title: Circulating plasma microRNA expression in early-onset and late-onset coronary artery disease patients

city: Riga

first: Evija

last: Kanašniece

address: Dzirciema street 16

country: Latvia

institute: Riga Stradins University

summary: The prevalence of coronary artery disease (CAD) is increasing among young adults. To improve CAD diagnosis, microRNAs are being explored as potential minimally invasive biomarkers. The aim of this study was to evaluate circulating microRNA (miRNA) expression profiles and assess their value in predicting the development of early-onset CAD. A total of 108 patients with early- and late-onset CAD and 29 individuals without CAD were included, and their miRNA expression was evaluated. The diagnostic value of differentially expressed miRNAs across the subgroups was tested by logistic regression models and ROC curve analysis. A total of 287 different circulating miRNAs were analysed following sequencing and preprocessing. Seven miRNAs (miR-10b-5p, miR-29c-3p, miR-142-5p, miR-320b, miR-451a, miR-486-3p, and miR-625-3p) were found to be differentially expressed across all the study groups, four of which (miR-142-5p, miR-29c-3p, miR-451a, and miR-486-3p) were significantly downregulated in the late-onset CAD group compared with the control group. ROC analysis demonstrated that the combination of the seven miRNAs had high diagnostic accuracy, with an AUC of 0.9924 for distinguishing late-onset CAD from the other groups, and moderate accuracy, with an AUC of 0.8235 for distinguishing early-onset CAD from the other groups. A combination of seven circulating miRNAs (miR-10b-5p, miR-29c-3p, miR-142-5p, miR-320b, miR-451a, miR-486-3p, and miR-625-3p) is a promising biomarker panel for CAD diagnosis, distinguishing between early-onset and late-onset disease. While the panel demonstrated high accuracy in classifying late-onset CAD, its ability to predict early-onset CAD requires further validation. Larger, independent populations are needed to validate the predictive ability of the panel for early disease detection, confirm these findings, and improve generalizability.

overall_design: Prospective single-centre study of patients hospitalised for elective coronary angiography. Participants were stratified into three groups according to age and angiographic findings: non-CAD controls, early-onset CAD, and late-onset CAD. Fasting EDTA blood was collected, plasma was separated by centrifugation and stored at −80°C until processing. Total RNA including small RNAs was extracted from plasma, and small RNA libraries were prepared.

first: Kanasniece

last: Evija

first: Dauksaite

last: Viktorija

first: Vilne

last: Baiba

first: Gailite

last: Linda

first: Caunite

last: Laima

first: Erglis

last: Andrejs

first: Trusinskis

last: Karlis


title: Wnt/FGF20 signaling axis promotes migration of proximal blastema cell during tail regeneration of Gekko japonicus

status: Public on Nov 26 2025

city: Nantong

first: Man

last: Xu

address: No. 19 Qixiu Road

country: China

institute: Nantong University

type: Expression profiling by high throughput sequencing

summary: The Wnt/FGF20 axis establishes an organizing center that is largely non-proliferative in the distal blastema during epimorphic regeneration across multiple model systems. However, the underlying mechanisms remain poorly characterized. In this study, we investigate the role of the Wnt/FGF20 axis during tail regeneration in Gekko japonicus. We also developed an in vitro system to evaluate the effects of Wnt agonists, FGF20, and FGFR4 on cultured blastema cells. Our results demonstrate that Wnt signaling is activated in distal blastema cells and contributes to a lower proportion of proliferative cells beneath the epidermal basal layer in the regenerating tail of Gekko japonicus. This Wnt-mediated suppression of proliferation is associated with reduced FGFR4 expression, as confirmed both in vitro and in vivo. Furthermore, Wnt pathway activation upregulates FGF20 expression in distal blastema cells, which promotes the migration of proximal blastema cells without affecting their proliferation. Our findings provide insights into the organizing center of regenerated tissue, revealing a reciprocal regulatory interaction between the epidermis and blastema cells during successful epimorphic regeneration.

overall_design: RNA-seq profiling of  cultured blastema cells following SKL2001 treatment versus negative control.

first: Zhen

last: Li


title: Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [Treatment_Study_RNA-seq]

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

country: USA

institute: Baylor College of Medicine

summary: Most pediatric acute myeloid leukemia (pAML) patients achieve complete remission after chemotherapy. However, relapse remains common, and nearly 40% ultimately die of the disease. Prognosis is guided by cytogenetic biomarkers and measurable residual disease (MRD) after one chemotherapy cycle, at which point the highest-risk patients are referred to targeted experimental therapies and stem cell transplantation (SCT). Because these therapies are most effective before relapse, accurate early risk prediction is essential for improving outcomes. To address help this need, we analyzed paired diagnosis–relapse samples from 33 pAML patients at single-cell resolution and identified chemoresistant pAML populations whose abundance at diagnosis significantly improved risk prediction. Incorporation of these populations into a risk model uncovered a previously unrecognized subgroup—representing 20% of pAML cases—with event-free survival (EFS) below 40%, accounting for half of the deaths among patients that were not prescribed SCT after a cycle of chemotherapy. Furthermore, molecular characterization of these chemoresistant populations revealed therapeutic targets and targeted interventions relevant to most high-risk patients, paving the way for more effective treatments for high risk pAML patients.

overall_design: We profiled bone marrow samples from pAML PDX models treated with FLT3 and CDK4/6 inhibitors using bulk RNA sequencing.

first: Michele

middle: L

last: Redell


title: Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure

city: Oxford

first: James

last: Davies

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin structure is a key determinant of gene expression in eukaryotes but it has not previously been possible to define the full structure of regulatory elements at the scale of the proteins determining gene expression. Here we generate multidimensional chromosome conformation capture (3C) maps at single base-pair resolution using Micro Capture-C (MCC). This allows contacts between individual transcription factor binding sites within regulatory elements to be defined. Using degrons-we investigate the structural role of transcription factors and the Mediator complex. We show that the biophysical properties of nucleosomes and DNA can replicate the nanoscale chromatin structures observed with MCC using a detailed chemically specific, molecular dynamics approach. The ultra-high resolution 3C enable molecular dynamics approaches to be linked to larger scale nuclear architecture defined by super-resolution microscopy and allow us to propose a unified model to describe chromatin structure based on these orthogonal approaches.

overall_design: MNase libraries were prepared from murine embryonic stem cells.  Further information can be found in the Methods section of the paper.

first: Hangpeng


title: Cell layer-specific functions of the petal identity regulator PhDEF in petunia [ChIP-seq]

city: Lyon

first: Marie

last: Monniaux

address: 46 allee d'Italie

country: France

institute: ENS de Lyon

summary: We have employed a ChIP-Seq approached to identify the direct target genes of the petal identity regulator PhDEF in petunia flowers. In particular, we have applied this approach to wt and mutant flowers (named star and wico) where PhDEF is only expressed in a single cell layer (epidermis or mesophyll), which yields drastically different phenotypes. This study gives insight into the layer-specific function of an homeotic regulator in plants.

overall_design: Petals from wild-type, star and wico flowers at stage 8 (tube at about half its final size) were collected, flash-frozen and ground. Nuclei were extracted, fixated and sonicated to release the chromatin, that was incubated with an anti-PhDEF antibody. The immunoprecipitated chromatin (IP) and the control chromatin (INPUT) were sequenced by Illumina.

first: Emma

last: Désert


title: Acetyl-CoA dependent processes are preferentially supported by local metabolite synthesis

city: Philadelphia

first: Julianna

middle: Grace

last: Supplee

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: Multiple metabolic enzymes that classically function in cytosolic or mitochondrial pathways have recently been documented within cell nuclei, where they can directly impact gene expression and therefore cell phenotypes. Thus, the cell nucleus has emerged as an active site of metabolism. However, metabolites can passively diffuse across nuclear pores, and the extent to which the nucleus and cytosol are continuous versus distinct metabolic compartments remains unclear. Both the nucleus and cytosol require acetyl-CoA for specific processes (e.g., histone acetylation and lipid synthesis, respectively), and the acetyl-CoA producing enzyme ATP-citrate lyase (ACLY) is present in both locations, yet the biological significance of its nuclear-cytosolic distribution is incompletely understood. Here, we leveraged cell lines in which ACLY is restricted to either the nucleus or cytosol to investigate its compartmentalized functions. We find that ACLY in either location can support both fatty acid synthesis and histone acetylation, but compartment-localized ACLY enables fine-tuning of both processes. Nuclear ACLY preserves histone H3K23 acetylation under glucose limitation and modulates specific transcriptional programs, including suppression of fatty acid and cholesterol synthesis genes. Conversely, cytosolic ACLY most efficiently supports fatty acid synthesis and elongation, reflecting both local substrate production and increased expression of lipogenic enzymes. The data indicate that metabolites such as acetyl-CoA can diffuse between the nucleus and cytosol, but that local synthesis defines a preferential metabolic fate for products, enabling finer control of cellular processes.

overall_design:
Acly KO mouse embryonic fibroblasts (MEFs) expressing WT mCherry-tagged human ACLY (ACLY WT) with a nuclear export sequence (NES; ACLY-Cyto) or additional nuclear import sequences (NLS; ACLY-Nuc) were generated to study the role of ACLY subcellular localization. Acly KO MEFs expressing mCherry alone in the same vector were used as a control. Cells were cultured in either 10mM glucose (high glucose; HG) or 1mM glucose (low glucose; LG) for 24h were analyzed.
Please note that the 'ACLY_Cyto_3' sample in 10mM glucose was an anomaly and not included in the final analysis/publication.

