title: Transcription-Replication Collision Shapes DNA Break Dynamics

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

institute: German Cancer Research Center

summary: Transcription and replication conflict (TRC) are one of the main driving forces for genome instability. Yet, TRC rarely been discussed without the context of DNA:RNA entanglement, rending the role of transcription in other TRC unclear . In neural stem and progenitor cells, genes encode protein regulating neuron adhesion are hotspots for recurrent DNA break clusters (RDC). While RDC-containing genes are all actively transcribed, most RDC lack DNA:RNA entanglement. We demonstrated that, through controlled gain and loss of function genetic approaches, transcription activity is essential while not sufficient to induce RDC formation. In combination of a deep neural network and single-nucleotide resolution DNA break mapping approaches, we found RDC break densities mirror the replication fork dynamics. We demonstrated that, for the first time that, head-on TRC results in higher DNA break density than its co-direction counterparts. In summary, our results revealed that transcription has a higher-level regulatory role that has to be coordinated with DNA replication.

overall_design: Two parental lines of mouse ES cell (NXP010, NXP047) were used for CRISPR-Cas genome editing to create daughter lines that lack one allele of Ctnna2 (47-5_Ctnna2_allele-B), Ctnna2 promoter-enhanced deleted ES cell clones (38-3_Ctnna2_allele-B_promoter-A and 18-4_Ctnna2_allele-B_promoter-A), or ES cell lines that lacks one allele of Nrxn1 (22_Nrxn1_allele-B), and ), and Nrxn1 promoter-enhanced deleted ES cell clones (22-5_Nrxn1_allele-B_promoter-A and 22-37_Nrxn1_allele-B_promoter-A). The parental ES cells and the derived ES cell clones were in vitro differentiated to neural progenitor cells (ESC-NPC). These ESC-NPC were used for nascent RNA analyses, the Global-run on Sequencing (GRO-seq). To determine early and late replciation profile, we performed two fraction Repli-seq to ESC-NPC lines that lack one allele of Ctnna2 or Nrxn1, and lines that removed the promoter-enhancer of Ctnna2 or Nrxn1. For mapping DNA breaks in aphidicolin treated ESC-NPCs, cells were treated with 0.3 uM aphidocolin with or without 5 nM ATR inhibitor VE-821 for 96 hours. For LAM-HTGTS in ESC-NPCs, we used Chr6 and Chr8 viewpoints (Chr6_70Mb, Chr8_61Mb). For mapping DNA breaks in the CAST/121-9 ES cells, we used an ES cell line that the Ptn promoter on the 121-9 allele is replaced with an tetracyclin reponding element. The ES cells were treated with or without 0.1 uM aphidicolin. To induce Ptn expression, cells were treated with 0.125, 0.25, or 0.5 uM tetracycline. Viewpoint on Chr6 (Chr6_70Mb) was used in the CAST/121-9 experiments.

first: Vivien

last: Ionasz

first: Sergej

last: Andrejev

first: Lorenzo

last: Corazzi

first: Ethan

last: Vouzas

first: David

middle: M

last: Gilbert


title: TertHigh Cells: Key Players in Salivary Gland Homeostasis and Regeneration after Radiation Therapy in Adult Mice

status: Public on Jan 01 2026

city: Stanford

first: Li

last: Guan

state: California

address: 269 Campus dr, CCSR, Room 1230

country: USA

institute: Stanford University, Radiation Oncology

type: Expression profiling by high throughput sequencing

summary: To gain insight into the mechanisms by which TertHigh populations regulate cell survival post radiation treatment, we conducted RNA-Seq analysis of sorted TertHigh and TertLow SMG cells treated with or without RT. In this experiment, 2-month-old TertCreERT2/+Rosa26LSL-tdTomato/+   mice were treated with tamoxifen, followed by RT after a 7-day interval. Subsequently, the SMGs were harvested and dissociated 36 hours after RT treatment. We isolated and separately sorted 10,000 TertHigh and TertLow cells for RNA sequencing.

overall_design: After sorting TertHigh  (DAPI-EpCAM+tdTomato+) and TertLow (DAPI-EpCAM+tdTomato-) cells from SMGs treated with or without RT, cells were subjected to RNA extraction and library preparation. 1ng of purified RNA was used for preparing the library according to the Dr. Picelli’s protocol. Illumina dual Indices were used for library multiplexing. RNA sequencing was performed by Novogene via Illumina platforms based on mechanism of SBS (Sequencing by synthesis).


title: Profiling R loop in mouse and human hematopietic cells with low cell input using S9.6 antibody coupled cut&tag [MOLM13]

city: NY

first: Bin

last: Lu

address: 417 East 68th Street New York,

institute: mskcc

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Present R loop profling oftern requires large amout of material, lacking information about R loop in primary cells. To overcome this setback, we delevopment low input method which integrates in vitro amplication capability of T7 promoter and high binding specificity between nanotag and IgH (mouse)

overall_design: R loop was first recognized and bond by S9.6 antibody, nanobody T5 which recognize mouse IgH kappa was later used to bind S9.6 and ennable the cutting of chromosome site in the vicinity of R loop loci. Fragmaentated DNA was in vitro trancribed by T7 promoter and reverse transcribed to get double strand DNA library for NGS sequencing.

first: Omar

last: Abdel-Wahab


title: Profiling R loop in mouse and human hematopietic cells with low cell input using S9.6 antibody coupled cut&tag

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Profiling R loop using S9.6 antibody coupled cut&tag

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

overall_design: Refer to individual Series


title: YTHDF1 mitigates acute kidney injury via safeguarding m6A-methylated mRNAs in stress granules of renal tubules

city: Nanjing

first: Wenwen

last: yang

address: 163 Xianlin Avenue, Qixia Districtc

country: China

institute: nanjing university

type: Methylation profiling by high throughput sequencing


title: YTHDF1 mitigates acute kidney injury via safeguarding m6A-methylated mRNAs in stress granules of renal tubules [MeRIP]

summary: The pathogenesis of acute kidney injury (AKI), a serious complication with no effective therapy available, is complex and multifactorial. Here we show that renal tubular m6A reader YTHDF1 mitigates AKI through selectively recruiting m6A-modified mRNAs, many of which are essential for cell proliferation and survival, into stress granules (SGs) and safeguarding these methylated mRNAs in SGs until stress relief. This study provides YTHDF1, as well as its associated m6A mRNAs and SGs, as novel therapeutic targets for AKI treatment.

overall_design: Detection of m6a methylated genes in human renal tubular epithelial cells(HK2 cells)

last: Yang

first: Ke

last: Zen

first: Limin

last: Li


title: YTHDF1 mitigates acute kidney injury via safeguarding m6A-methylated mRNAs in stress granules of renal tubules [RIP-Seq]

overall_design: Detect genes that binding with YTHDF1 in human renal tubular epithelial cells(HK2 cells)


title: ATACseq of human pancreatic acinar and ductal cells

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

department: Cell Systems & Anatomy

institute: University of Texas Health San Antonio

summary: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to molecular characterization to identify lineage-specific expression and epigenetic properties. Cells of both lineages were cultured and transformed via lentiviral mutation to form pancreatic ductal adenocarcinoma.

overall_design: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to ATACseq for differential analysis of chromatin accessability by lineage

first: Yi

last: Xu

first: Michael

middle: H

last: Nipper

first: Zhengqing

last: Ye

first: Naoki

last: Akanuma

first: Kevin

last: Lopez

first: Janice

middle: J

last: Deng

first: Aatur

middle: D

last: Singhi

first: Francis

middle: E

last: Sharkey

first: Huamin

first: Luzhe

last: Sun

first: Yidong

last: Chen

first: Jun

last: Liu


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [RNA-Seq]

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Fusing VP16  transcription activation domain with OCT4 and SOX2 (OvSvK) promoted the generation of induced pluripotency stem cells (iPSCs) by remodeling cell cycle and epigenetic modification. Multiomic analyses revealed that the other 80% upregulated genes experienced increase in H3K4me3 and decrease in H3K27me3 and were enriched with genes which undergo more intensive DNA demethylation during cell proliferation. Consistent results were obtained when siCcnd1, siCdkn2a and Ccne1 were screened out and used to mimic the cell cycle remodeling. In summary, these studies set up a correlation between epigenetic modification during cell cycle remodeling and cell fate conversion.

overall_design: For bulk RNA-seq, cells were infected with O, S, K, OS, OK and SK respectively and collected at  post-infected Day0. For single-cell RNA-Seq, reprogramming cells were collected at post-infected Day0, Day1, Day2, Day3 and Day4 using Fluidigm C1. For ATAC-seq, cells were infected with hCdt1 and hGeminin and also OSK or OvSvK. Cells at different cell cycle stage were isolated by fluorescence-activated cell sorting (FACS). For CUT&Tag, cells infected with OSK or OvSvK and collected at post-infected Day3 and Day2 respectively.

first: Lin

last: Guo


title: Hypertension has stage-dependent signatures in the hypertensive rat frontal brain

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

country: Germany

institute: University Wuerzburg

summary: Long-term arterial hypertension causes cerebral microvascular dysfunction and doubles dementia risk in aging. However, cognitive health preservation by therapeutical blood pressure lowering alone might be limited by disease duration, the degree of irreversible tissue damage and whether microvascular function can be restored. This study aimed to understand cellular and molecular temporo-spatial pathomechanisms in the course of arterial hypertension. We investigated initial, early chronic and late chronic hypertension effects in the frontal brain of hypertensive rats by applying behavioral tests, histology, immunofluorescence, FACS and microvascular/neural tissue RNA sequencing as well as 18F-FDG PET imaging. Chronic hypertension caused frontal brain-specific behavioral deficits. From a mechanistic perspective our results suggest continuous microvascular stress and wounding due to hypertension, which in turn leads to an early recruitment of activated microglia and peripheral immune cells, blood-brain-barrier breakdown and an energy-demanding hypermetabolic state. Vascular adaptation mechanisms e.g., vessel wall strengthening by production of cellular adhesion molecules and extracellular matrix (ECM), and angiogenesis were first observed first in late chronic stages. Additionally, we identified late-chronic vascular accumulation of Igfbp-5 in the brains of rats and humans with hypertensive cerebral small vessel disease, possibly attenuating protective Igf-1 signaling in the cerebral microvasculature. Thus, we characterized cellular and molecular temporo-spatial pathomechanisms in the course of arterial hypertension, that might represent critical points for clinical decision-making and could therefore be used to prevent irreversible tissue damage.

