in the presence of host-derived fluids. These findings describe a previously unrecognized host–pathogen–drug interaction with potential clinical implications, suggesting that vitamin B12 exposure could contribute to cefiderocol treatment failure. Our results underscore the urgent need to consider vitamin supplements potential contribution in antimicrobial therapy and CRAB management strategies.

overall_design: Total mRNA of Acinetobacter baumanii AB5075 or Acinetobacter baumannii AMA17 was isolated from bacteria incubated either in LB broth or in LB broth supplemented with vitamin B12 (methylcobalamin, 100 µg/mL).

first: Maria

first: Rodrigo

last: Sieira


title: NMN protects cisplatin induced AKI via NAD+/SIRT1 pathway

city: nantong

first: Zhaozhi

last: Wen

state: jiangsu

address: Seyuan Road 9

institute: Nantong University

summary: Acute kidney injury (AKI) is a critical public health concern with high morbidity and mortality.Using male mice and HK-2 cells, we found that the NAD⁺ precursor NMN restored renal NAD⁺ levels and activated SIRT1, markedly lowering plasma creatinine and BUN, reducing NGAL and KIM-1 expression, suppressing IL-6/IL-18 and neutrophil infiltration, and attenuating ROS and LDH release. Thus, NMN protects against CIS-AKI via the NAD⁺–SIRT1 pathway and represents a promising therapeutic strategy.

overall_design: RNA-seq profiling of saline-treated control and cisplatin-treated mouse kidneys at 72 h post-injection.

first: Yihang

last: Yang

first: Jiazeng

last: Wang

first: Longlong

last: Chen

first: Xiangge

last: Ji

first: Dong

last: Liu

first: Chongxu

last: Shi