middle: G

first: Pedro

last: Costa-Pinheiro

first: Karl

last: Wessendorf-Rodriguez

first: Christina

last: Demetriadou

first: Qihua

last: Yang

first: Stephanie

last: Stransky

first: Joy

first: Jennifer

last: Pennise

first: Mariola

middle: M

last: Marcinkiewicz

first: Simone

last: Sidoli

first: Nathaniel

middle: W

last: Snyder

first: Christian

last: Metallo

first: Ronen

last: Marmorstein

first: Kathryn

middle: E

last: Wellen


title: Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [ChIP-seq]

first: James

overall_design: To ensure the fully degradation of transcriptional factor NANOG, and Mediator subunit: MED14. We established mouse embryonic stem E14 cell lines in which target protein has been depleted employing degradation tag (dTAG) system, and check the level of occupancy of the target protein after dTAG13 treatment in different time points/

first: Hangpeng

last: Li


title: Transcriptomic profiling in equine IVF and ICSI embryos

city: Jouy-en-Josas

first: Alice

last: Jouneau

address: Domaine de vilvert

institute: INRAE

summary: In vitro production of equine embryos has been performed using intracytoplasmic sperm injection (ICSI) for the last two decades. Since 2022, a repeatable protocol for conventional in vitro fertilization (IVF) provides a successful alternative. However, little is known about the influence of the fertilization method on embryo quality and the transcriptomic profile. In this study, we aimed to examine differentially expressed genes (DEGs) between ICSI and IVF embryos in the horse. Therefore, ten equine sibling blastocysts, produced in vitro by either ICSI or IVF from three different mares, were subjected to Full-Length Single-Cell RNA-Sequencing (FLASH-sequencing). As such, 11,518 genes were identified, with only 1 DEG between ICSI and IVF embryos. Interleukin 4 induced 1 (IL4I1), a protein coding gene related to sperm cell death, was upregulated in IVF embryos (adjusted P-value = 0.01, FC = 2.84). Cleavage rates, calculated on collected COCs, of IVF zygotes (55.0%) were similar to those of ICSI zygotes (51.9%; P = 0.74), but blastocyst rates were higher following ICSI (37.0% vs 22.5% calculated on collected COCs and 71.4% vs 40.9% calculated on cleaved zygotes; P = 0.04 and 0.004, respectively). The average day of blastocyst development did not differ (P = 0.55). In conclusion, gene expression was similar for the two fertilization techniques, aside from one sperm related DEG, supporting the safety of equine IVF for further clinical studies. Overall, the horse provides a valuable model to study long-term effects of assisted reproductive technologies with potential extrapolation to human medicine. Keywords: Transcriptome, FLASH-seq, embryo, horse, IVP, fertilization

overall_design: Equine sibling embryos were created using OPU-ICSI or OPU-IVF from three mares (R, V, T) and a single stallion. Blastocysts were individually frozen (5 replicats). Library preparation was performed using the FLASH-seq method.

first: Klaartje

last: Broothaers

first: Daniel

last: Angel-Velez

first: Tine

last: De Coster

first: Nicola

last: Festuccia

first: Catherine

last: Archilla

first: Sophie

last: Calderari

first: Luc

first: Emma

last: Van den Branden

first: Sofie

last: Peere

first: Ellen

last: Polfliet

first: Manon

last: Dewulf

first: Jan

last: Govaere

first: Pascale

last: Chavatte-Palmer

first: Katrien

last: Smits


title: Venetoclax Enhances gamma-deltaT cell Antileukemia Activity via Fatty Acid Oxidation in Relapsed Acute Myeloid Leukemia.

city: hefei

first: Xing

middle: chi

last: Chen

state: Anhui

address: No. 9, Lujiang Road, Luyang District, Hefei City

institute: University of science and technology of China

summary: Relapse remains a leading cause of death in acute myeloid leukemia (AML), in part because host immune surveillance declines over time. Gamma delta (gamma-delta) T cells contribute to immune surveillance and have been linked to better outcomes in AML. Here we show that gamma-deltaT cells from patients with relapsed AML display reduced effector programs compared with those from patients in complete remission. In a targeted screen of approved AML drugs, the B-cell lymphoma 2 (Bcl-2) inhibitor venetoclax emerged as a potent enhancer of gamma-deltaT-cell cytotoxicity against primary AML blasts from both newly diagnosed and relapsed patients. Short ex vivo venetoclax exposure activated gamma-deltaT cells, increased proliferation, and lowered markers of exhaustion, thereby sustaining antileukemia activity over time. Venetoclax also increased mitochondrial respiration (oxidative phosphorylation) and respiratory reserve and shifted metabolism toward fatty acid oxidation. In AML xenograft models, adoptive transfer of venetoclax-pretreated gamma-deltaT cells, including chimeric antigen receptor (CAR)–engineered gamma-deltaT cells, produced superior tumor clearance compared with untreated cells. These findings indicate that venetoclax rejuvenates gamma-deltaT-cell function through metabolic remodeling and supports combining venetoclax with gamma-deltaT-cell–based immunotherapy for relapsed AML.

overall_design: This study investigated the effects of venetoclax on the transcriptomic profile of gamma-delta T cells in the context of acute myeloid leukemia (AML). Peripheral blood mononuclear cells (PBMCs) were collected from healthy donors. gamma-delta T cells were isolated and expanded ex vivo under standard conditions. For experimental samples, expanded gamma-delta T cells were treated with venetoclax for 18 hours; untreated gamma-delta T cells from the same donors served as controls. RNA was extracted from gamma-delta T cells (both untreated and venetoclax-treated) using, followed by poly(A) selection and library preparation. Sequencing was performed on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads. The dataset includes N = 3 donors with matched gamma-delta T (control) and venetoclax-treated gamma-delta T (experimental) samples. The primary comparison is venetoclax-treated vs untreated gamma-delta T cells.

first: Xingchi

first: Xiaoyu

last: Zhu

first: Lin

last: Zhang

first: Bingbing

last: Yan

first: Yinqiang

last: Sui

first: Weiwei

last: Ma

first: Yining

last: Wang


title: Single cell transcriptome profiling of Lrig1 quiescent stem cell populations

city: Madison

first: Yujia

last: Cai

address: 425 Henry Mall

institute: University of Wisconsin-Madison

summary: Identifying progenitor cells in laryngeal and vocal fold (VF) mucosa is essential for advancing stem cell-based tissue engineering and therapies for treatment of VF diseases. In this study, we used the Lrig1 gene as a marker for tissue-resident stem cells within murine laryngeal and VF mucosa. We show that Lrig1⁺ cells exhibited hallmark features of quiescent stem cells: slow-cycling, persistence and differentiation potential. Transcriptionally, they suppress transcription of cell type–specific genes and proliferation, while activating a global transcriptional program related to RNA metabolism, epigenetic regulation and protein ubiquitination – supporting quiescence and readiness for activation. Lrig1+ cells were enriched in basal, parabasal, and immature secretory populations and were spatially shielded from direct stress exposure to prevent their premature or chronic mobilization. Notably, we detected analogous Lrig1-expressing cells in human laryngeal and VF tissues, emphasizing the translational relevance of our findings. To investigate how Lrig1⁺ cell quiescence is regulated, we conditionally deleted Notch1, leading to epithelial hyperplasia, expansion of secretory cell populations, and mucus hyperproduction. In summary, Lrig1 marks a conserved, quiescent stem cell population in the larynx and VFs, with quiescence maintained through Notch1 signaling.

overall_design: We first genetically labeled Lrig1⁺ cells in Lrig1CreERT2/+;ROSALSL-tdTomato/+reporter mice, induced the Cre-recombination using tamoxifen injections and collected tissue at various timepoints - 1day, 3days, 1week, 2weeks and 2 months post recombination (for lineage tracing experiments). For transcriptional profiling, we used the same labeling and recombination approach and collected tissue 24 hours post-recombination. WT and ROSALSL-tdTomato/+ were included as negative and background controls for flow cytometry cell sorting. Cells were dissociated to generate single-cell suspensions, sorted based on tdTomato signal, and subjected to single-cell RNA sequencing using the 10x Genomics pipeline. To experimentally disrupt Lrig1⁺ cell quiescence in vivo, we conditionally deleted the Notch1 gene in Lrig1⁺ cells and investigated whether Notch1 deletion can lead to pathological mucosal remodeling, including epithelial hyperplasia and/or increased mucus secretion.

first: Vlasta

last: Lungova

first: Jessica

last: Fernandez

first: Christina

last: Kendziorski

first: Susan

last: Thibeault


title: Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis

city: Kansas City

first: Wen-Xing

last: Ding

state: Kansas

address: 3901 Rainbow Blvd.

department: Department of Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

summary: In this study, we first demonstrate that the expression levels of DNM1L, a key mitochondrial fission gene, are highly heterogeneous in human HCC samples. Specifically, DNM1L expression was significantly higher in some HCC samples and lower in others, suggesting abnormal expression patterns in human HCC. To investigate the role and mechanisms of mitochondrial dynamics in liver pathophysiology and tumorigenesis, we generated several genetically engineered mice that were either deficient in fission, fusion, or both, followed by rigorous histological and biochemical analyses, as well as multiple omics approaches.

overall_design: 2M and 6M Dnm1l KO, Mfn1/2 KO, and Dnm1l/Mfn1/2 TKO mouse liver were collected and send for RNA-Seq analysis.

first: Xiaowen

first: Xiaoli

last: Wei

first: Zheyun

last: Peng

first: Wanqing

last: Liu

first: Hongmin

last: Ni


title: Gene Expression Profiling Identifies Potential Biomarkers for Vaso-Occlusive Episodes in Sickle Cell Disease

city: Atlanta

first: Varsha

last: Bhat

state: Georgia

address: 950 Atlantic Drive, EBB1

institute: Georgia Institute of Technology

summary: Vaso-occlusive episodes (VOE) or acute pain events, involving complex interactions between sickle erythrocytes and other blood cells, are a hallmark symptom of sickle cell disease (SCD). In this study, we analyzed changes in peripheral blood transcriptomes between steady state and VOE in individuals with SCD. We followed a cohort of 174 individuals with SCD with or without chronic pain and collected peripheral blood at clinic visits (steady state) and during hospitalizations (VOE). We performed RNA-Seq profiling of CD45+ leukocytes and CD71+ erythroid cells. Pathways linked to complement activation, coagulation, and IL6-JAK-STAT3 signaling were enriched at VOE in the CD45+ cells. Contrastingly, the CD71+ cells showed an enrichment of pathways related to the cell cycle such as mTORC1 signaling and the G2M checkpoint. Expression of four genes—FAM20A, IL1B, MS4A4A, and SERPINB2—were elevated during VOE compared to steady state in a majority of patients.

overall_design: CD45+ cells and CD71+ cell samples were collected at steady state, during a vaso-occlusive episode and during follow-up. Gene expression profiling was peformed by RNA-Seq.