overall_design: Total number of samples is 38

first: Philipp

last: Ulbrich

first: Lorena

last: Morton

last: Briese

first: Naomi

last: Lämmlin

first: Hendrik

last: Mattern

first: Mohammed

last: Hasanuzzaman

first: Melina

last: Westhues

first: Mahsima

last: Khoshneviszadeh

first: Daniel

last: Gündel

first: Magali

last: Toussaint

first: Peter

last: Brust

first: Torsten

last: Kniess

first: Anja

last: Oelschlegel

first: Jürgen

last: Goldschmidt

first: Sven

last: Meuth

first: Hans-Jochen

last: Heinze

first: Grazyna

last: Debska-Vielhaber

first: Stefan

last: Vielhaber

first: Axel

last: Becker

first: Alexander

last: Dityatev

first: Deniz

last: Yilmazer-Hanke

first: Solveig

last: Jandke

last: Sendtner

first: Ildiko

last: Dunay

first: Stefanie

last: Schreiber


title: CUT&Tag sequencing of human pancreatic acinar and ductal cells

first: Pei

last: Wang

overall_design: Flow-sorted pancreatic acinar and ductal cells from fresh human pancreatic exocrine tissue were subjected to CUT&Tag sequencing with antibodies for H3K4me1 and H3K27ac, for differential analysis of epigenetic state by lineage

first: Yi

last: Xu

first: Michael

last: Nipper

first: Zhengqing

last: Ye

first: Naoki

last: Akanuma

first: Kevin

last: Lopez

first: Janice

last: Deng

first: Aatur

last: Singhi

first: Francis

last: Sharkey

first: Huamin

first: Luzhe

last: Sun

first: Yidong

last: Chen

first: Jun

last: Liu


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [ATAC-Seq]

first: Hui

last: Zheng

overall_design: Cells were infected with hCdt1-mCherry and hGeminin-mCitrine and also OSK or OvSvK. Cells at different cell cycle stage were isolated by fluorescence-activated cell sorting (FACS).

first: Lin

last: Guo


title: Role of RNA-binding protein PTBP1 in viral RNA nucleocytoplasmic transport and in HSV-1 infection

first: Zhang

last: Mengyu

address: HanKou road 22

institute: Nanjing university

summary: Here we show that HSV-1 infection promoted PTBP1 nucleocytoplasmic translocation. PTBP1, an RNA binding protein, interacted with both cellular and viral RNA. Suppression of PTBP1 expression blocked HSV-1 lytic infection. Furthermore, we observed that acute PTBP1 suppression during HSV-1 lytic infection promoted HSV-1 latency that occurred with cell type conversion from fibroblast cells to neuronal-like cells. This demonstrates that a cellular factor PTBP1 plays an essential role in viral RNA nuclear export and in HSV-1 lytic infection. Additionally, a cell type conversion based on PTBP1 suppression may provide a basic model for delineation of host and viral factors governing HSV-1 lytic and latent infection within the same cell lineage of transcription regulation.

overall_design: Utilize  a native RNA immunoprecipitation (RIP) assay to identify PTBP1-interacted host and viral RNAsRNA-seq  in human HeLa cells. Utilize RNA-seq to comprehensively analyze the effect of PTBP1 suppression on host gene expression in N2a cells

first: Weikang

first: Mengyu

last: Zhang

first: Zhiqiang

last: Huang

first: Ergang

last: Li


title: YTHDF1 mitigates acute kidney injury via safeguarding m6A-methylated mRNAs in stress granules of renal tubules [RNA-Seq]

first: Wenwen

last: yang

overall_design: RNA sequencing was used to detect mRNAs in stress granules from HK2 cells which induced by hydrogen peroxide, heat shock or FG4592.

last: Yang

first: Ke

last: Zen

first: Limin


title: Comparative analysis of the cardiac structure and transcriptome of scallop and snail, perspectives to heart evolution

city: Qingdao

first: Long

last: Zhao

address: 5 Yushan Rd

institute: Ocean University of China

summary: As a vital organ to pump blood in the circulatory system, the heart has undergone gradual refinement in its structure and functional efficiency along animal evolution. The occurrence of cardiac chambers, the atrium and the ventricle, is an important event during heart evolution.The two-chambered heart, consisting of a single atrium and a single ventricle, first appeared among mollusks, prior to the evolution of multi-chambered hearts in higher vertebrates. The molecular bases driving the evolution of cardiac chambers, however, are largely unknown. In this study, we studied two common mollusks, the giant African snail (Lissachatina fulica) and scallops (Mizuhopecten yessoensis), to explore the gene profiles of atrium vs. ventricle in mollusks. By examining their heart structures, we found that the snail heart possesses a more compact muscle layer than the scallop heart. Then, RNA sequencing and differentially expressed genes (DEGs) analysis of the atrium and ventricle revealed that these two chambers are distinct in gene expression preference and functional features. Moreover, by comparing with the zebrafish heart, a typical two-chambered heart in vertebrates, mollusk ventricles share similar gene function enrichments with the zebrafish ventricle, but their atria exhibit obvious variation in functional clusters from the zebrafish atrium. Interestingly, we also found that the scallop hearts contain a high amount of collagens, which could be beneficial for heart repair after damage. Together, our work presented novel gene profiling data in the mollusk atria and ventricles, thereby providing new insights into the evolution of cardiac chambers.

sample_organism:
Mizuhopecten yessoensis
Lissachatina fulica

overall_design: To systematically profile the cardiac gene expression in adult scallop and snail hearts, their atria and ventricles were separately  collected, and RNA sequencing for these samples was performed.

first: Meina

last: Lu

first: Xuejiao


title: Triclocarban affects early embryo development in mouse through disrupting maternal-to-zygotic transition and epigenetic modifications

city: Wuhan

first: Jing-Jing

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

summary:
To explore the effect of TCC on mouse preimplantation embryo development, we collected the in vivo fertilized eggs, treated them with 0, 2, 4 and 6 µM TCC, respectively, and observed the early embryo development of the control and TCC treatment groups.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control and TCC-treated embryos.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and TCC-treated embryos.

first: Zhi-Ming

last: Ding

first: Shang-Ke

last: Wang

first: Yi-Liang

last: Miao


title: Dual inhibition of CDK4/6 and XPO1 induced senescence with acquired vulnerability to CRBN-based PROTAC drugs

city: Shanghai

first: Hui

address: Building 5, No.1630 Dongfang Road

institute: Shanghai Cancer Institute

summary: We treated liver cancer cells with vehicle, CDK4/6 inhibitor, XPO1 inhibitor and the combination. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or CDK4/6 inhibitor, XPO1 inhibitor and the combination treated liver cancer cells. CDK4/6 inhibitor, XPO1 inhibitor and the combination induced expression changes were obtained based on the processed data.

overall_design: Examination of the transcriptome changes of liver cancer cells treated with CDK4/6 inhibitor, XPO1 inhibitor or the combination.


title: Induced regulatory B cells stably expressing IL-10 cure CNS autoimmunity by targeting microglia

city: Saarbrücken

first: Annemarie

last: Jungmann

address: Campus, building A 2.4

department: Genetics / Epigenetics

institute: Saarland University

summary: B cells can control autoimmunity through interleukin(IL)-10 production. However, there is no protocol to efficiently generate IL-10-producing B cells, which limits the understanding of their differentiation and their development for cell therapy. To overcome this limitation, we performed a high throughput screen and identified a novel small molecule enabling the induction of quasi pure and stable IL-10-producing B cells. These B cells prevented the development of experimental autoimmune encephalomyelitis and cured recipient mice from disease within a few days upon administration at the peak of clinical signs. Their therapeutic effect involved IL-10 provision to microglia and was independent of their cognate interaction with CD4+ T cells. This study reports the generation of induced regulatory B cells (iBregs) for cell therapy against immune-mediated inflammatory diseases.

overall_design: B cells were isolated from spleens and cultured for up to 7 days in different conditions: either with N6 compound, CpG or DMSO controls. Cells were harvested, nuceli were prepared and tagmentation was performed. Libraries fro ATAC-seq were generated and sequenced.

first: Benoît

last: Manfroi

first: Gilles

last: Gasparoni

first: Abdulrahman

last: Salhab

first: Jörn

last: Walter

first: Simon

last: Fillatreau


title: Effect of olanzapine and aripiprazole supplemented diet treatments on gene expression of WT and PTP1B KO mice liver

city: Madrid

first: Mónica

last: Ruíz Rosario

state: Madrid

address: 7, Calle Faraday

country: Spain

institute: NIMGenetics

summary: Aripiprazole and olanzapine are atypical antipsychotics used mainly for schizophrenia treatment. Despite their advantages, they produce endocrine and cardiometabolic side effects. To understand their impact on the development of metabolic diseases, we compared the gene expression of liver samples from treated and untreated mice. Because PTP1B deficient mice are protected against insulin resistance and obesity induced through the diet, we also compared the gene expression of treated PTP1B KO Vs WT mice to understand if PTP1B deficient may confer protection against these antipsychotics metabolic side effects.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver samples from WT mice treated with olanzapine Vs WT mice untreated, WT mice treated with aripiprazole Vs WT mice untreated, PTP1B KO mice treated with olanzapine Vs PTP1B KO mice untreated, PTP1B KO mice treated with aripiprazole Vs PTP1B KO mice untreated, PTP1B KO mice treated with olanzapine Vs WT mice treated with olanzapine, PTP1B KO mice treated with aripiprazole Vs WT mice treated with aripiprazole and PTP1B KO mice untreated Vs WT mice untreated

first: Vítor

last: Ferreira

first: Ángela

last: Valverde

first: Juan

middle: C

last: Cigudosa


title: Arsenite exposure disturbs maternal-to-zygote transition by attenuating H3K27ac during mouse preimplantation development [ChIP-seq]

last: Zhang

summary: Arsenite is mainly used as insecticides, antiseptic and herbicides. It enters the food chain through soil contamination, and then impedes human health, including of reproductive systems. Early embryos, as the initial stage of mammalian life, are very sensitive to the environmental toxins and pollutants. However, whether and how arsenite disturbs the early embryo development remains unknown.  Here, we used mouse early embryo as a model and found that arsenite exposure did not induce reactive oxygen species production, DNA damage and apoptosis in early mouse embryos. However, arsenite exposure made embryonic development arrest at the 2-cell stage by altering their gene expression patterns. The transcriptional profile in the arrested embryos showed abnormal maternal-to-zygote transition (MZT). More importantly, arsenite exposure attenuated H3K27ac modification enrichment at the promoter region of Brg1 (a key gene for MZT), which inhibited its transcription, and further affected MZT and early embryonic development. Taken together, these results suggest that arsenite exposure affects MZT by reducing the enrichment of H3K27ac on the embryonic genome, and ultimately induces early embryonic development arrest at the 2-cell stage.