first: Justin

middle: J

last: Yoo

first: Srija

last: Ponna

first: Alka

middle: A

last: Potdar

first: Ashwin

middle: P

last: Patel

first: Guoying

middle: K

last: Yu

first: Greg

last: Gibson

first: Vivien

last: Sheehan


title: Dynamics of chaperonin function in live human cells

city: Martinsried/Planegg

first: Martin

last: Mueller

address: Am Klopferspitz 18

country: Germany

institute: MPI of Biochemistry

summary: The eukaryotic chaperonin TRiC/CCT plays an essential role in protein folding1-4. As shown in vitro, the cylindrical TRiC complex captures unfolded client proteins and facilitates their folding through ATP-regulated encapsulation5-8. However, the functional dynamics of the chaperonin system within the cellular environment remain largely unexplored. In this study, we developed single-particle tracking in live human cells to monitor the interactions of TRiC with newly synthesized proteins, as well as its interplay with the co-chaperone PFD. We found that PFD and TRiC engage nascent protein chains in repeated, brief probing events—typically lasting around one second—with PFD acting to recruit TRiC. Using actin as an obligate chaperonin client7, the co-translational interactions of PFD and TRiC increased in both frequency and lifetime during nascent chain elongation. Near the point of translation termination, PFD interactions lasted for ~6 seconds, enabling TRiC recruitment for post-translational completion of folding via multiple reaction cycles of ~2.5 seconds. Notably, the lifetime of TRiC cycles was 3-4 times longer when a folding-defective actin mutant was analyzed, indicating that the conformational state of the client protein modulates TRiC function. Mutant actin continued cycling on TRiC until being targeted for proteasomal degradation. Unexpectedly, TRiC remained confined near its client protein between successive binding cycles, suggesting that folding occurs within a localized ‘protective zone.’ Together, these findings offer the first detailed insights into the dynamic behavior and supramolecular organization of the chaperonin system in living cells. The methodology developed in this study offers a framework for systematically investigating protein folding within the intact cellular environment.

overall_design: Selective Ribo-seq of TRiC and PFDN performed in U2OS cells

first: Rongqin

last: Li

first: Niko

last: Dalheimer

middle: B

last: Müller

first: Ulrich

last: Hartl


title: IPSC-Derived CAR-NK Extracellular Vesicles Remodel Macrophage Immunity and Enhance Tumor Eradication

city: Chicago

first: Hao

last: Zhang

address: 1101 E. 58th Street, Chicago

institute: University of Chicago

summary: Chimeric antigen receptor (CAR) cell therapy has revolutionized the treatment of hematological malignancies; however, its efficacy in solid tumors remains limited due to dense stromal barriers and the immunosuppressive tumor microenvironment (TME), which hinder immune cell infiltration and persistence. To overcome these challenges, we propose an innovative strategy utilizing induced pluripotent stem cell (iPSC)-derived CAR-NK extracellular vesicles (CAR-iNEV), engineered from iPSC-differentiated NK cells. Unlike conventional CAR-NK cell therapies that rely on immortalized NK92 cell lines, our approach leverages iPSC-derived NK cells, reducing tumorigenic risk and enhancing CAR transduction efficiency. Additionally, we incorporate nanobody-based CAR constructs in place of traditional single-chain variable fragments (scFv), significantly improving CAR stability and expression efficiency. Beyond direct cytotoxicity, CAR-iNEV offers superior therapeutic advantages, including reduced systemic toxicity and enhanced drug delivery capabilities compared to CAR-iNK cells. In vivo studies demonstrate that CAR-iNEV exhibits exceptional safety and potent antitumor activity across multiple solid tumor xenograft and patient-derived xenograft (PDX) models in humanized mice. Mechanistically, CAR-iNEV not only directly eliminates tumor cells but also reprograms the TME by activating macrophage-derived nitric oxide synthase (NOS2), amplifying host antitumor immunity. These findings establish CAR-iNEV as a promising platform for solid tumor immunotherapy, particularly in relapsed and metastatic settings, providing a novel and effective strategy that bridges direct tumor targeting with immune microenvironment remodeling. This study lays the foundation for future clinical translation, advancing the next generation of cell-free CAR-based immunotherapies.

overall_design: To further elucidate the impact of CARCD133-iNEV on the TME, we performed single-cell RNA sequencing (scRNA-seq) on CD45⁺ immune cells isolated from tumor tissues collected two weeks post-treatment. Preliminary analysis revealed significant alterations in the composition of tumor-infiltrating immune cell subsets in the CARCD133-iNEV treatment group, suggesting a profound reprogramming effect on immune cells

first: Peng

last: Xia

first: Bin

last: Jin

first: Minghe

first: Jie


title: Flexible Nanoelectronics Show Reduction of Arrhythmogenesis in Transplanted Human Cardiomyocytes

city: Cambridge

first: Richard

last: Lee

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: The transplantation of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offers a promising avenue for cardiac repair. However, challenges such as arrhythmogenic automaticity arising from transplanted cells limit clinical translation. In this study, we investigated the effects of RADA16, a clinically approved self-assembling peptide that forms nanofibers after injection, on the vascularization, myofibril structure, and electrophysiological adaptation of hiPSC-CMs transplanted into rat hearts. RADA16 accelerated the transition of hiPSC-CMs to adult-like gene expression profiles, enhanced sarcomere organization, and improved vascularization in the transplanted site. Flexible mesh nanoelectronics revealed fibrillation of transplanted hiPSC-CMs within the beating recipient heart, and RADA16 dramatically reduced the automaticity of hiPSC-CMs. Our findings demonstrate the potential of self-assembling nanofibers to advance cardiac cell therapy.

sample_organism: Homo sapiens/Rattus norvegicus xenograft

overall_design: Human iPSC-derived cardiomyocytes were implanted into the left ventricles of athymic rats with or without co-injection of the self-assembling peptide RADA16 in order to assess sarcomeric maturation and vascularization at 7 and 21 days following implantation. All conditions were assessed utilizing a Slide-seqV2 protocol.

first: Lee

middle: T

last: Richard

first: Chen

last: Fei

first: Liu

last: Jia


title: Metabolic tuning enables immediate adaptation to energy stress in yeast

city: Edinburgh

first: Katherine

last: Bexley

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: In Saccharomyces cerevisiae, glucose depletion induces metabolic reprogramming through widespread transcriptional and translational reorganization. We report that initial very rapid translational silencing is driven by a specialized metabolic mechanism. Following glucose withdrawal, intracellular NTP levels drop drastically over 30 sec, before stabilizing at a regulated, post-stress set-point. Programmed translational control results from the differential NTP affinities of key enzymes; ATP falls below the (high) binding constants for DEAD-box helicase initiation factors, including eIF4A, driving mRNA release and blocking 80S assembly. Contrastingly, GTP levels always greatly exceed the (low) binding constants for elongation factors, allowing ribosome run-off and orderly translation shutdown. Translation initiation is immediately lost on all pre-existing mRNAs, before being selectively re-established on newly synthesized, upregulated stress-response transcripts. This response is unique to, and potentially de-risks, rapid glycolytic growth. We conclude that enzymatic constants are tuned for metabolic remodeling, allowing hierarchical inhibition of energy-consuming processes on very rapid timescales.

overall_design: RNAseq samples for BY4741 Saccharomyces cerevisiae in two conditions: 1) 'Sucrose', in which cells were grown at 30° in SC medium with 2% sucrose; and 2) 'NoSucrose', in which sucrose grown cells were collected by filtration, then transferred to sucrose-free medium containing 2% each of glycerol and ethanol.

first: Michaela

last: Ristová

first: Sushma

last: Sharma

first: Andrei

last: Chabes

first: David

last: Tollervey


title: Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery [Cut & Tag]

first: Fei

last: Ji

address: 250 Massachusetts Ave

institute: Novartis Biomedical Research

summary: Despite the improvement of therapeutic options for melanoma, patients with advanced metastatic disease are still in high need of durable and tolerated treatments. Analysis of clinical data from patients receiving targeted and/or immunotherapy, along with genetic and functional studies in preclinical melanoma models, show that lineage addiction to MITF is retained throughout disease progression, thus providing the rationale to pursue therapeutic inhibition of MITF. However, direct targeting of MITF or other basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors is unprecedented. Here, we report on the fragment-based discovery of high-affinity ligands for MITF. Fragment screening by NMR led to the discovery of weak binders to the kink pocket of MITF, which were optimized to sub-micromolar affinity by structure-based design enabled by crystallography and biophysics. Furthermore, NMR experiments and molecular dynamics simulations revealed a dynamic conformational exchange of the two helices in the asymmetric homodimer, which is perturbed by ligand binding. This work advances our knowledge on direct targeting of bHLH-LZ domains and sets the basis to further explore pharmacological inhibition of MITF.

overall_design: RNA-seq profiling of wild-type and MITF knocked-down (KD) in naïve (parental) or resistant to the Dabrafenib and Trametinib combination MELHO cells. MITF Cut&Tag chromatin profiling in WT and MITF mutant expressed UACC-257 cells

first: Deborah

last: Castelletti

first: Fanny

last: Mermet-Meillon

first: Aurore

last: Desplat

first: Kayhan Gabriel

last: Akyel

first: Edward

last: Oakeley

first: Ulrike

last: Naumann

first: Louise

last: Barys


title: Spatial molecular profiling of amygdalar neurons enables precision pharmacology against pain unpleasantness

city: Mountain View

first: Daniel

last: Berg

state: CA

address: 2005 California Street

institute: Stanford University

summary: Spatially resolved the expression of 97 genes encoding amygdala cell-type-selective marker genes, including novel gene markers identified from our scRNA-seq study of the amygdala.

overall_design: Individual mouse brains were dissected and amygdalas sections for single-molecular fluorescence in situ hybridization using Resolve Biosciences' Molecular Cartography platform.

first: Berg

last: Daniel

first: Scherrer

last: Gregory


title: Cell layer-specific functions of the petal identity regulator PhDEF in petunia

first: Marie

last: Monniaux

summary: We have employed a single-cell RNA-Seq approach using 10X Genomics Chromium to explore how the regulator PhDEF specifies petal identity in petunia. In particular, we have applied this approach to wt and mutant flowers (named star and wico) where PhDEF is only expressed in a single cell layer (epidermis or mesophyll), which yields drastically different phenotypes. This study gives insight into the layer-specific function of an homeotic regulator in plants.

overall_design: Petals from wild-type, star and wico flowers at anthesis were colleceted and cut into pieces in an enzymatic mix to obtain protoplasts. Protoplasts were purified by filtration and centrifugation, and viability was assessed before loading into the 10X chip.

first: Quentin

last: Cavallini-Speisser


title: Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands.