overall_design: The ChIP-Seq experiments of the control and arsenite treatment 2-cell embryo.

first: Longtao

last: Yu

first: Xin

last: Liu


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [CUT&Tag]

last: Zheng

overall_design: Cells infected with OSK or OvSvK and collected at post-infected Day3 and Day2 respectively.

first: Lin

last: Guo


title: Activity of PDGFRA inhibitor Avapritinib in H3K27M Diffuse Midline Glioma

city: Boston

first: Jenna

last: LaBelle

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary:
PDGFRA is commonly altered in pediatric high grade gliomas including in histone 3 lysine 27-mutated diffuse midline gliomas (H3K27M DMG), a disease with almost no long-term survivors.
We describe effective CNS penetration of a PDGFRA inhibitor with pharmacologically relevant concentrations in brain tumor tissue resulting in dramatic clinical effect and minimal side effects in a cohort of 9 pediatric high grade glioma cases.

overall_design: Gene expression profiling of 3 pediatric high grade glioma cases

first: Petra

last: Pokorná

first: Štěrba

last: Jaroslav

first: Lisa

last: Mayr

first: Maria

last: Trissal

first: Kallen

last: Schwark

first: Mariella

last: Filbin

first: Johannes

last: Gojo

first: Carl

last: Koschmann


title: Circular RNA as new serum metabolic biomarkers in patients with Premature Ovarian Insufficiency

first: Yuqi

address: Sanyuanli

summary:
Quantitative Real-time PCR (qrt-PCR) is used to detect the differential expression of Circular RNA in patients of Premature Ovarian Insufficiency, in order to explore the biomarkers of POI that can be detected from blood as soon as possible.
Quantitative Real-time PCR (qrt-PCR) is used to detect the differential expression of Circular RNA in patients of Premature Ovarian Insufficiency, in order to explore the biomarkers of POI that can be detected from blood as soon as possible.

overall_design: The study collected blood samples from 30 patients in POI group and 30 normal people group that met the inclusion criteria but did not meet the exclusion criteria, who visited the gynecology clinic of The First Affiliated Hospital of Guangzhou University of Chinese Medicine from July 2019 to December 2020. Then circRNAs in plasma were extracted for qRT-PCR validation.

first: Z

last: Wang

first: Y

first: C

last: Zhong

last: Ou

last: Lin

last: Zhao


title: Arsenite exposure disturbs maternal-to-zygote transition by attenuating H3K27ac during mouse preimplantation development

first: Jing-Jing

last: Zhang

overall_design: Refer to individual Series


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle

first: Hui

last: Zheng


title: Endogenous Real Time Imaging Reveals Dynamic Chromosomal Mobility During ER-Mediated Transcriptional Burst Events [ChIP-seq]

city: La Jolla

first: Amir

last: Gamliel

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

summary: Enhancers serve as the major activators of mammalian signal-dependent transcriptional programs, exemplified by responses to liganded nuclear receptors, where their acute initial activation, is characterized by alternating periods of target gene “bursting” and “non-busting”, followed by a protracted chronic period of diminished transcriptional activation. Linking these responses to alterations in induced enhancer condensates and locus motility in real time would provide insights into these dynamic regulatory events. Here, endogenous live cell imaging reveals the altered chromosomal dynamics during estrogen receptor  (ER)-dependent target gene bursting/post-bursting and chronic activation events. We first observed that acute stimulation of ER results in increased frequency of bursting compared to the unstimulated state, but bursting actually diminishes with prolonged, chronic E2 stimulation. Second, while acute ligand-dependent activation results in higher levels of mobility of the chromosomal locus than in the unstimulated condition, this mobility further increases during chronic E2 stimulation. Simultaneous DNA/RNA endogenous live imaging of enhancer regulated target gene transcription revealed that the increased mobility of acutely ER-stimulated loci observed during the bursting phase was, unexpectedly, further increased in the subsequent non-burst phase, revealing that the transcription burst event is not the mechanism underlying increased motility. Single molecule tracking (SMT) of ER showed that the relatively high-burst, lower-mobility acute state was indeed enriched for high-viscosity, 1,6-hexanediol-sensative ER molecules. Interestingly, the increased proximity of E2-stimulated loci to interchromatin granules remained unchanged between the bursting and non-bursting phases of acute activation. Together these findings support a dynamic, multi-state condensate model for enhancer-regulated transcriptional programs.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Estrogen Recepetor alpha (ESR1), GATA3, AP2 gamma and RAR alpha in MCF7 cells treated with vehicle or 1 hour or 16 hours of 100 nM 17-beta Estradiol.

first: Susan

first: Michael

middle: G

last: Rosenfeld


title: Endogenous Real Time Imaging Reveals Dynamic Chromosomal Mobility During ER-Mediated Transcriptional Burst Events [PRO-seq]

overall_design: Precision Run-on sequencing (PRO-seq) of MCF7 cells treated with ICI 182,780 for 3 hours (control), or 1 hour or 16 hours of 100 nM 17-beta Estradiol.


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [scRNA-Seq]

overall_design: For bulk RNA-seq, cells were infected with O, S, K, OS, OK and SK respectively and collected at  post-infected Day0. For single-cell RNA-Seq, reprogramming cells were collected at post-infected Day0, Day1, Day2, Day3 and Day4 using Fluidigm C1. For ATAC-seq, cells were infected with hCdt1 and hGeminin and also OSK or OvSvK. Cells at different cell cycle stage were isolated by fluorescence-activated cell sorting (FACS). For CUT&Tag, cells infected with OSK or OvSvK and collected at post-infected Day3 and Day2 respectively.

first: Lin

last: Guo


title: Expression data from mouse adrenal gland at 2 month of age

city: Shimotsuke

first: Taka-aki

last: Koshimizu

state: Tochigi

department: Pharmaclogy

country: Japan

institute: Jichi medical university

summary:
V1a vesopressin receptor knockout mouse and wild type mouse were compaired
Lipofuscin is an autofluorescent pigment that accumulates in aging cells. We previously found that lipofuscin deposition was accelerated in the adrenal cortex of mice lacking V1a vasopressin receptor gene (V1aKO mice). However, the mechanism underlying V1a receptor- mediated regulation of lipofuscin deposition remains unclear. Upon analysis of the time course of lipofuscin accumulation, we found that autofluorescence in the adrenal cortex first appeared intracellularly and became evident at 2 months of age in male V1aKO mice but not in wild- type mice. At the age of 12 months, the area of the lipofuscin deposit in the adrenal section was 6.8-fold larger in V1aKO mice than that in wild-type mice. Analysis of the expression profiles revealed two upregulated genes, Xaf1 and Serpina1b, and two downregulated genes, Adi1 and Abhd1, in the adrenal cortex of V1aKO mice. The changes in gene expression were confirmed using real-time PCR analysis of adrenal samples from both groups of male mice at 2 months of age. In the adrenocortical Y1 cell line, the V1a receptor was the dominant subtype among the vasopressin/oxytocin receptor family members. Stimulation of Y1 cells with arginine-vasopressin increased intracellular calcium signaling, which was suppressed by a V1a antagonist. Furthermore, in Y1 cells, vasopressin stimulation significantly reduced the Xaf1 transcript levels; this effect has been reported to enhance p53 function and lead to senescence. These data indicate a novel role for the V1a receptor in regulating the aging phenotype in the adrenal cortex.

overall_design: Mouse adrenal glands of male V1a knockout (KO) mouse and wild-type (WT) mouse at 2 month of age were used for RNA extraction and hybridization on Affymetrix microarrays.


title: Single-cell transcriptomic profiling reveals sex-specific microglial responses to simulated galactic cosmic radiation without classical inflammatory activation

status: Public on Dec 31 2025

city: Rochester

first: Mark

middle: Ayor

last: Osabutey

state: New York

address: 601 Elmwood Avenue

institute: University of Rochester Medical Center

summary: Long‑duration deep space missions expose astronauts to galactic cosmic radiation (GCR), a complex mixture of high‑ and low‑LET ions that can compromise central nervous system (CNS) health. Microglia, the resident immune cells of the brain, are highly sensitive to radiation, yet their cell‑state adaptations to space‑relevant mixed‑field exposure remain poorly defined. Here, we performed single‑cell RNA sequencing (scRNA‑seq) of hippocampal microglia isolated from male and female C57BL/6J mice 53 days after acute 100 cGy 5‑ion GCR simulation. Behavioral testing showed no overt deficits, but scRNA‑seq revealed subtle, sex‑specific transcriptional remodeling. Male microglia engaged a stress‑adaptive program characterized by upregulation of Fkbp5, Rtp4, Creb5, and metabolic regulators, with concurrent downregulation of ER chaperone and ribosomal genes. Female microglia displayed a transcriptionally blunted phenotype with selective induction of Fkbp5, Ccnd3, and Tnfaip3, and broad downregulation of inflammatory and NOD/TNF pathways. Canonical inflammatory or disease‑associated microglia signatures were absent and homeostatic markers (P2ry12, Cx3cr1) were preserved. These findings define a non‑inflammatory, sex‑specific microglial response to space‑relevant GCR and provide a cellular framework for sex‑informed CNS risk assessment and countermeasure development for deep space travel.

overall_design: Six‑month‑old male and female C57BL/6J mice were randomly assigned to sham irradiation or exposure to 100 cGy simplified 5‑ion galactic cosmic radiation simulation (GCRsim) at the NASA Space Radiation Laboratory (Brookhaven National Laboratory). Behavioral testing (open field, novel object recognition, contextual fear conditioning) was performed 48–51 days post‑irradiation. At 53 days post‑irradiation, mice were euthanized by injection with a mixture of xylazine (10 mg/kg, i.p.) and ketamine (100 mg/kg, i.p.) and perfused intracardially with 0.15 M PBS containing 0.5% sodium nitrite and 2 IU heparin/mL. Hippocampus and overlying cortex were dissected and CD11b+ microglia were isolated by fluorescence‑activated cell sorting. Samples were multiplexed using TotalSeq‑B anti-CD45 antibody hashing and profiled by 10x Genomics single‑cell 3′ gene expression sequencing. Single‑cell transcriptomes were analyzed to quantify sex‑ and radiation‑dependent changes in microglial cell states, differential gene expression, and pathway enrichment.