city: Gif-sur-Yvette

first: Virginia

last: Lioy

address: 1 Avenue de la Terrasse

department: Genome Biology

institute: Institute for Integrative Biology of the Cell (I2BC)

summary: Salmonella Pathogenicity Islands (SPIs) are horizontally acquired genetic elements integrated in the chromosome of Salmonella species, which allow them to infect and survive within their hosts. The nucleoid associated protein H-NS silences SPI gene transcription and this repression is counter-silenced at precise stages of the Salmonella infectious cycle. Bistable expression of the Type Three Secretion System 1 encoded in SPI-1 is a key step in the invasion of epithelial cells by Salmonella. In bacteria, transcriptionally active units form chromatin domains with specific dynamics and subcellular localization.  How chromatin domains are formed in physiological conditions remains poorly characterized. By applying a functional genomics approach to phenotypically similar Salmonella populations, we studied the remodeling of SPI-1 chromatin upon H-NS counter silencing. Our results show that although H-NS significantly reduces pervasive transcription, high H-NS occupancy co-exists with a low spurious transcriptional activity and low RNA polymerase occupancy at silent SPIs. When SPI-1 is expressed, we observe a remodeling of SPI-1 chromatin into domains that is dependent on the HilD transcriptional regulator. We uncovered the transcriptional signature of Salmonella cells expressing SPI-1 and determined that SPI-1 chromatin domains are associated with a variable distribution of H-NS occupancy and localized close to the nucleoid periphery. Our findings support a model in which the transcriptional activation of SPI-1 genes drives the chromatin remodeling and subcellular re-localization of this pathogenicity island.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Chromomosome conformation capture, RNA-seq and ChIP-seq of Salmonella enterica serovar Thyphimurium SL1344 WT and hilE mutant.

first: Mounia

last: Kortebi

first: Mickael

last: Bourge

first: Romain

last: Le Bars

first: Erwin

last: Van Dijk

first: Charles J

last: Dorman

first: Stéphanie

last: Bury-Moné

first: Frédéric

last: Boccard

first: Virginia S


title: Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery

first: Fei

last: Ji

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

overall_design: Refer to individual Series


title: Exploring the anti-influenza mechanism of erucic acid based on network pharmacology and transcriptomics

city: Guangzhou

first: liu

last: lifu

state: Guangdong

address: Panyu xinzao NO.1 Road

institute: Guangzhou Medical University

summary: Exploring the pharmacological mechanism of erucic acid in preventing and treating influenza pneumonia through transcriptomics

overall_design: A549 cells were infected with H1N1 virus and subjected to different concentrations of EA(0.3/0.6/0.9mM) or not. After a period of culture, total RNA was extracted for sequencing.


title: Humanized Monoacylglycerol Acyltransferase 2 mice Become Obese and develop Metabolic Dysfunction-Associated Steatotic Liver Disease when fed a High Fat Diet

city: Hamilton

first: Joseph

last: Nickels

state: New Jersey

address: 1000 Waterview Drive

department: Institute of Metabolic Disorders

institute: Genesis Biotechnology Group

summary: Objective: Elevated monoacylglycerol acyltransferase 2 (hMOGAT2) expression is seen in individuals having obesity and mice lacking mMGAT2 activity are resistant to diet-induced obesity. Whether hMOGAT2 inhibitors have therapeutic value in treating obesity requires the use of physiologically relevant pre-clinical models to test for drug efficacy. Methods: Here we characterized how humanized hMOGAT2 mice globally expressing hMOGAT2 responded metabolically to being fed a high fat diet.   Results: hMOGAT2 and mMgat2 mice  fed a high fat diet became obese, glucose-intolerant, and insulin resistant.  Blood triglycerides and cholesterol levels were markedly elevated, as were liver triglycerides.  Histological staining revealed the presence of metabolic dysfunction-associated steatotic liver disease (MASLD) and the beginning stages of metabolic dysfunction-associated steatohepatitis (MASH).  Liver and adipose pAKTSer473 levels were decreased indicating defects in insulin signaling leading to pre-diabetes.  Liver gluconeogenesis and de novo lipogenesis were likely increased based on the elevated gene expressions of Srebp2, Fasn, Pck1, and G6pc.  TGF-β1-driven hepatic stellate cell activation led to extracellular matrix formation and increased pJNK-pSMAD2 and pJAK2-pSTAT5 signaling, contributing to hepatocyte apoptosis.  Liver IL-4 and IL-13 levels were elevated further driving collagen deposition and the transition from MASLD to MASH. Conclusions: Results showing that humanized hMOGAT2  mice respond like mMgat2 mice lend support for their use as an in vivo preclinical efficacy model for testing hMOGAT2 inhibitors and for studying hMOGAT2 activity in the context of obesity

overall_design: RNA-Seq profiling of mMgat2 wild type and humanized HuMgat2 mice expressing human MOGAT2 fed a chow diet or a HFD for 16 weeks.  RNA-Seq analysis was performed at the end of the study.

first: Jose

last: Corbalan

first: Pranavi

last: Jagadeesan


title: Differential expression profiles of plasma exosomal microRNAs in obstructive sleep apnea patients

city: changsha

first: xing

last: lyu

address: NO.139 Renmin road

department: Laboratory Medicine

institute: The Second Xiangya Hospital, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Obstructive sleep apnea (OSA) is a prevalent respiratory disorder, with an estimated global prevalence of over one billion individuals, exhibiting a wide spectrum of severity. In this study, clinical data and whole blood samples were obtained from non-OSA individuals and OSA patients.we performed high-throughput sequencing to analyze differential expression of miRNAs between non-OSA exosomes (n=4) and OSA-Exos (n=6). This analysis identified 15 miRNAs exhibited significantly different expression levels between the two groups, with 7 upregulated and 8 downregulated in OSA-Exos compared to CON-Exos.

overall_design: miRNA profiling by high throughput sequencing

first: Xing

last: Lyu

first: Jingyao

last: Cai

first: Hui

last: Gong

first: Shisheng

last: Li

first: Min

last: Hu

first: Shengyu

last: Tan

first: Xiangyu

last: Zhang


title: Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [TT-Seq]

city: Oxford

first: James

last: Davies

address: John Radcliffe Hospital/Headley Way

institute: MRC Weatherall Institute of Molecular Medicine

summary: Chromatin structure is a key determinant of gene expression in eukaryotes but it has not previously been possible to define the full structure of regulatory elements at the scale of the proteins determining gene expression. Here we generate multidimensional chromosome conformation capture (3C) maps at single base-pair resolution using Micro Capture-C (MCC). This allows contacts between individual transcription factor binding sites within regulatory elements to be defined. Using degrons-we investigate the structural role of transcription factors and the Mediator complex. We show that the biophysical properties of nucleosomes and DNA can replicate the nanoscale chromatin structures observed with MCC using a detailed chemically specific, molecular dynamics approach. The ultra-high resolution 3C enable molecular dynamics approaches to be linked to larger scale nuclear architecture defined by super-resolution microscopy and allow us to propose a unified model to describe chromatin structure based on these orthogonal approaches.

overall_design: To investigate the transcriptional function of key transcriptional factors: SOX2 and NANOG, and Mediator subunites: MED14, MED13/13l and MED1. We established mouse embryonic stem E14 cell lines in which target protein has been depleted employing degradation tag (dTAG) system.  Differential experssion analysis was done between DMSO and coresponding dTAG-13 ligand treated samples using Deseq2.

first: Hangpeng


title: Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery [RNA-seq]

first: Deborah

last: Castelletti

first: Fanny

last: Mermet-Meillon

first: Aurore

last: Desplat

first: Kayhan Gabriel

last: Akyel

first: Edward

last: Oakeley

first: Ulrike

last: Naumann

first: Louise

last: Barys


title: Transcriptomic responses of the cyanobacterium Synechococcus sp. PCC 7002 under growth-inhibiting high CO2 concentration

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

summary: RNA-seq study that inverstigated the transcriptomics landscape of Synechococcus sp. PCC 7002 under air (0.04%), optimal growth (4 & 8%) and growth-inhibiting high (30% CO2) aeration.

overall_design: Grown in aqua culture with constant pH but varying CO2 levels

first: Adrian

middle: S

last: Geissler

first: Elena

last: Carrasquer-Alvarez

first: Jan

last: Gorodkin

first: Niels-Ulrik

last: Frigaard

first: Stefan

last: Seemann


title: Intragenic Epigenetic Deregulation by IDH2 Mutations Synergizes with SRSF2 Mutations Causing Mis-splicing of Key Transcriptional Regulators [BiSulfite-seq]

city: Miami

first: Aristeidis

last: Telonis

state: FL

address: 1550 NW 10th Ave

department: Biochemistry & Molecular Biology

institute: University of Miami

type: Methylation profiling by high throughput sequencing

summary: Genes impacting DNA methylation (DNAme), like IDH2, are frequently co-mutated with splicing factors, like SRSF2, in acute myeloid leukemia (AML). These co-occurring mutations are associated with more aggressive phenotypes but the underlying molecular mechanisms remain elusive. To address this gap, we profiled wild-type, IDH2R140Q or SRSF2P95 single-mutants and IDH2R140Q/SRSF2P95 double-mutant AMLs at a deep resolution level. We find a unique set of mis-spliced genes and differentially methylated CpGs in double-mutants. Mis-spliced exons are enriched in CCNG splicing enhancers and in the corresponding DNAme changes. Using a machine-learning model, we can accurately predict exon inclusion levels from proximal CpGs. These CpGs are more likely to overlap with footprints of RNA-binding and chromatin-modifying complexes but not transcription factors. We also report unique gene expression profiles associated with each genotype; however, the differentially expressed genes do not overlap with mis-spliced transcripts. Instead, the mis-spliced genes encode for proteins that interact with the gene regulatory complexes that control the expression of these differentially expressed genes. Thus, we propose a mechanism where synergism between aberrant DNAme and splicing leads to the mis-splicing of key components in gene regulatory complexes, thus resulting in the aberrant gene expression profiles characteristic of these AMLs.

overall_design: Clinical bone marrow or peripheral blood specimens were collected from 25 de-identified AML specimens. Mononuclear cells (MNC) were isolated through Ficoll density centrifugation at diagnosis. RNA and DNA were extracted for RNA sequencing and Whole Genome Bisulfite Sequencing, respectively.

first: Maria

last: Figueroa


title: Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [Capture-C]

first: James

overall_design: MCC libraries were prepared from murine primary erythroid cells, embryonic stem cells or hematopoietic stem and progenitor cells. Micro-Capture-C-Ultra (MCCu) integrates Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment to enable in-depth, targeted sequencing of chromatin interactions in specific regions of interest. Further information can be found in the Methods section of the paper.