middle: A

first: Lia

last: Calcines-Rodríguez

first: Lee

last: Trojanczyk

first: John

last: Oslchowka

first: M.

middle: K

last: O'Banion


title: Oncolytic virotherapy and platinum-based chemotherapy synergize to potentiate anti-tumor immunity through targeted engagement of chemo-persistent bystander CD8+ T cells

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

summary: The efficacy of combined chemotherapy and PD-1 immune checkpoint blockade (ICB) is constrained by a fundamental pharmacological conflict, as chemotherapy indiscriminately eliminates the proliferating tumor-specific CD8+ T (TTST) cells that PD-1 ICB aims to expand. To overcome this limitation, we targeted the chemotherapy-resistant bystander CD8+ T (TBYS) cell niche. We found that within the tumor microenvironment, CD8+ TBYS cells persist in a quiescent state, in stark contrast to chemotherapy-susceptible TTST cells. Leveraging this, we developed an oncolytic virus (OV-BYTE) engineered to redirect TBYS cells against tumors. In preclinical models and patient-derived organoids, OV-BYTE synergized with chemotherapy to control tumor progression. This synergy stemmed from direct engagement of the TBYS cell reservoir and concurrent restoration of TTST cell function via reduced apoptotic susceptibility and promotion of a polyfunctional effector state. Importantly, integrating OV-BYTE into standard chemo-PD-1 ICB regimens yielded superior anti-tumor efficacy. Collectively, our work establishes TBYS cells as a pivotal therapeutic target and presents OV-BYTE as a translatable strategy that resolves a core constraint in current cancer therapy, unlocking more effective combination regimens.

overall_design: The library preparation for single-cell RNA sequencing (scRNA-seq) using the BD Rhapsody platform to study P14/OT1 CD8+ T cells in tumor when undergoing OV-BYTE treatment w/o chemotherapy. Here, we further demonstrate that OV-BYTE and chemotherapy activate tumor-specific and bystander T cells in pre-clinical models, thus jointly killing tumor cells. This study gives a transcriptome profiles of P14/OT1 CD8+ T cells in tumor with administration of OV-BYTE treatment and chemotherapy.

first: Yang

last: yang

first: Shuai

last: Yue

first: Junjian

last: He

first: Lilin

last: Ye

first: Xiangyu

last: Chen


title: Exposure to di(2-ethylhexyl) phthalate and diisononyl phthalate during adulthood disrupts hormones and ovarian folliculogenesis throughout the prime reproductive life of the female mouse.

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

summary: Di(2-ethylhexyl) phthalate (DEHP) is a phthalate commonly used for its plasticizing capabilities. Because of the wide production and use of DEHP, humans are exposed to DEHP on a daily basis. Diisononyl phthalate (DiNP) is often used as a DEHP replacement chemical, and because of the increased use of DiNP, humans are increasingly exposed to DiNP over time. Of concern is that DEHP and DiNP both exhibit endocrine disrupting capabilities, and little is known about how short-term exposure to either of these phthalates affects aspects of female reproduction. Thus, this study tested the hypothesis that short-term exposure to DEHP or DiNP during adulthood has long-lasting consequences on ovarian follicles and hormones in female mice. Female CD-1 mice aged 39–40 days were orally dosed with either vehicle control (corn oil), DEHP (20 μg/kg/day or 200 ug/kg/day), or DiNP (20 μg/kg/day or 100 ug/kg/day) for 10 days. Total ovarian RNA was collected either immediately post-dosing (0 month) or 3 months post-dosing. The results indicate that 10 days of exposure to DEHP and DiNP changed the distribution of ovarian follicle populations and sex steroid hormones both immediatly after treatment as well as 3 months after treatment. These data show that short-term exposure to either DEHP or DiNP has long-term consequences that persist long after cessation of exposure. RNA sequence analysis was preformed to elucidate the ovarian molecular pathways altered by DEHP or DiNP exposure immediatly after treatment or 3 months after treatment.

overall_design: Ovarian mRNA profiles from adult female mice treated for 10 days of either DEHP, DiNP or vehicle control. Ovaries were collected either immediatly after 10 days of treatment (0 month) or 3 months after treatment. DEHP doses included 20 ug/kg/day and 200 ug/kg/day. DiNP doses included 20 ug/kg/day and 100 ug/kg/day. Each treatment group at each time point was completed in a replicate of 3 for a total of 30 RNA samples.

first: Catheryne

last: Chiang

first: Jodi

last: Flaws


title: Endogenous Real Time Imaging Reveals Dynamic Chromosomal Mobility During ER-Mediated Transcriptional Burst Events

first: Amir

last: Gamliel

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


title: Single-nucleus RNA sequencing of the cells obtained from acupoint BL23 (Shenshu) in low back pain.

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: The cellular and molecular dynamics at human acupuncture points remain largely unexplored. To address this, we developed a novel acupuncture-needle technique capable of collecting sufficient numbers of cells from acupuncture points during treatment. Using this approach in combination with single-nucleus RNA sequencing (snRNA-seq), we identified heterogeneous cell populations at the acupoint BL23. This study enabled characterization of the cellular and transcriptional changes occurring before and after acupuncture treatment in patients with lower back pain (lumbar sprain), offering new insights into the mechanisms underlying acupuncture-induced pain relief.

overall_design: Cells adhering to the acupuncture needles were collected at the initial intervention and again two weeks later following twice-weekly acupuncture treatments. Paired samples from the acupoint BL23 (Shenshu) were obtained, and single nuclei were subsequently isolated for transcriptomic analysis.

first: Gexin

last: Zhao


title: Arsenite exposure disturbs maternal-to-zygote transition by attenuating H3K27ac during mouse preimplantation development [RNA-seq]

first: Jing-Jing

last: Zhang

overall_design: The RNA-Seq experiments of the control and arsenite treatment 2-cell embryo.

first: Longtao

last: Yu

first: Xin

last: Liu


title: APOE Genotype Differentially Modulates Prion Pathology in a Mouse Model

city: New York

first: Martin

last: Sadowski

state: NY

address: 435 E 30th St

department: Neurology

institute: NYU Langone

summary: Background: APOE polymorphism affects the risk of occurrence and the rate of progression in several neurodegenerative diseases including late-onset Alzheimer’s disease, primary tauopathies, α-synucleinopathy, and age-related macular degeneration, but its role in prion pathogenesis remains unestablished. Using APOE targeted replacement (TR) mice, we investigated how APOE genotype affects key neurodegenerative mechanisms involved in prion pathology.  Methods: Male and female ε2/ε2, ε3/ε3, and ε4/ε4 APOE-TR mice were inoculated with 22L mouse adapted scrapie strain or normal brain homogenate and followed using serial behavioral testing from 10-week post inoculation (wpi.) onward. Mice were euthanized at 23 wpi. when all prion-infected animals were visibly symptomatic. Multiple neuropathological, biochemical, and transcriptomic metrics were analyzed and compared across animals of different APOE genotypes.   Results: ε4/ε422L mice featured the shortest disease latency time, the worst neurological score at the end of the study, and the highest load of spongiform lesions. ε2/ε222L mice performed significantly better compared to  ε4/ε422L mice but also significantly worse than ε3/ε322L animals.  Numerous aspects of PrP proteinopathy were exacerbated in the presence of the ε4 allele including increased PrPSc accumulation, reduced PrP solubility, and increased PrP oligomerization. These metrics were comparable between  ε2/ε222L and  ε3/ε322L mice. Prion pathology significantly increased brain apolipoprotein (apo) E levels, with the greatest increase in  ε4/ε422L mice. All apoE isoforms formed complexes with conformationally altered PrP, but in ε4/ε422L mice the PrP/apoE interaction was the strongest. The load of reactive microglia and astrocytes, transcriptomic markers representative of neurodegenerative microglia and chronically reactive astrocytes were the highest in  ε4/ε422L mice, but they also were significantly upregulated in  ε2/ε222L mice compared to  ε3/ε322L animals.   Conclusions: APOE polymorphism differentially regulates the progression of prion pathology. We identified two mechanisms attributable to the detrimental effect endowed by the  ε4 allele: the increased conversion and accumulation of the PrPSc conformer, and the worsening of prion-associated neuroinflammation. Although less severe than ε4, the  ε2 allele also is associated with an increased inflammatory response, rendering disease outcome worse compared to the  ε3 allele.  Findings of this animal model study suggest both  ε4 and  ε2 alleles are disadvantageous determinants in prion pathology.

overall_design: 4 animals per APOE genotype were analyzed in 22L inoculated experimental group and 4 animals from matched APOE genotype in NBH inocluated control group


title: Gene expression analysis using the NanoString nCounter® Human AutoImmune Profiling Panel for T cells from PRAAS patients carrying a de novo PSMB8 variant

city: Greifswald

first: Sophie

last: Wolfgramm

address: Ferdinand-Sauerbruch Straße

department: Medical Biochemistry and Molecular Biology

institute: University Medicine Greifswald

summary:
Elucidation of a heterozygous de novo PSMB8 variant on transcriptional level using the NanoString nCounter® Human Autoimmune Profiling panel
Two seperate analyses were performed for normalization (1st and 2nd batch). HD_A-C and Pt A,B, and C were analyzed together and represents the first batch. HD_E, HD_F, β5i_IH_A, and β5i_IH_B were analyzed together and reprensent the second batch.

overall_design: Isolated peripheral blood mononuclear cells (PBMCs) from patients and healthy controls were co-cultured with irridated feeder cells and stimulated with interleukin-2 (IL-2) and phytohemmagglutinin-L (PHA-L) for T cells expansion. Isolated RNA from T cells were used for NanoString measurements.