last: Li

first: Joseph

middle: C

last: Hamley

first: Gianna

last: Bloye

first: Nicholas

last: Denny


title: Coordinated gene expression within persistent STAT3-associated chromatin conformations contributes to hepatocellular carcinoma progression [HiChIP]

city: Seoul

first: Sunyoung

last: Jang

state: Not required for this country

address: Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul

country: South Korea

institute: Sookmyung Women's University

summary: p-STAT3 has emerged as a critical modulator of hepatocellular carcinoma (HCC) progression; however, its role in 3D chromatin architecture and the expression of genes linked to HCC aggressiveness remains largely unexplored. Here, we elucidate the function of p-STAT3 in establishing stable regulatory regions known as FIREs, characterized by highly active interactions and the potential to alter topologically associated domains (TADs). Our results demonstrate that expression of genes located within FIREs is highly correlated, and upregulation, these genes play a crucial role in driving phenotypes, including HCC invasion and tube formation. Notably, p-STAT3-associated FIREs maintain chromatin activation despite pharmacological interventions targeting STAT3, suggesting a mechanism that failure to suppress the expression of genes associated with HCC aggressiveness leads to drug resistance. These findings provide novel insights into how the 3D genome structure associated with p-STAT3 promotes HCC progression and drug resistance, highlighting the therapeutic potential of targeting 3D chromatin dynamics in HCC.

overall_design: To further explore active chromatin interactions in HCC, HiChIP was conducted about active marker, H3K27ac in HCC cell lines.

first: Sumin

last: Yoon

first: Kyung

middle: H

last: Yoo


title: Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML PDX scRNA-seq]

city: Houston

first: Pavel

last: Sumazin

address: 1102 Bates St

institute: Baylor College of Medicine

summary: Most pediatric acute myeloid leukemia (pAML) patients achieve complete remission after chemotherapy. However, relapse remains common, and nearly 40% ultimately die of the disease. Prognosis is guided by cytogenetic biomarkers and measurable residual disease (MRD) after one chemotherapy cycle, at which point the highest-risk patients are referred to targeted experimental therapies and stem cell transplantation (SCT). Because these therapies are most effective before relapse, accurate early risk prediction is essential for improving outcomes. To address help this need, we analyzed paired diagnosis–relapse samples from 33 pAML patients at single-cell resolution and identified chemoresistant pAML populations whose abundance at diagnosis significantly improved risk prediction. Incorporation of these populations into a risk model uncovered a previously unrecognized subgroup—representing 20% of pAML cases—with event-free survival (EFS) below 40%, accounting for half of the deaths among patients that were not prescribed SCT after a cycle of chemotherapy. Furthermore, molecular characterization of these chemoresistant populations revealed therapeutic targets and targeted interventions relevant to most high-risk patients, paving the way for more effective treatments for high risk pAML patients.

overall_design: We profiled diagnosis-relapse pairs of samples from pediatric AML PDX models using sc-RNA-Seq technology.

first: Michele

last: Redell


title: Base pair resolution chromosome conformation capture reveals mechanistic insights into the nature of chromatin structure [ATAC-Seq]

last: Davies

first: Hangpeng


title: Coordinated gene expression within persistent STAT3-associated chromatin conformations contributes to hepatocellular carcinoma progression [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-Seq data depending IL-6 induction in Hep3B and Huh7 cell lines.


title: Coordinated gene expression within persistent STAT3-associated chromatin conformations contributes to hepatocellular carcinoma progression [CHIP-seq]

overall_design: To further explore the underlying epigenetic mechanisms of p-STAT3 and 3D genome structure in HCC, Chromatin Immunoprecification DNA-Sequencing (ChIP-Seq) was conducted about conventional markers of active euchromatin such as H3K27ac and H3K4me3, and transcription factors related with chromatin structure, CTCF, SMC1 and SMC3, as well as, p-STAT3. The profiling of these selected histone modifications and transcription factores were performed using ChIP-seq on control, IL-6-treated and sorafenib-treated cells.


title: Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML


title: Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML Patients Bulk RNA-seq]

overall_design: We profiled diagnosis-relapse pairs of samples from pediatric AML patients using bulk RNA-Seq technology.


title: Single-cell RNA Sequencing analysis of the impact of diabetes on the host response in periodontitis

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

summary: Diabetes exert a disruptive immune respose process. We use single-cell RNA-sequencing (scRNA-seq) data from gingiva from normalglycemic and diabetic mice to investigate the impact of diabetes on immune cells and to understand their role in host response.

overall_design:
Wild-type mice were CD11CCre-/-;FoxoLL mice, which are on a mixed C57B6 - FVB background. The loxP sites flank exon 2 of the Foxo1 gene and the Foxo1 protein produced in Cre- mice is normal.  To ensure that there was no insertion of LoxP sites in the exons, we checked alligned files and did not find any evidence of insertions.  Type-I diabetes mellitus was induced in mice using streptozotocin. Bacterial induced inflammation for two weeks, waiting period was two weeks. Cells were isolated from the gingiva, pooled from 4 mice per group with negative selection of dead cells (DAPI+), endothelial cells (CD31+), RBC (Ter-119+)and positive selection of CD45+ cells with 20% enrichment of CD11c+CD45+ cells by FACS sorting. 10,000 FACS sorted cells were loaded per lane of a 10x Genomics Chromium instrument for scRNA-seq analysis

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Submitter states they no longer have access to the raw data files.
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first: Bushra

last: Alghamdi

first: Min

last: Liu

first: Mi

last: Zhou

last: Troka

first: Dana

last: Graves


title: Molecular Plasticity Results in Oncofetal Reprogramming and Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

city: Heidelberg

first: Maximilian

last: Schönung

address: Im Neuenheimer Feld 280

department: Division Translational Medical Oncology

institute: German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg

summary: Single cell RNA-sequencing (scRNA-seq) of bone marrow hematopoietic cells from Ptpn11E76K/+ Scl-CreERT mice and Ptpn11+/+ Scl-CreERT controls.

overall_design: Bone marrow cells from three hematopoietic compartments (LSK, LK and total hematopoietic cells) were FACS-isolated 18 week after tamoxifen injection. Sequencing libraries were generated using the Single Cell 3’ Reagent Kit v2 (10x Genomics) and sequenced using a NovaSeq 6000 (Illumina) in PE 26/96 bp mode .

first: Daniel

last: Lipka

first: Mark

last: Hartmann


title: X chromosome crossover formation and genome stability in Caenorhabditis elegans are independently regulated by xnd-1

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The germ line efficiently combats numerous genotoxic insults to ensure the high fidelity propagation of unaltered genomic information across generations. Yet, germ cells in most metazoans also intentionally create double-strand breaks (DSBs) to promote DNA exchange between parental chromosomes, a process known as crossing over. Homologous recombination is employed in the repair of both genotoxic lesions and programmed DSBs and many of the core DNA repair proteins function in both processes. In addition, DNA repair efficiency and crossover distribution are both influenced by local and global differences in chromatin structure, yet the interplay between chromatin structure, genome integrity, and meiotic fidelity is still poorly understand. We have used the xnd-1 mutant of C. elegans to explore the relationship between genome integrity and crossover (CO) formation. Known for its role in ensuring X chromosome CO formation and germline development, we show that xnd-1 also regulates genome stability. xnd-1 mutants exhibited a mortal germ line, high embryonic lethality, high incidence of males, and sensitivity to ionizing radiation. We discovered that a hypomorphic allele of mys-1 suppressed these genome instability phenotypes of xnd-1 but did not suppress the CO defects, suggesting it serves as a separation-of-function allele. mys-1 encodes the histone acetyltransferase whose homolog Tip60 acetylates H2AK5, a histone mark associated with transcriptional activation that is increased in xnd-1 mutant germlines, raising the possibility that thresholds of H2AK5ac may differentially influence distinct germ line repair events. We also show that xnd-1 regulated him-5 transcriptionally, independently of mys-1, and that ectopic expression of him-5 suppressed the CO defects of xnd-1. Our work provides xnd-1 as a model in which to study the link between chromatin factors, gene expression, and genome stability.

overall_design: Identification of genes expressed in three groups (N2, XND-HC, XND-LC), with 2 groups of three replications and 1 group of two replications.

first: Judith

last: Yanowitz

first: M

last: Krause


title: YAP targets TEAD4-NF-κB complex and inhibits ccRCC tumor growth

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

summary: The prevalent understanding of Hippo signaling is one inhibitory pathway in tumor growth via deactivating the potential of YAP-TEAD transcriptional complex. The aberrant activation of YAP was observed in a series of human malignancies. However, recent studies implicate that in certain cancer types, YAP could be a tumor suppressor. Here, we reported a context-dependent function of YAP in clear cell renal carcinoma (ccRCC). Inhibition of Hippo kinase activity impeded ccRCC tumor growth and NF-κB transcriptional programs. Pharmacological blocking Hippo kinase activity or ectopic activation of YAP suppressed tumor growth in xenograft and PDX models. Mechanism studies revealed that TEAD could synchronize with P65 for NF-κB signaling activation, while YAP disrupted TEAD-NF-κB interactions and dissociated P65 from its target gene promoter, thereby inhibiting NF-κB transcriptional programs and ccRCC tumor growth. Our study identified a novel crosstalk between Hippo and NF-κB pathway, uncovered a non-canonical regulation of Hippo/YAP axis in renal cancer and suggested a novel strategy to ccRCC treatments by YAP activation.

overall_design: clear cell renal carcinoma mRNA samples were summarized in six samples, divided into two groups, Vehicle and XMU_MP_1

last: Li

first: Miao

last: YU

first: Jian

last: Zhu


title: Extensive remodelling of XIST regulatory networks during primate evolution

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

institute: Université Paris Cité

type: Genome variation profiling by high throughput sequencing

sample_organism:
Callithrix jacchus
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Refer to individual Series


title: Inactivation of Pkd2 in adult mice results in delayed cyst formation and identifies sex as a major modifier of disease severity

first: Luis Fernando

last: Menezes

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

institute: National Institutes of Health

summary: Autosomal Dominant Polycystic Kidney Disease (ADPKD) is caused by mutations in PKD1 or PKD2 and is the most common single gene disorder resulting in end-stage kidney disease. Since deletion of either Pkd1 or Pkd2 in mice is lethal, conditional alleles have become indispensable tools for studying the pathobiology of ADPKD as well as for preclinical testing. The rapidity of cyst formation in Pkd1 conditional mice depends on the timing of gene inactivation but this has never been formally studied for Pkd2. The objective of the present study was to characterize the kinetics of cystogenesis in a Pkd2 conditional mouse model and to identify associated alterations in gene expression. Here, we show that there is a similar developmental switch in Pkd2 conditional mice with delayed cyst formation after Pkd2 inactivation at or beyond P14. In addition, we find that similar to Pkd1, cystogenesis is associated with differential expression of genes involved in metabolism, cell proliferation and immune response. Our study confirms that sex is a key modifier of ADPKD progression with differences in disease severity occurring in the context of significant transcriptional differences between males and females that are independent of Pkd2 genotype. In summary, Pkd2 conditional mice are a useful model for understanding ADPKD pathogenesis and for testing therapeutics. Our data highlight the importance of sex as a biological variable that should be taken into account in any study design using orthologous mouse models with late Pkd2 inactivation.