first: Frédéric

last: Ebstein


title: Adverse Childhood Experiences, DNA Methylation, and Depressive Symptoms in Black Pregnant Women

city: Maywood

first: Alexandra

middle: L

last: Nowak

state: IL

institute: Loyola University Chicago

type: Methylation profiling by genome tiling array

summary: Background: Prenatal depression, affecting up to a quarter of all pregnancies in the United States, contributes to morbidity and mortality and is associated with increased risk of adverse birth and long-term mental health outcomes. Adverse childhood experiences (ACEs, or experiences of abuse, neglect, or family dysfunction experienced prior to age 18) are a strong predictor of adult depression and adverse health outcomes. The present study investigated whether epigenetic modification in the form of DNA methylation (DNAm) of four stress-related, glucocorticoid pathway genes (CRH, CRHR1, FKBP5, NR3C1) me-diates associations between ACEs and depressive symptoms among Black pregnant women. Methods: Using a cross-sectional design, we examined the mediating role of DNAm on the relationship between depressive symptoms (Center for Epidemiologic Studies Depression Scale (CES-D)) and ACEs (Centers for Disease Control and Prevention 10-item questionnaire), in a subsample (n = 61) of Black pregnant women who were participants of the Biosocial Impacts of Black Births (BIBB) study. Results: A significant association was found between ACEs and depressive symptoms scores (TE α_X = 2.29 with p_TE = 6.60 × 105). DNAm on five CpG sites within two genes significantly mediated the relationship between ACEs and depressive symptoms (cg03238273 on CRHR1, and cg08845721, cg16594263, cg19820298, and cg23430507 on NR3C1). Conclusions: This study provides evidence that DNAm partially mediated the association of ACEs and depressive symptoms during pregnancy among Black pregnant women. Understanding the mo-lecular pathways underlying the mediating effect of ACEs on depressive symptoms among Black pregnant women can illuminate biological markers that help identify and treat pregnant women who are at an increased risk for depression following childhood trauma.

overall_design: We aimed to examine whether DNAm of four stress-related, gluco-corticoid pathway genes (CRH, CRHR1, FKBP5, NR3C1) mediates associations between ACEs and depressive symptoms in a subsample (n = 61) of Black pregnant women who were participants of the Biosocial Impacts of Black Births (BIBB) study.

first: Marvin

last: Schlit-Solberg

first: Xiaoyu

last: Liang

first: Fabiola

last: Magana

first: Dawn

middle: P

last: Misra

first: Carmen

last: Giurgescu


title: The bZIP Transcription Factor AtfA Coordinates Asexual Sporulation with Primary Metabolism in Aspergillus nidulans

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

summary: Asexual sporulation (conidiogenesis) in filamentous fungi is a complex developmental process that requires precise coordination with primary metabolism and environmental stress responses. In the model fungus Aspergillus nidulans, we demonstrate that the bZIP-type transcription fac-tor AtfA plays a central role in integrating conidiogenesis with the underlying metabolic and regulatory networks. Using combined ChIP-seq and RNA-seq analyses in wild-type, ∆atfA, and atfA-complemented strains under stress-free and oxidative stress (menadione) conditions, we identify a conserved AtfA binding motif and map its functional targets genome-wide. Our data reveal that AtfA binding to its target promoters is largely stress-independent, suggesting a preemptive regulatory mechanism in conidial development. AtfA directly controls genes in-volved in the MAPK signaling cascade, light-dependent sporulation, antioxidant defense, ei-sosome biogenesis, and the biosynthesis of trehalose and polyols—key metabolites supporting spore maturation and dormancy. Importantly, AtfA acts predominantly as a transcriptional acti-vator, and its regulatory scope extends beyond stress adaptation to the orchestration of metabolic processes essential for spore integrity and germination. These findings position AtfA as a master regulator that synchronizes morphological development with metabolic preparedness during asexual reproduction in A. nidulans.

overall_design: ChIP-seq was performed to map the binding sites of the AtfA transcription factor in the filamentous fungus Aspergillus nidulans. Analyses were carried out in untreated 2- and 3-day-old spores, as well as in 3-day-old spores exposed to menadione.

first: Sandugash

last: Ibragimova

first: Beatrix

last: Kocsis

first: Tibor

last: Nagy

first: Hee-Soo

last: Park

first: Tamás

last: Emri

first: Jae-Hyuk

first: Éva

last: Leiter

first: István

last: Pócsi


title: Vitamin B12 Ameliorates Diabetic complications: potential role of Circadian pathway and the NAMPT–NAD⁺–SIRT1 Pathway

city: CHAPEL HILL

first: Yukako

last: Kayashima

state: NC

address: 710 BRINKHOUS-BULLITT BUILDING CB #7525

department: Pathology Lab Med

institute: University of North Carolina at Chapel Hill

summary: Vitamin B12 is emerging as a potential therapeutic agent for diabetes-associated complications, with roles in redox balance, methylation, and mitochondrial function. Recent evidence suggests that B12 may also regulate circadian rhythms, which are closely linked to metabolic health. However, the connection between B12, circadian regulation, and protection against early diabetic liver and kidney damage remains unclear. Diabetic (Elmo1H/HIns2Akita/+) and non-diabetic (Elmo1HH) mice were treated with or without Vitamin B12 (10 mg/kg/day) in drinking water for 8 weeks, starting at 8 weeks of age. At 16 weeks, blood, liver, and kidney samples were collected for biochemical, transcriptomic, and histological analysis. Vitamin B12 significantly reduced serum triglycerides, improved mesangial expansion in kidneys, and improved liver cellular structure in diabetic mice. B12 also modulated circadian gene expression, downregulating Clock, Bmal1, and Npas2 (40–50%) while upregulating Cry1/2, Per1–3, Nr1d2, and Dbp in both liver and kidney (130–180%), regardless of diabetic status. Importantly, B12 significantly increased Nampt expression in the liver (p = 0.0062) and kidney (p = 0.0013) of diabetic mice, suggesting enhancement of the NAMPT–NAD⁺–SIRT1 axis, a key pathway for mitochondrial redox control and circadian stability. Additionally, B12 upregulated several solute carrier (SLC) transporters involved in nutrient and ion homeostasis. Together, these findings indicate that Vitamin B12 offers early protective effects against diabetic complications by improving metabolic balance and enhancing Nampt expression, supporting its potential role in preventing liver and kidney damage via circadian and NAD⁺-dependent mechanisms.

overall_design: RNA Seq profiling of liver and kidney tissues of non-diabetic Elmo1H/HIns2+/+  and diabetic Elmo1H/HIns2Akita/+ mice were tretaed with and without vitamin B12 via drinking water.

first: Niroshani

last: Wariyapperuma

first: Anshulika

last: Deshmukh

first: Rachel

last: Moser

first: Qiing

last: Ma

first: Feng

last: Li

first: John

last: Hagaman

first: Nobuyo

last: Maeda


title: An epigenetic basis for sustained inflammatory epithelial progenitor cell states in Crohn’s disease

city: Philadelphia

first: Yusen

last: Zhou

state: PA

address: 3401 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

summary: Defining consequential differences in intestinal epithelial stem cells in healthy humans versus those with inflammatory bowel disease (Crohn’s disease (CD) and ulcerative colitis) is essential for the development of therapies to restore the epithelial barrier and maintain its fidelity post-injury. Our study objective was to define transcriptomic, epigenomic, and functional divergence between healthy and CD epithelium.

overall_design:
We used single cell RNA sequencing and single nuclei ATAC-sequencing (n= 27 CD, 26 control) to evaluate transcriptomic and epigenomic differences in non-inflamed CD epithelium. Matched patient organoids from the same specimens were used to investigate durable epithelial-intrinsic changes at transcriptional and functional levels.
This submission contains scRNA-Seq submission.

first: Tatiana

last: A Karakasheva

first: Clara

last: Morral Martinez

first: Jingya

last: Qiu

first: Kathryn

last: E. Hamilton


title: A novel role of BPCs in the control of medial domain differentiation during gynoecium development in Arabidopsis thaliana

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

summary: The gynoecium, a highly specialized structure in flowering plants, ensures their high reproductive success through the control of different crucial steps spanning from ovule protection to fertilization and seed maturation and dispersion. Multiple bpc mutants show reduced vigor, small fruit size and height, a reduced number of seeds and problems in septum fusion and formation. BPCs are known to be involved in the regulation of key factors involved in plant development, and they are thought to function both as activators and repressors of target gene expression. Here we showed that gynoecium development is affected in different multiple mutants of the Basic PentaCysteine (BPC) genes, where the septum fails to develop properly, and that BPCs of class I and II regulate the expression of different genes involved in carpel development and phytohormonal pathways regulation. Considering the fundamental role of the gynoecium, which affects the reproductive success of the plants, we focused on understanding which genes could be putative direct targets of BPCs and thus involved in gynoecium development. We demonstrated that SPATULA and NO TRANSMITTING TRACT (NTT), which play pivotal roles in carpel and transmitting tract development, are downregulated. As a consequence, bpc multiple mutants fail to properly develop the septum and the transmitting tract. Interestingly, among the downregulated genes, we also found PIN-LIKES3, whose promoter can be directly bound by BPCs, which is an auxin efflux carrier that regulates and controls cytoplasmatic availability of auxin and could contribute also to various growth processes.

overall_design: RNAseq: Total RNA was extracted from 3 biological replicates from both wild type and bpcV mutant inflorescences apexes with flowers up to stage 12

first: Veronica

last: Gregis

first: Francesca

last: Caselli


title: TGF-βRII/IL-15 Immunotherapeutic complex targets exhausted CD8+ T cell subsets in lymph nodes and tumors

city: Columbus

first: Mark

last: Rubinstein

address: 460 W 12th Ave

department: Internal medicine

institute: The Ohio State University

summary: Exhausted CD8+ T cells, located within the tumor-draining lymph nodes (TDLNs) are responsible for maintaining tumor-specific responses in cancer. Here, we demonstrate that a bifunctional TGF-βRII/IL-15 protein complex (HCW9218), with TGF-β neutralization and IL-15 immunostimulatory activities, is capable of localizing to the TDLNs and tumors after subcutaneous administration, neutralizes TGF-β, expands progenitor stem-like exhausted T cells (TPEX) in TDLNs, and promotes their infiltration into tumors. Immune-checkpoint-inhibitors (ICIs) significantly enhanced the effects of HCW9218 on TPEX, and synergistically improved HCW9218 anti-tumor efficacy in melanoma and reduced spontaneous lung metastasis in breast cancer models. In a dose-escalating clinical trial in patients with chemo-refractory/relapsed solid tumors, HCW9218 monotherapy was well-tolerated, reduced serum TGF-β levels, promoted CD8+ T cell expansion in peripheral blood and CD8+ T cell infiltration in tumor biopsies. These findings provide a strong basis for using HCW9218 to enhance the efficacy of ICIs against solid tumors in the clinical setting.