overall_design: We performed RNA sequencing to investigate the transcriptional underpinnings of cyst formation in Pkd2 mutant kidneys using a late induction model. We induced Pkd2 deletion in Pkd2fl/fl; Pax8rtTA; TetOCre and control mice with IP DOX at P27-P29 and harvested kidneys at P125 from ten males and 10 females.  For each sex, there were N=5 Cre positive experimental mice and N=5 negative controls. At this stage (P125), both male and female kidneys were cystic with KW/BW ratio and cystic index significantly increased compared with controls of the same sex

first: Patricia

last: Outeda

first: Perry

last: Summers

first: Denis

last: Basquin

first: Ruizhen

last: Xu

first: Jessica

last: Hunt

first: Luis

middle: F

first: Terry

last: Watnick


title: Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML Patients scRNA-seq]

first: Pavel

last: Sumazin

overall_design: We profiled diagnosis-relapse pairs of samples from pediatric AML patients who were enrolled in AAML1031 treatment protocol using sc-RNA-Seq technology.

first: Michele

middle: L

last: Redell


title: scMultiome-seq and single-cell spatial HD data for the developing human knee

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. Compromises to the integrity of joint-lining articular cartilage in particular lead to debilitating chronic degenerative diseases including osteoarthritis. To better understand how human articular cartilage develops in vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femora at 2 fetal timepoints. We used these multiomic data to predict transcription factor-based regulatory networks that are important for articular chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and identified new biological roles for CREB5. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro.

overall_design:
Single cell epigenetic and transcriptomic profiling of cells isolated from human fetal femur at E59 and E72
Fresh knee samples were dissected out (along with the soft tissues surrounding them), flash frozen in OCT, and were processed using 10X Genomics visium spatial HD transcriptomics protocol. Each 10X genomics visium run has raw fatq files and input files

first: G

last: Senevirathne

first: Andrew

first: Divya

last: Venkatasubramanian

first: Terence

middle: D

last: Capellini


title: Combining CDK12 and BAF inhibition synergistically impairs cancer cell survival in triple-negative breast cancer line

status: Public on Nov 25 2025

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Chromatin profiling with CUT&Tag and CUTAC reveals that while CDK12 inhibition primarily disrupts DNA accessibility at Brg1 and CDK12 co-occupied promoters, BAF inhibition leads to widespread loss of enhancer accessibility. Co-inhibition causes a compounded disruption at shared co-occupied regulatory sites, resulting in loss of chromatin accessibility and transcriptional dysregulation at key loci.

overall_design: CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library.

first: Cassidy

last: Danyko

first: Monika

last: Macakova

first: Kami

last: Ahmad

first: Steven


title: AKAP2 coordinates a focal adhesion signaling scaffold to promote growth and metastasis in triple-negative breast cancer

first: John

last: Scott

address: 1959 NE Pacific St

institute: University of Waqshington

summary: A Kinase Anchoring Proteins (AKAPs) that coordinate spatiotemporal signaling are increasingly implicated in cancer. Elevated AKAP2 protein correlates with an invasive phenotype in triple-negative breast cancer cell lines. A combination of biochemical, cellular, and omics approaches show that AKAP2 cytoskeleton and focal adhesion associated scaffolds contribute to the progression of basal-like triple-negative breast cancer. Proximity proteomics identifies AKAP2 as an element of focal adhesions in MDA-MB-231 cells. Molecular and immunofluorescent microscopy studies demonstrate that AKAP2 indirectly constrains focal adhesion kinase (FAK). Gene silencing of AKAP2 not only decreases FAK levels but also attenuates the phosphorylation of the cell motility adapter protein paxillin on Tyr118. Cell-derived xenograft studies in mice establish that AKAP2 is required for triple-negative breast cancer growth and metastasis, phenotypes that are linked to FAK action. These findings discover a new role for focal adhesion-associated AKAP2 in triple-negative breast cancer pathology.

overall_design: RNAseq profiling of shScramble MDA-MB-231 cells and shAKAP2 MDA-MB-231 cells in the presence or absence of doxycycline. Doxycycline induces the expression of the shRNA promoter.

first: Kacey J

last: Rosenthal

first: John D


title: NF-𝜅B is a Central Regulator of Hypoxia-Induced Gene Expression

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

institute: University of Liverpool

summary: RNA-seq analysis investigating NF-𝜅B dependent transcriptional response following hypoxia stimulation

overall_design: HeLa cells were grown at 21% oxygen, treated with control siRNA and exposed to 0 hrs (control) or 24 hrs (control) 1% oxygen (hypoxia). HeLa cells were also treated with RelA, RelB or cRel siRNAs and exposed to 24 hrs 1% oxygen. RNA-seq was performed to measure differential transcript expression.

first: Dilem

last: Shakir


title: Lymphotoxin alpha eradicates acute myeloid leukemia and simultaneously promotes healthy hematopoiesis in mice

city: Graz

first: Sebastian

last: Vosberg

address: Auenbruggerplatz 15

country: Austria

institute: Medical University of Graz

summary: Acute myeloid leukemia (AML) is characterized by frequent relapse, which is driven by resistant leukemic stem or progenitor cells (LSCs). Here, we reported on a tumor-suppressive mechanism that can be harnessed to simultaneously clear LSCs and promote healthy hematopoiesis. Genetic deletion of the tumor necrosis factor (TNF) superfamily member lymphotoxin alpha (Lta) blocked cell death and accelerated leukemogenesis in murine AML models. Accordingly, exposure of leukemic cells to exogenous recombinant lymphotoxin alpha (LTα3) induced myeloid differentiation and, in part, cell death in AML progenitors. In syngeneic and patient-derived xenograft mouse models, exposure to recombinant LTα3 resulted in deep and durable remissions. LTα3 repressed leukemia by depleting tumor necrosis factor receptor (TNFR)-associated factor 2 (TRAF2) through activation of TNF receptors TNFR1 and TNFR2. In contrast with conventional therapies, LTα3 exerted only minimal toxicity on the healthy hematopoiesis but instead promoted hematopoietic progenitors. Leveraging this endogenous tumor-suppressive mechanism may decouple treatment efficacy on malignant cells from undesired bone marrow suppression.

overall_design: Cell lines or bone marrow from AML patients and healthy CD34+ HSPCs were treated with rhLTα3 and TNF for 24 hours and total RNA from primary cells was isolated using miRNeasy Mini Kit (Qiagen). Total RNA from AML cell lines (OCI-AML3 and MOLM-13) were isolated using peq gold total RNA kit (VWR). mRNA library was made with poly A enrichment using akit developed by Novogene (Novogene GmbH) and 150bp paired end sequencing was performed on Illumina Sequencing platform NovaSeq 6000. Raw sequencing data from cell lines and the count tables from primary samples were deposited in NCBI’s Gene Expression Omnibus (S.V. to include). NGS reads were mapped using STAR and differential gene expression was calculated with DESeq2. The reference genome for mapping was hg38, default parameters have been used for all individual steps. To count the gene expression the program “featureCounts” was used.


title: Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML PDX Bulk RNA-seq]

first: Pavel

overall_design: We profiled paired diagnosis and relapse samples from pAML PDX models using bulk RNA sequencing technology.

first: Michele


title: Intragenic Epigenetic Deregulation by IDH2 Mutations Synergizes with SRSF2 Mutations Causing Mis-splicing of Key Transcriptional Regulators [RNA-seq]

first: Aristeidis

middle: G

last: Telonis

overall_design: Clinical bone marrow or peripheral blood specimens were collected from 25 de-identified AML specimens. Mononuclear cells (MNC) were isolated through Ficoll density centrifugation at diagnosis. RNA and DNA were extracted for RNA sequencing and Whole Genome Bisulfite Sequencing, respectively.

first: Maria

last: Figueroa


title: Alloreactivity and autoreactivity converge to support B cell epitope targeting

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Ave. South

institute: University of Alabama at Birmingham

summary: Donor-specific antibody (DSA) responses against human leukocyte antigen (HLA) proteins mismatched between kidney transplant donors and recipients cause allograft loss. Using single cell, molecular, structural, and proteomic techniques, we profiled the HLA-specific (alloreactive) B cell response in kidney and blood of a transplant recipient with antibody-mediated rejection (AMR). We identified 14 distinct alloreactive B cell lineages, which spanned the rejected organ and blood and expressed high-affinity anti-donor HLA-specific B cell receptors – many of which were clonally linked to circulating DSA. The alloreactive B cell response was focused on exposed, solvent-accessible mismatched HLA residues, while also demonstrating extensive contacts with self-HLA residues. Consistent with structural evidence of self-recognition, measurable autoreactivity by donor-specific B cells was common and positively correlated with anti-donor affinity maturation. Thus, allo- and self-reactive signatures appeared to converge, suggesting that during AMR, the recognition of non-self and breaches of tolerance conspire to produce a pathogenic donor-specific adaptive response.

overall_design: After tissue processing, B cells and antibody-secreting cells (ASCs) from a rejected transplanted kidney and the peripheral blood of that same patient were sort-purified for bulk B-cell receptor IgVH sequencing and generation of single HLA-reactive recombinant monoclonal antibodies (rmAbs). rmAbs were utilized for experiments testing fine specificity, affinity, and binding structures. Plasma was affinity-purified against the donor HLA-A*01:01 to produce affinity-purified plasma Abs (appAbs) which were analyzed via proteomics.

last: Killian Jr

first: R

last: King

first: James

last: Kizziah

first: Christopher

last: Fucile

first: Ruben

last: Diaz-Avalos

first: Shihong

last: Qiu

first: Aaron

last: Silva-Sanchez

first: Betty

last: Mousseau

first: Kevin

last: Macon

first: Amanda

middle: R

last: Callahan

first: Guang

last: Yang

first: M

last: Hossain

first: Jobaida

last: Akther

first: Daryl

last: Good

first: Susan

last: Kelso

first: Julie

last: Houp

first: Frida

last: Rosenblum

first: Paige

middle: M

last: Porrett

first: Song

last: Ong

first: Vineeta

last: Kumar

first: Erica

last: Ollmann Saphire

last: Kearney

first: Troy

last: Randall

first: Todd

last: Green

first: Frances

last: Lund

last: Lucander


title: Venom-gland transcriptomic analysis of the predatory stink bug, Picromerus lewisi (Hemiptera: Pentatomidae)

city: Jingzhou

first: Jinmeng

last: Li

address: Chengnan

institute: Yangtze University

summary: Comparative gene expression profiling analysis of RNA-seq data from six  venom-gland samples belonging to the Ag and Ng groups. The transcriptome data of the venom gland of P. lewisi obtained in this study provide a theoretical foundation for identifying the components and studying the biological functions of P. lewisi venom.