overall_design: B16F10 tumor bearing C57Bl6/J female mice received a single subcutaneous dose of HCW9218 (n=9) or saline (n=9) when tumors reached 50-100mm3, a single s.c. dose of HCW9218 (3mg/kg) was administered following which the mice were sacrificed on day 5 post treatment. Total CD8+ T cells were isolated from TDLN, sorted and pooled from 3 mice in each group (total 3 samples from each group) and subjected to single cell RNA Seq analysis.


title: Developmentally dynamic chromatin state at loci regulating interorgan communication

first: Aditya

last: Parmar

department: Pathology

summary: Interorgan communication, metabolite regulation and drug handling all require fine-tuned transport of small molecules across cellular membranes. Approximately 1000 protein-coding genes – including hundreds of solute carrier (SLC) and ATP-binding cassette (ABC) transporters as well as enzymes and transcription factors-mediate small molecule organ crosstalk via a process known as “remote sensing and signaling (RSS)”. The RSS protein coding genes greatly overlap with those regulating absorption, digestion, metabolism and excretion (ADME) of small molecule drugs. However, it is not known how chromatin and epigenetic state at these loci are coordinately regulated during the development of the liver and kidney, which control the small molecule composition of the blood, or the brain, whose physiology relies upon proper regulation of this process. Understanding how epigenetic state changes during development at these loci provides insight into how the body attains autonomous functionality.

overall_design: CUT&RUN of the histone modifications H3K4me3, H3K27ac, H3K9ac, and H3K27me3 in mouse kidney, liver, and brain

first: Sanjay

last: Nigam

first: Kun

last: Cai

first: Kian

last: Falah

first: Vladimir

middle: S

last: Ermakov

first: Kelly

last: Wang

first: Jonathan

last: Tawil

first: Cole

last: Ferguson


title: Tet2 and Tp53 cooperate to promote leukemia and modulate response to inflammation

first: Alan

last: Shih

address: 1 Gustave L Levy Place

institute: Icahn School  of Medicine at Mount Sinai

overall_design: Refer to individual Series


title: Contemporary highly pathogenic avian influenza (H5N1) viruses retain neurotropism in human cerebral organoids

city: Hamilton

first: Emmie

last: de Wit

state: MT

address: 903 S 4th St

institute: NIAID

summary: Background Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 viruses are widely circulating in North America with unprecedented transmission into novel host species. A high incidence of neurologic disease is observed in carnivores infected with clade 2.3.4.4b HPAI H5N1 viruses and historical outbreaks of HPAI H5N1 in humans are also associated with neurologic complications, raising concerns about neurotropism and neurovirulence of clade 2.3.4.4b HPAI H5N1 viruses. Methods We analyzed virus replication kinetics, cellular tropism, and host responses to infection in human cerebral organoids (hCOs) inoculated with clade 2.3.4.4b HPAI H5N1 viruses compared to a historical clade 1 HPAI H5N1 virus and a seasonal influenza A virus. Results HPAI H5N1 viruses replicated to high titers in hCOs, but replication of the seasonal influenza A virus was not detected. Viral antigen and RNA were detected primarily in neuron- and astrocyte-like cells. Interferon responses to infection with HPAI H5N1 viruses were observed in a small population of bystander cells. Higher levels of cell death and proinflammatory cytokines and chemokines were observed in organoids inoculated with the historical HPAI H5N1 isolate. Conclusions Clade 2.3.4.4b HPAI H5N1 viruses exhibit similar neurotropism compared to a historical clade 1 HPAI H5N1 virus. Lower levels of cell death and inflammatory cytokine production induced by clade 2.3.4.4b viruses may indicate reduced neuropathogenic potential of these viruses in humans.

sample_organism:
Homo sapiens
Influenza A virus

platform_organism:
Homo sapiens
Influenza A virus

overall_design: Human cerebral organoids (hCOs) were inoculated with historical HPAI H5N1 isolate VN2004, contemporary HPAI H5N1 isolates mMT2024 or bOH2024, seasonal influenza A virus isolate BR2007, or mock-inoculated. scRNA-seq aanlysis was conducted at 1 or 3 days post-inoculation. Libraries were prepared using PIPseq T2 3’ Single Cell RNA kit v4.0 PLUS (Fluent Biosciences). Samples were indexed using the PIPseq UDI-96 kit (Fluent Biosciences), pooled, and sequenced on an Illumina NextSeq instrument.

first: Kerry

last: Goldin

first: Meaghan

last: Flagg

first: Tessa

last: Lutterman

first: Bridget

last: Brackney

first: Katie

last: Williams

first: Cathryn

last: Haigh


title: Global transcriptomic analysis identifies gene expression programs regulated by α-factor in yeast

city: Chuncheon-si, Gangwon-do

first: soojin

last: yeom

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: In yeast, the mating pheromone α-factor triggers a signaling cascade in haploid "a" cells, leading to G1 cell cycle arrest, polarized growth ("shmoo" formation), cell wall remodeling, and ultimately cell fusion. While the physiological responses to α-factor are well established, a genome-wide analysis of transcriptional changes in response to α-factor has not been previously reported. Here, we performed RNA sequencing (RNA-seq) to profile gene expression changes in "a" mating type yeast cells treated with α-factor. We identified 957 differentially expressed genes (DEGs), including 448 upregulated and 509 downregulated genes. Gene ontology (GO) analysis revealed enrichment of upregulated genes in pheromone signaling, cell wall biogenesis, and cell shape regulation. In contrast, downregulated genes were mainly associated with cell cycle progression, chromatin remodeling, histone gene expression, and nucleosome organization. Our dataset validates known pheromone-responsive genes and identifies novel candidates potentially involved in mating responses. These findings provide a valuable resource for understanding how transcriptional regulation and chromatin dynamics are coordinated during pheromone signaling in yeast.

overall_design: RNA-seq profiling of wildtype FM391 and their knockout derivates (dsir2, dcdc73) before and after α-factor

first: Soojin

last: Yeom

first: Jung-Shin

last: Lee


title: High throughput identification of genetic regulators of microglial inflammatory processes in Alzheimer's disease.

first: Andrew

last: Sproul

department: Pathology and Cell Biology

institute: Columbia University

summary: We sought to assess at scale how AD GWAS hits influence human microglial inflammatory responses. We conducted CRISPR inhibition screens of 119 AD GWAS hits in parallel along with 52 control genes in human iPSC-derived microglia, with reactive oxygen species produced in response to the viral mimic poly(I:C) as a readout. Top hits that either decreased or increased ROS in response to poly(I:C) when knocked down were then interrogated via perturb-seq.

overall_design: Human iPS-derived microglia were infected with sgRNA targeting hit of interest on day 21. Cells were treated with either vehicle or poly(I:C) on day 35 for 2 hours and collected for single-cell RNA-sequencing. CRISPR guide libraries were also generated for downstream analysis.

first: Christopher

last: Cardona

first: Lai

last: Wei

first: Joonwon

last: Kim

first: Ellen

last: Angeles

first: Gunjandeep

last: Singh

first: Shiye

last: Chen

first: Ronak

last: Patel

first: Nkechime

last: Ifediora

first: Peter

last: Canoll

middle: F

last: Teich

first: Gunnar

last: Hargus

first: Alejandro

last: Chavez


title: Global gene expression in S. mutans UA159 treated with and without LSOS

city: Changsha

first: Jianying

last: Zhang

state: Hunan

address: NO.72 Xiangya Road

department: Xiangya School of Stomatology

institute: Central South University

overall_design: S. mutans UA159 was cultured to mid-logarithmic phase (OD600 = 0.5) with or without LSOS treatment (0 or 2.5 mM), and cells were harvested by centrifugation. Microarray analysis was performed to examine global gene expression changes in response to LSOS treatment. Each treatment condition was performed with two biological replicates.


title: CDK7 regulates pre-mRNA splicing via CDK11

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Cyclin-dependent kinase 11 (CDK11) is essential for the regulation of pre-mRNA splicing by phosphorylating SF3B1, a core spliceosome component. This phosphorylation is a marker of the catalytically active spliceosome, so it is important to identify the mechanisms that regulate CDK11. Herein, we report that a small subset of CDK11 is phosphorylated on the activation T-loop threonine 595 (Thr595) and is associated with the activated spliceosome on chromatin in gene bodies. Mutational analyses revealed that Thr595 is essential for the formation of the active CDK11 complex with cyclin L and SAP30BP. CDK11 transiently associates with CDK7, a transcriptional kinase that also promotes the activation of other CDKs. The time course of the inhibition of CDK7 initially decreases transcription, but later produces unspliced pre-mRNAs. The dynamics of onset of the CDK7-mediated splicing defect correlates with the sequential dephosphorylation of CDK11 Thr595 and SF3B1. SILAC-based phospho-proteomics upon brief CDK11 inhibition identified SF3B1, CDC5L and ESS2 as CDK11 substrates, an overlap with the previously identified CDK7 substrates in the spliceosome. In summary, our study suggests that CDK7 likely acts via CDK11 Thr595 phosphorylation to regulate pre-mRNA splicing in cells. The identification of additional CDK11 substrates indicates its more complex role in spliceosome regulation.

overall_design:
ChIP-Seq of CDK11 phosphorylated on its activation T-loop threonine after inhibition of CDK7 kinase by SY-351 inhibitor. In HCT116 cells.
Comparison of 2 antibodies for ChIP-Seq recognising CDK11 phosphorylated on its activation T-loop threonine. In HCT116 cells.
ChIP-Seq of SF3B1 protein. In HCT116 cells.

first: Michal

last: Rájecký

first: Pavla

last: gajdušková

last: Maník

first: Milan

last: Hluchý

first: Eva

last: Hegedűsová

first: David

last: Potěšil

first: Petra

last: Martinková

first: Zuzana

last: Slabá

first: Marek

last: Šebesta

first: Prashantkumar

last: Khirsariya

first: Kamil

last: Paruch

first: Zbyněk

last: Zdráhal

first: Dalibor

last: Blažek


title: Single-Cell Transcriptome Profiling of PBMCs in Response to Diverse Immune Adjuvant Stimuli

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

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

department: Department of Immunology

institute: Kumamoto University

summary: Immune adjuvants are agents that enhance the immunogenicity of vaccines when co-administered with antigens. While their primary mode of action involves activation of innate immune pathways in antigen-presenting cells such as myeloid cells—leading to cellular maturation and enhanced antigen presentation—how adjuvants affect other hematopoietic cell types remains largely unclear. To address this, we performed single-cell RNA sequencing of human PBMCs treated with various immune adjuvants, aiming to characterize cell type–specific transcriptional responses at single-cell resolution.

overall_design: Human PBMCs were treated for 24 hours with saline, ARNAX-120 (10 µg/mL), poly(I:C) (10 µg/mL), Alum (500 µg/mL), or miR-192-LNP (200 pmol/mL). Following treatment, cells were cryopreserved in CELLBANKER 1(Takara) at –80 °C. For multiplex analysis, cells were barcoded using BioLegend Hashtag DNA. Single-cell capture and reverse transcription were performed using the BD Rhapsody system, and cDNA amplification was carried out using the Terminator-assisted solid-phase cDNA amplification sequencing (TAS-Seq) method (Shichino et al., Commun. Biol., 2022), in collaboration with ImmunoGeneTeqs Inc. The correspondence between samples and tags is as follows: Control (Saline): A0955, ARNAX-120: A0962, poly(I:C): A0963, Alum: A0964, and miR-192-LNP: A0965.

first: Hiroyuki

last: Oshiumi


title: Early skin seeding regulatory T cells modulate PPARγ-dependent skin pigmentation [IC_scRNAseq]

city: London

first: Niwa

last: Ali

address: King’s College London, 28th Floor, Tower Wing  Guy’s Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

summary: To understand the role of early skin-seeding neonatal Tregs, we performed scRNA-seq of Treg-sufficient and Treg-depleted skin on postnatal day 9 (P9). Further, we performed bulk RNA-seq of sorted Tregs from P9 and Treg-sufficient and Treg-depleted skin from P9 and P13 mice.

overall_design: Skin tissues were harvested and pooled (n=3) for each whole skin scRNA-seq. Skin tissues were digested and dead cell removal was performed using the Miltenyi's dead cell removal kit. Single cell RNA-seq libraries were generated by the Blizard Institute at the Queen Mary University of London using the 10X platform.

first: Inchul

last: Cho

first: Jessie

middle: Z

last: xu

first: Monica

last: Sen


title: TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment [ATAC-seq]

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

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

overall_design: ATAC-seq of BT549-D, BT549-P, BT549-PB, BT549-NP, BMDM-D, BMDM-P, BMDM-PB, BMDM-NP were harvested and analyzed

first: Hongquan

last: Zhang

first: Jun

last: Zhan


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

overall_design: D tumor and  P tumor were harvested and analyzed using Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies).


title: Integrated transcriptomic and epigenomic profiling of mouse lung cells at the single-cell level

city: Paris

first: Olivier

last: Mirabeau

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Our previous scRNA-seq data suggest that immune and stromal cells exhibit memory properties that contribute to the long-term regulation of lung allergic responses, which are cross-regulated by the co-administration of TLR ligands or bacterial extracts. To further investigate these mechanisms, we performed single-cell multiome sequencing (scMulti-omics) to integrate transcriptomic and epigenomic profiling, focusing on the characterization of immune and stromal cell populations during long-term resolution.

overall_design: To assess long-term changes induced by allergen exposure and cross-regulation, we performed scMulti-omics on whole lung cells from mice under four conditions: Long-Term Phase (6 Weeks): Control, papain, papain+CpG or papain+OM85, analyzed 6 weeks post-administration (no recall).

first: Jaechan

last: Ryu

first: Victoire

last: Baillet

first: Gérard

last: Eberl


title: TNF-α Driven m6A Modification Disrupts MSCs Immune Regulatory Function by Regulating HDAC5-dependent Super Enhancer [CUT&Tag]

city: shenzhen

first: weihao

last: zhang

address: futian

department: Department of Orthopedics, The Eighth Affiliated Hospital

institute: Sun Yat-sen university

summary: Mesenchymal stem cells (MSCs) are widely used to treat inflammatory diseases due to their strong immunosuppressive functions. However, these functions were greatly affected by inflammatory microenvironment in vivo and therefore limited the therapeutic effect of MSCs. The present study demonstrates that TNF-α impairs immunosuppression capability of MSCs on T cells proliferation. Mechanistically, TNF-α treatment decreased the expression of H3 deacetylation eazyme HDAC5, therefore leading to the enhanced super enhancer (SE) signals and upregulated expression of leukemia inhibitory factor (LIF) in MSCs. Moreover, TNF-α downregulated HDAC5 expression through promoting WTAP-mediated m6A modification of HDAC5 mRNA, which was subsequently regulated by YTHDF2 to reduce the mRNA stability. Notably, intravenous infusion of MSCs overexpressing HDAC5 showed improved therapeutic efficacy in SKG mice with inflammatory arthritis. Our results elucidate a synergistic epigenetic regulatory mechanism between super-enhancer and m6A modification of the MSCs immunosuppressive functions, and provide a novel strategy to enhance the clinical therapeutic potential of MSC infusion in inflammatory diseases.

overall_design: The first CUTTAG-seq  performed in MSCs with/without TNF-α treatment, while another CUTTAG-seq in OE-NC MSCs without TNF-α , OE-NC MSCs with TNF-α and OE-HDAC5 MSCs with TNF-α.


title: Effect of eyelid UVB irradiation on gene expression of rat meibomian gland

first: Min

last: ZHAO

state: France

address: 15 rue de l'Ecole de Médecine

institute: INSERM U1138, Centre de Recherche des Cordelier, University Paris Descartes

summary: We have developed a rat model of UVB-induced ocular surface and eyelid damages mimicking ocular rosacea, a common chronic inflammatory and neurovascular ocular surface disease associated with meibomian gland dysfunction. Rat eyelids were exposed to UVB for 5 minutes daily (300mJ/cm2) for 5 days. UVB-exposed rats displayed altered meibocyte activity and lipid production, ductal epithelial hyper-keratinization, apoptosis, mitochondrial dysfunction and oxidative stress. Corneal epithelial defects, barrier disruption and abnormal innervation occurred 2 weeks after UVB exposure, subsequent to meibomian gland dysfunction. The aim of this study was to investigate the transcriptomic signature associated with meibomian gland dysfunction induced by UVB in rats. We revealed pathways related to keratinization, cell cycle and proliferation, DNA damage and repair, inflammation, immune responses, oxidative responses, and fatty acid metabolism. These regulations supported the observed functional changes of meibomian gland and were consistent with the transcriptomic signature of human meibomian gland dysfunction.

overall_design: We compared gene expression profile in meibomian gland between UVB-irradiated and non-irradiated rats.

first: Linxin

last: ZHU

first: Francine

last: Behar-Cohen


title: Single-cell transcriptomic and spatial subcellular landscape of the articular disk synovium in mouse temporomandibular joint osteoarthritis

city: Sinagawa-ku

first: Kazuhiro

last: Shibusaka

state: Tokyo-to

address: 1-5-8, Hatanodai,1st building, 343

institute: showa university

summary: This study aimed to elucidate the molecular mechanisms underlying TMJ-OA by integrating subcellular spatial transcriptomics with single-cell RNA sequencing analysis in TMJ-OA mouse models.

overall_design: The TMJ-OA model mouse experiments were conducted using 9-week-old female C57Black/6J mice. The TMJ-OA models were divided into three groups: Control (n=7), Mechanical Stress (MS) model (n=7), and Articular Disc Displacement (ADD) model (n=4). scRNA-seq was performed on cells obtained from the articular disc, including the synovium, three weeks after establishing the TMJ models.

first: Asuka

last: Terashima

first: Soichiro

last: Negishi

first: Masahiro

last: Hosonuma

first: Miki

last: Maemura

first: Hiroshi

last: Yoshida

first: Nobuhiro

last: Sakai

first: YoungKwan

last: Kim

first: Yutaka

last: Suzuki

last: Okada

first: Fumiko

last: Yano


title: Epigenetic Memory of Cross-Regulation by Papain and CpG in Lung Stromal Cells

last: Baillet

address: 25-28 rue du Dr Roux

summary: This study investigates the long-term epigenetic memory induced by the cross-regulation of type 2 and type 1 inflammation in lung stromal cells. Using bulk ATAC-seq, we examined chromatin accessibility changes associated with the chemokine CCL11, a key driver of eosinophil recruitment, under long-term conditions.

overall_design: This experimental design explores how recombinant cytokines (rIL-4, rIL-13, and rIFNγ) and antibody-mediated blockade (aIL-4, aIL-13, and aIFNγ) influence chromatin accessibility in lung stromal cells during allergic inflammation and cross-regulation. Papain, a type 2 inducer, is hypothesized to drive IL-4 and IL-13 production, which not only induces CCL11 expression in stromal cells but also promotes epigenetic imprinting. Conversely, CpG, a type 1 inducer, likely mediates cross-regulation through IFNγ, repressing both CCL11 expression and its associated epigenetic changes. To test these hypotheses, anti-IL-4 and anti-IL-13 are used with papain to determine whether these cytokines are necessary for CCL11 epigenetic imprinting. Anti-IFNγ is used with CpG to identify IFNγ's role in CpG-mediated cross-regulation. Finally, rIL-4, rIL-13, and rIFNγ are used to confirm whether these cytokines are the key drivers of CCL11 induction and repression, as well as the corresponding epigenetic modifications in stromal cells

first: Jaechan

last: Ryu

first: Gerard


title: Exosomal SNHG26 derived from drug-resistant tongue squamous cell carcinoma cells inhibits the anticancer effect of NK cells in the microenvironment_scRNAseq

city: Nanchang

first: Jiaxuan

last: Qiu

state: Jiangxi

address: 17 Yongwai Zheng Street

institute: The First Affiliated Hospital of Nanchang University

summary: Cisplatin resistance is a common occurrence among patients diagnosed with tongue squamous cell carcinoma (TSCC), resulting in a bleak prognosis. The immune microenvironment, specifically the involvement of Natural killer (NK) cells, plays a significant role in the development of drug-resistant tumor cells and subsequently impacts patient prognosis. However, the precise interaction mode and the underlying mechanisms governing this process remain elusive.

overall_design: In this study, a variety of research subjects were utilized, including clinical samples, patient-derived organoids (PDO), TSCC/NK cell co-culture system, patient-derived tumor xenograft (PDX) models, and humanized mice. Various methods were employed, such as drug sensitivity testing, single cell and transcriptome sequencing analysis, gene regulation, DNA/RNA/protein interaction experiments, to investigate and confirm the cascade reaction of TSCC cisplatin resistance-induced NK-related immunosuppression.

first: Qingkun

last: Jiang


title: Epigenetic Activation of BCL11B Mediates Profibrotic Cardiac Remodeling Triggered by Colitis-Associated Gut Dysbiosis