overall_design: Eukaryotic Non-reference Transcriptome Sequencing of adult and 5th instar nymph of Picromerus lewisi

first: Xu

last: Tian

first: Hancheng

last: Wang

first: Wenhong


title: EGFR-mutant transformed small cell lung cancer harbors intratumoral heterogeneity targetable with MEK inhibitor combination therapy

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Small cell lung cancer (SCLC) transformation is an incompletely characterized mechanism of resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in EGFR mutant cancers, limiting development of optimal treatment approaches. Through single-cell RNA sequencing of malignant pleural effusions from patients who underwent SCLC transformation, we identified heterogeneity and diversity including distinct neuroendocrine (NE) and mesenchymal non-NE cancer cell subsets, which was maintained in patient-derived cell lines. We demonstrate that EZH2 regulates EGFR expression in NE cells where EGFR expression is silenced at baseline. Although neither epigenetic derepression nor exogenous overexpression of mutant EGFR sensitized the cells to EGFR inhibition, non-NE cells exhibited selective sensitivity to MEK inhibitors. Combined MEK inhibitor and chemotherapy effectively inhibited growth of both NE and non-NE cells in vitro and in vivo. Our findings demonstrate that EGFR mutant SCLC is composed of mixed cell states with distinct therapeutic vulnerabilities and offer a novel therapeutic strategy to target tumor heterogeneity in highly plastic and treatment-resistant malignancies such as SCLC transformed cancers.

overall_design: 4 Whole exome sequencing samples and 3 single cell RNA-Seq samples were generated from small cell lung cancer patient derived model

first: Ogino

last: Atsuko

first: Book

last: Matthew

first: Tolstorukov

last: Michael

first: Jänne

last: Pasi

first: Barbie

last: Dave

first: Oser

first: Paweletz

last: Cloud

first: Gokhale

last: Prafulla


title: An ancestral transmembrane transcription factor couples cell envelope regulation and the SOS response in Caulobacter crescentus

city: Odense

first: Clare

last: Kirkpatrick

address: Campusvej 55, 5230 Odense

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

summary: The DNA damage (SOS) response in bacteria involves derepression of a set of genes in order to activate mechanisms to tolerate stress, repair DNA and slow down cell division. While some of these genes are well characterized, many genes exist which are clearly induced by DNA damage but for which the function is unclear. In Caulobacter crescentus, the toxin-antitoxin (TA) system higBA and a closely associated downstream transcription factor (higX) are strongly induced as part of the SOS response, but the role of higX is unknown. We show that, unexpectedly, HigX functions independently of HigBA as a cell membrane-associated regulator and is toxic when overexpressed. ChIP-Seq indicated that it binds to several promoters associated with cell envelope regulation. In cells with the SOS response constitutively activated, HigX was overproduced, but at the same time was unable to bind the majority of its target promoters. higX was highly conserved in genomic context among many alpha-proteobacteria, while higBA was only found upstream of it in a small number of Caulobacter genomes, including the universal laboratory strain C. crescentus NA1000. Compositional analysis suggested that higBA originated from a foreign source, while higX is likely ancestral to the alpha-proteobacteria. Our data support a model where dysregulation of HigX production and activity in filamentous ΔlexA cells contributes to cell envelope instability and antibiotic sensitivity. Thus, the protective effect of inhibiting cell division during the SOS response in order to repair the DNA, carries the hidden cost of interference with HigX-mediated cell envelope maintenance.

overall_design: ChIP-Seq profiling of HigX in wild-type and delta-lexA strains to determine its binding sites

first: Kamilla

last: Brejndal

first: Nikolaj

middle: V

last: Hansen

first: Koyel

last: Ghosh

first: Sebastian

last: Nielsen

first: Lykke

first: Lene

last: Jakobsen

first: Martin

last: Larsen


title: Loss of KAT6B causes premature ossification and promotes osteoblast differentiation during development

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: The MYST family histone acetyltransferase gene, KAT6B (MYST4, MORF, QKF) is mutated in two distinct human congenital disorders characterised by intellectual disability, facial dysmorphogenesis and skeletal abnormalities, Say-Barber-Biesecker-Young-Simpson variant of Ohdo syndrome and Genitopatellar syndrome. Despite its requirement in normal skeletal development, the cellular and transcription effects of KAT6B in skeletogenesis have not been thoroughly studied. In this dataset, we examined the effects of loss of KAT6B on gene expression in proliferating primary mouse embryonic fibroblasts (MEFs) and MEFs induced to differentiated towards chondrocytes, osteoblasts and adipocytes. We show that loss of KAT6B in mesenchymal progenitor cells promotes transition towards an osteoblast-progenitor state with upregulation of gene targets of RUNX2, a master regulators of osteoblast development and concomitant downregulation of SOX9, a critical gene in chondrocyte development.

overall_design: RNA-sequencing data of mouse primary embryonic fibroblasts isolated from N = 4 Kat6b+/+ and N = 4 Kat6b–/– E12.5 mouse embryos, expanded and then grown in proliferating conditions and in conditions promoting chondrocyte, osteoblast and adipocyte differentiation.

first: Anne

last: Voss

first: Tim

last: Thomas


title: The retromer complex promotes apoptotic cell degradation during efferocytosis

city: Los Angeles

first: Bishuang

last: Cai

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

summary: Efficient clearance of dead cells, termed efferocytosis, is essential for maintaining tissue homeostasis. Although the cellular and molecular mechanisms regulating apoptotic cell (AC) internalization are well established, our understanding of AC digestion upon engulfment remains elusive. Here, we show that the retromer subunits are recruited to AC-containing phagosomes during efferocytosis and promote AC corpse degradation. Mechanistically, retromer stabilizes NOX2, a key regulator for LC3 recruitment to AC-containing phagosomes, leading to the maturation of phagolysosomes and corpse degradation. Meanwhile, TBC1D5, a binding partner for both retromer and LC3, also accelerates phagolysosomal maturation and AC degradation. Hence, our study indicates that retromer promotes LC3 recruitment and phagolysosomal maturation through stabilizing NOX2 and interacting with TBC1D5. This work elucidates a novel role of retromer in AC degradation and suggests a new avenue to explore the potential of retromer-stabilizing strategies to restore efficient AC clearance in disease.

overall_design: Mouse BMDMs treated with siVps35 and incubated with apoptotic cells (AC)

first: Xin

last: Huang


title: DNA methylation analysis of 293T cells expressing wild-type RUNX1 and a chimera protein RUNX11-299-SPI11-102

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: Transcription factor (TF)-dependent DNA demethylation is associated with generation of specific DNA methylation profiles in normal cellular development and disease, although only a small fraction of TFs are known to promote DNA demethylation. We examined DNA methylation profiles of 293T mock, 293T wild type RUNX1, and 293T RUNX11-299–SPI11-102 cells by reduced representation bisulfite sequencing analysis. Genome-wide DNA demethylation was observed specifically at RUNX1-binding sites in 293T cells expressing a chimeric protein consisting of RUNX11-299 and SPI11-102, similar to 293T cells expressing wild type RUNX1.

overall_design: 293T cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 U/mL, 100 mg/mL). The cells were infected overnight with the lentivirus vectors at a multiplicity of infection of 7–15 in the presence of 8 mg/mL polybrene, followed by puromycin selection at 3 µg/mL for 10 days. Genomic DNA was extracted from the 293T cells and subjected to the reduced representation bisulfite sequencing.

first: Xian-Yang

last: Qin

first: Harukazu

last: Suzuki


title: Effect of age, lysosomal degradation and mitochondrial replication on mouse hematopoietic stem cell

city: New York

first: Saghi

last: Ghaffari

state: , New York

address: 1468 Madison Ave

institute: Icahn  School of Medicine at Mount Sinai

summary: Aging impairs the function of hematopoietic stem cells (HSCs), promotes clonal hematopoiesis and myeloid malignancies, and contributes to immune decline in the elderly. The role of lysosomes – the cell’s primary degradation organelles –  beyond their passive mediation of autophagy in HSC aging remains unknown. Here, we show that lysosomes in aged HSCs are depleted, damaged, hyperacidic, and aberrantly activated compared to those in young HSCs. Using single-cell RNA sequencing (scRNA-seq) and functional analyses, we demonstrate that pharmacological inhibition of damaged hyperactivated lysosomes – by a vacuolar ATPase (v-ATPase) inhibitor  that blocks lysosomal hyperacidification – restores lysosomal integrity, as well as metabolic and epigenetic homeostasis in aged HSCs. This intervention also resolves inflammatory and interferon-related transcriptional programs by enhancing lysosomal processing of mitochondrial DNA (mtDNA) and suppressing intrinsic inflammation mediated by the cGAS–STING DNA-sensing pathway.

overall_design:
Freshly FACS-isolated hematopoietic stem cells [HSCs; lineage negative (Lin-) Sca1+ cKit+ (LSK) CD150+CD48- cells] from 8 weeks (young, Y) or 20 month-old (old, O) mice or HSCs cultured 16 hours in vitro in the presence of ConA (40 nM) or ddC (40uM) or non treated (NT). All conditions were assessed by scRNA-seq in addition to freshly isolated HSC from young or old mice.
Note: HSC from young mice cultured 16h without drug were labelled "Old-like_mHSC_Cultured".
For each samples, a barcodes.tsv, a features.tsc and a matrix.mtx are available.

first: Hossein

last: Khademian

first: Maxime

last: Batignes

first: Jiajing

last: Qiu

first: Mickaël

last: M. Ménager


title: Expansion of Pluripotent Stem Cells in a Closed Bioreactor System Guided by Automated In-Process Monitoring [CytoScanOptima_Array]

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

summary:
PluriTest score for iPSCs cultured for 7 days in a small bioreactor received a pluripotency score of 36.87 ± 0.12. n = 3. PluriTest score for iPSCs cultured in a standard bioreactor for 6 or 7 days was 41.28 ± 0.32. n = 3.
KaryoStat assays revealed no chromosomal or genetic mutations occurred in the iPSCs cultured in the small and standard bioreactors. n = 3.

overall_design: Quantum Flex Cell Expansion System (n = 3)

first: Itsuki

last: Kinoshita

first: Takaki

last: Yamaguchi

first: Nathan

last: Frank

first: Mindy

last: Miller

first: Masatsugu

last: Igarashi

first: Masayoshi

last: Tsukahara


title: Zone Equalisation Normalisation For Improved Alignment of Epigenetic Signal

city: Oxford

first: Simone

last: Riva

state: England

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington Oxford OX3 9DS

institute: University of Oxford

summary: High-throughput genomic technologies have transformed our understanding of biological systems, but analysing these complex datasets remains challenging. Existing normalisation methods often struggle to accurately correct for technical variations across different experimental conditions, potentially leading to misleading biological interpretations. We introduce Zone Equalisation Normalisation (ZEN), a novel approach designed to improve signal normalisation across genomic datasets. By developing a flexible method that reduces technical noise whilst preserving biological signals, ZEN addresses critical limitations in current normalisation techniques. By applying ZEN to diverse genomic techniques, we reveal its robust performance in managing technical variations across different experimental platforms. ZEN provides researchers with a robust tool for more accurate and reliable genomic data analysis, potentially revealing biological insights that were previously obscured by technical variations.

overall_design: CD34+ cells were harvest on day 13 for donors 002 and 003 and 7 replicates of bulk ATAC-seq performed for each.

first: Jim

last: Hughes


title: CSF1R-inhibitor resistant model for CNS-wide microglia replacement strategies

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: Recent advances in cell-based therapies have demonstrated therapeutic safety and efficacy for a variety of diseases. However, significant challenges remain in their development for the treatment of neurological disorders. Preclinical studies have explored microglial replacement strategies utilizing bone marrow transplantation and CSF1R-inhibitor (CSF1Ri) treatment. However, these approaches often require highly invasive strategies and result in engrafted cells that remain transcriptionally and functionally distinct from microglia. To assess less invasive microglia replacement strategies capable of preserving microglial ontogeny, we developed a Csf1r-G793A knockin mouse. We found G793A mice develop typical microglial densities and peripheral hematopoietic populations which exhibit broad CSF1Ri resistance enabling widespread microglia replacement following direct intraparenchymal injection or bone marrow transplantation. Furthermore, we demonstrate that widespread microglia replacement can be achieved via less invasive intracisternal delivery of CSF1Ri-resistant murine and iPSC-derived human microglia. Together with the accompanying study by Lombroso and colleagues, our findings demonstrate that G793A mice provide a robust and broadly applicable source of engraftable donor microglia and peripheral macrophages for the preclinical investigation of microglia replacement strategies.

overall_design: WT or Csf1R-G793A (C57BL/6J) mice were fed control, PLX3397 (290mg/kg), or PLX5622 (1200mg/kg) for 14 days to examine the effects of Csf1R-G793A  mutation (WT-control vs G793A-control), PLX3397 (WT-control vs WT-3397), and PLX5622 (WT-control vs WT-5622) on the brain transcriptome and whether CSF1R-inhibitor effects were prevented by Csf1R-G793A (WT-control vs G793A-3397) (WT-control vs G793A-5622). WT-control, n=3. G793A-control, n=4. WT-3397, n=4. G793A-3397, n=4. WT-5622, n=4. WT-5622, n=4

first: Jean Paul

last: Chadarevian


title: Mutant p53 binds RNA to drive mitochondrial dysfunction [RNA-seq]

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Tumor suppressor protein 53 (p53) is a transcription factor that is deregulated in 50% of cancers. Often termed the guardian of the genome, p53 is responsible for maintenance of genomic stability, cell cycle arrest, DNA repair, senescence, and apoptosis. In cancer cells, deregulation of p53 often occurs through mutations in the DNA binding domain which lead to a loss of the transcriptional activity. While 100’s of somatic mutations in the DNA binding domain are known, a small number of mutants are enriched in cancer, suggesting a gain-of-function role. Here we deploy an intein-based approach to localize µMap photoproximity labeling to p53 to define novel interactions contributing to the loss and gain of function roles of 5 separate hotspot mutants. These data revealed that G245S and R273H binds to RNA through its C-terminal domain. We show through CLIP experiments that mutant p53 has an RNA binding motif that conserved across mutants and is enriched in 3’UTRs, promoting ribosomal localization and labeling of proteins at the mitochondrial surface. We further demonstrate that the RNA binding ability of mutant p53 promotes altered miRNA processing and mitochondrial dysfunction providing mechanistic rationale for historically reported but poorly understood phenotypes.

overall_design: RNA-seq of HEK cells stably expressing wild-type or mutant p53, collected in biological triplicates. HEK cells expressing wild-type p53 served as the control.

first: Alice

last: Long

first: Cameron

last: Douglas

first: Dalila

last: Gallegos

first: James

last: Burke

first: David

last: MacMillan

first: Ezgi

last: Hacisuleyman

first: Ciaran

last: Seath


title: Beta vulgaris-Derived Exosome-like Nanovesicles Mitigate Photoaging by Attenuating Oxidative Stress and Promoting Collagen Biosynthesis Abstract

city: Changsha

first: Zhou

last: jian

address: renming road

institute: The Second Xiangya Hospital

summary: Differential gene expression (DEG) analysis identified a total of 1,316 significantly altered genes, with 852 genes upregulated and 464 downregulated in the BVNV-treated group compared to the UVB-irradiated control group. The significant upregulation of SPRR1A, SPRR1B, and KRT17, genes known to be crucial for keratinocyte proliferation and the formation of the epidermal barrier, indicates that BVNVs actively promote the restoration of the skin's physical barrier, a key defense mechanism compromised by UV exposure. Additionally, the expression of INHBA, which encodes the βA subunit of Activin A, was significantly increased. Activin A, a key ligand of the TGF-β signaling pathway, is a primary regulator of collagen synthesis. This provides a strong molecular link to the promotion of dermal matrix integrity. In summary, transcriptomic analysis shows that BVNV treatment modulates a series of genes critical for skin barrier integrity, cell proliferation, and extracellular matrix (ECM) remodeling. The data reveal that BVNVs coordinate multifaceted cellular responses by simultaneously enhancing skin barrier function and driving ECM remodeling through key signaling pathways, offering new insights into how BVNVs exert protective and restorative effects on photo-damaged skin through complex molecular networks.

overall_design: RNA sequencing analysis was performed on UVB-irradiated HaCaT cells and BVNV-treated UVB-irradiated HaCaT cells (n=3).

first: Jian

first: Meng-En

last: Guo


title: KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival

city: Stuttgart

first: Steven

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal cancer with a 5-year survival rate of 13%. Despite recent molecular stratification of tumors into distinct classical and basal-like cell states, most tumors are heterogeneous and contain both subtypes. Therefore, therapeutic approaches targeting only one subtype are unlikely to be effective as standalone PDAC treatments. Here, we integrated chromatin accessibility (ATAC-seq), genome-wide occupancy (ChIP-seq) for epigenetic status (H3K27ac) and H3K4me3-anchored chromatin topology (HiChIP) to uncover subtype-independent highly interactive enhancers that interact with essential genes in PDAC. Motif analysis revealed these common enhancers were bound by KLF5 with subsequent depletion leading to decreased cell viability via induction of apoptosis. To elucidate the transcriptional and epigenetic mechanisms by which KLF5 functions in PDAC, we employed rapid depletion of KLF5 with dTAG technology and profiled the effects on the open and active chromatin landscape and transcription with nascent RNA and mRNA-seq over time. Enhancer inactivation via KRAB domain Zim3-dCas9 fusion protein confirmed KLF5-bound enhancers regulate target genes, including the anti-apoptotic gene BCL2L1. Multiplex immunofluorescence confirmed co-staining of KLF5 and Bcl-xL in patient samples and overexpression of Bcl-xL rescued the induction of apoptosis after KLF5 depletion. Taken together, this study provides new insights into common mechanisms to target highly heterogeneous PDAC tumors.

overall_design: To investigate KLF5-dependent mechanisms of cell survival in pancreatic cancer, we performed ATACseq after dTAG treament in clonal L36pl cells with endogenous knockin of GFP-FKBP12 into the KLF5 locus after dTAG treatment. We also performed ATACseq under normal conditions in PDAC cell lines.

first: Thomas

last: Ekstrom


title: ERG lacking endothelium identifies IL8-CXCR2 axis as a therapeutic target  for resolving neutrophilic lung vascular injury

city: Chicago

first: Vijay Avin

last: Balaji Ragunathrao

state: IL

address: 835 S Wolcott Ave

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

summary: Neutrophilic inflammation and hyperpermeable lung microvasculature are consequential to lethal acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). The vascular endothelium is the first point of entry for neutrophils to breach and cause tissue injury. In this study we demonstrate that conditional deletion of ERG (ETS related gene) in adult endothelium of iEC-ERG-/- mice, spontaneously induces accumulation of neutrophils in the lungs. The infiltrated neutrophils showed altered transcriptome, enriched with genes that induce neutrophil recruitment and activation. These activated neutrophils induced lung vascular inflammatory injury. This study shows that endothelial ERG, instructs EC anti-inflammatory niche and thereby controls neutrophil accumulation and activation in the lungs. As the loss of ERG is observed in chronic lung injury, including ARDS, pulmonary hypertension (PAH) and fibrosis, our findings will have implications for understanding and therapeutically mitigating neutrophil function in inflammatory diseases.

overall_design: RNA sequencing (RNA-seq) was performed to investigate the endothelial ERG deletion effect of pulmonary neutrophils lungs in ERGfl/fl  & iEC-ERG-/- mice. Lung neutrophils were flow sorted using anti-CD45 and anti-Ly6G antibodies after tamoxifen injection and drug washout period from both ERGfl/fl  & iEC-ERG-/- mice (six mice per group pooled together). Total RNA was extracted using the RNeasy mini kit (Qiagen USA), and ribosomal RNA was depleted using the RiboMinus™ Eukaryote kit v2 (Thermo Fisher Scientific). RNA integrity was assessed using an Agilent 2100 Bioanalyzer; only samples with RNA integrity number (RIN) > 8 were used. RNA libraries were then constructed with the TruSeq RNA library prep kit v2 (Illumina) and sequenced using the NovaSeq 6000 platform with paired-end 150 bp reads.

first: Vigneshwaran

last: Vellingiri

last: Balaji Raghunathrao

first: Jagdish Chandra

last: Joshi

first: Md Zahid

last: Akhter

first: Mumtaz

last: Anwar

first: Somenath

last: Banerjee

first: Sayanti

last: Datta

first: Viktor

last: Pinneker

last: Dudek

first: Yoshikazu

last: Tsukasaki

first: Sandra

last: Pinho

first: Dolly

last: Mehta