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Boulevard

department: Internal Medicine

institute: UTMB

summary: Inflammatory bowel disease (IBD) is linked to elevated cardiovascular risk, but the mechanisms connecting gut dysbiosis to heart pathology are unclear. This study investigated whether transplanting a dysbiotic microbiome (DM) from colitic mice could alter cardiac function in germ-free recipients. Results showed that DM transplantation impaired cardiac contractility and increased collagen deposition, indicating fibrosis. Transcriptomic analysis revealed widespread gene upregulation, particularly in females, with enrichment in histone acetylation and immune signaling pathways. Key epigenetic regulators, Nat8f7 and Tet1, were significantly upregulated, leading to increased histone acetylation and reduced DNA methylation at the Bcl11b promoter. This enhanced RNA polymerase II recruitment and Bcl11b transcription. In a model of dextran sodium sulfate (DSS)-induced colitis, similar upregulation of Nat8f7, Tet1, and Bcl11b occurred alongside increased fibrotic markers. Crucially, fecal microbiota transplantation from healthy donors reversed these molecular and fibrotic changes, normalizing Bcl11b expression and epigenetic status. Furthermore, functional assays demonstrated that BCL11B overexpression drives fibroblast proliferation and collagen production. In conclusion, these findings identify a novel gut-heart axis where a dysbiotic microbiome promotes cardiac fibrosis through the epigenetic activation of Bcl11b, and restoring a healthy microbiome mitigates these effects, pointing to microbiome-targeted strategies as potential therapies for IBD-related cardiovascular complications.

overall_design: Germ-free mice were colonized with either normal microbiomes from wild-type donors or dysbiotic microbiomes from Il10-/- donors. Cardiac function was assessed via echocardiography. The gut microbiome was profiled using 16S rRNA sequencing, and transcriptomic changes were analyzed by RNA-sequencing. Chronic colitis was induced in mice using repeated oral dextran sodium sulfate (DSS) administration, with a subset receiving fecal microbiota transplantation from healthy controls. To investigate epigenetic mechanisms, techniques including transient transfection, chromatin immunoprecipitation, and methylation-specific qPCR were employed, alongside functional assays in C2C12 myoblast cells.

first: Rongliwen

last: Ou

first: Thierry

last: Kochkarian

first: Kevin

last: Lopez

first: Christian

last: Garza

first: Kamil

last: Khanipov

first: Don

middle: W

last: Powell

first: Xiaowei

last: Liu


title: Cell of origin alters myeloid-mediated immunosuppression in lung adenocarcinom

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

summary: Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer with extensive biological heterogeneity, such as varying cells of origin from alveolar epithelial cells (AECs) in the distal lung. The predominant types of AECs include surfactant-producing alveolar epithelial type II (AT2) cells and large, delicate alveolar epithelial type I (AT1) cells, which are responsible for facilitating gas exchange. Although AT1 cells have been thought to be terminally differentiated and consequently unable to proliferate, we, and others, have previously reported that Gramd2+ AT1 cells can give rise to a histologically-defined LUAD1,2 on transgenic mouse model. Immunotherapy has shown a major impact on treatment of solid tumors over the past 10 years, particularly on LUAD, where it significantly improves patients’ survival rates3. However, because of the largely unknown immunosuppressive states of LUAD, there is considerable variability in patient response to therapy across LUAD patients, making immunotherapeutic treatment challenging. To determine whether cells of origin for LUAD reprogram differently tumor immune microenvironment (TIME) landscape, we employed single nucleus RNA sequencing (snRNA-Seq) on mouse KRASG12D-overexpressing Gramd2+ AT1 cell and Sftpc+ AT2 cell-derived LUADs to comprehensively characterize transcriptomic, molecular, and cellular aberrations within the TIME. We demonstrate that myeloid cells within the AT1-LUAD TIME manifest a disordered cell composition and disrupted transcriptome: increased cell number of inflammatory monocytes and macrophages but decreased cell number of myeloid-derived suppressor cells (MDSCs) were observed in AT1-LUAD TIME compared with its AT2 counterpart. In addition, a series of bioinformatic analyses, gene set enrichment analysis (GSEA), ingenuity pathway analysis (IPA) and cell-cell communication (CCC) analysis, along with immunostaining confirmed LUAD TIME derived from different cells of origin exhibits altered suppressive gene expression patterns and disparate pro-inflammatory signaling activities. Taken together, AT1-LUAD presents a proinflammatory, immunoreactive TIME, while the TIME of AT2-LUAD is relatively immunosuppressive. This study suggests that LUAD cell of origin is associated with transcriptomic aberrations and immune landscape changes that may inform ongoing translational work to improve patient responses.

overall_design: Whole lungs of each sample B6 mouse were perfused and dissociated into a single cell suspension for nuclei isolation

first: Minxiao

last: Yang

first: Edgar

last: Gonzalez

first: Jonathan

last: Castillo

first: Chunli

last: Yan

first: Keqiang

last: Zhang

first: Leonidas

last: Arvanidis

first: Zea

last: Borok

first: W.

last: Wallace

first: Dan

last: Raz

first: Evanthia

last: Roussos Torres

middle: N


title: A peptide that regulates metalation and function of the Arabidopsis ethylene receptor

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

institute: Durham University

summary: Ethylene signalling represents one of the classic hormonal pathways in plants, with diverse roles in development and stress responses. The dimeric ethylene receptor localizes to the endoplasmic reticulum (ER) and contains Cu(I) ions essential for ethylene binding and signalling. As for other vesicular cupro-proteins, the final step of Cu(I) maturation at the ER is undefined. We previously discovered that mutants in the Arabidopsis gene POLARIS (PLS), encoding a 36 amino acid peptide, exhibit enhanced ethylene signalling responses. Here we report a 1:2 thiol-dependent Cu(I):PLS2 complex, with an affinity of 3.79 (±1.5) x1019 M-2. We demonstrate PLS interactions with the transmembrane domain of receptor protein ETR1, the Cu(I) chaperones ATX1 and CCH, and Cu(I)-transporting P1B-type ATPase RAN1 at the ER. Formation of Cu(I)-dependent PLS-cuproprotein interactions at the ER provides a mechanism to modulate the metalation of ETR1, thereby regulating its activity and representing a novel mechanism for plant hormone receptor regulation.

overall_design: To investigate the pls molecular phenotype, we carried out an RNA-seq analysis on loss-of-function pls mutant and PLS transgenic overexpressor seedlings, each compared with the wildtype seedlings of the same ecotype as controls. There were triplicates in each of the four groups (C24 pls mutant, C24 wild type, COL-0 PLS overexpressor, COL-0 wild type)

first: Anna

last: Mudge

first: Saher

last: Mehdi

first: Will

last: Michaels

first: Beatriz

last: Orosa-Puente

first: Weiran

last: Shen

first: Charlie

last: Tomlinson

first: Ari

last: Sadanandom

first: Flora

middle: M

last: Hetherington

first: Claudia

last: Hoppen

first: Buket

last: Uzun

first: Georg

last: Groth

first: Jennifer

last: Topping

first: Nigel

last: Robinson

first: Keith

last: Lindsey


title: Efficacy of Melflufen in Patients with Relapsed/Refractory Multiple Myeloma and Mutated or Deleted TP53

city: Helsinki

first: Philipp

last: Sergeev

address: Tukholmankatu 8

country: Finland

institute: University of Helsinki

summary: Clinical challenges remain for patients with relapsed/refractory multiple myeloma (MM), especially for high-risk patients with del(17p) and TP53 mutation who have poor response and significantly shorter survival compared to patients without these aberrations. Here, we present the mechanism of action of melphalan flufenamide (melflufen) in TP53 wild type and double mutant (TP53-/-) isogenic myeloma cells in relation to DNA damage, apoptosis kinetics, and mitochondrial function. Melflufen demonstrated superior in vitro efficacy in comparison to melphalan or cyclophosphamide. Differential gene expression and DNA damage pathway analysis upon treatment of TP53 wild type and TP53-/- MM cell lines revealed qualitative differences between melflufen and melphalan. In addition, we investigated response of primary bone marrow (BM) patient samples with del(17p)/TP53 mutation to melflufen. In accordance with the cell line data, ex vivo sensitivity to melflufen was independent of BM TP53 mutation status. Gene set enrichment analysis of single cell transcriptome data from MM cells highly or less sensitive to melflufen revealed differences related to p53 and DNA damage repair pathways. These findings provide molecular understanding of results from post-hoc analysis of the del(17p) patient population from the OCEAN randomized, open label, head-to-head, phase III clinical trial. From this analysis, we observed favorable progression free survival in the del(17p) subgroup treated with melflufen plus dexamethasone compared to the pomalidomide plus dexamethasone arm. Our insights into the molecular mechanisms of melflufen activity in mutant TP53 MM support its clinical efficacy and application in the del(17p) and mutant TP53 patient population.

overall_design: Myeloma plasma cells from viably frozen myeloma patient bone marrow mononuclear cells were isolated using Fluoresence-activated cell sorting (FACS) according to the presence or absence of CD138 cell surface marker. scRNAseq analyis was performed to CD138 positive and CD138 negative cells that were mixed in 1:1 ratio.

first: Klara

last: Acs

first: Juho

last: Miettinen

last: Segeev

first: Tobias

last: Heckel

first: Yumei

last: Diao

first: Kristin

last: Witt-Mulder

first: Marcus

last: Thureson

first: Thorsten

last: Bischler

first: Maiju-Emilia

last: Huppunen

first: Jakob

last: Obermüller

first: Umair

last: Munawar

first: Ana

last: Slipicevic

first: Ralf

last: Bargou

first: Fredrik

last: Lehmann

first: Stefan

last: Svensson Gelius

last: Norin

last: Schjesvold

first: Pieter

last: Sonneveld

last: Stühmer

first: Caroline

last: Heckman


title: Gene expression dynamics at the single cell level in mouse lung cells

first: Olivier

last: Mirabeau

summary: We performed single-cell RNA sequencing (scRNA-seq) to dissect the heterogeneity of lung cells from mice exposed to papain, with or without co-administration of TLR ligands or bacterial extracts, identify key transcriptional signatures associated with type 2 inflammation, and uncover molecular changes induced by cross-regulatory signals.

overall_design: Experimental design : To assess acute effects, long-term changes, and recall responses induced by allergen exposure and cross-regulation, we performed scRNA-seq on whole lung cells from mice under six conditions:  1.Acute Phase (Day 3): Papain or papain+CpG, analyzed 3 days after administration. 2.Long-Term Phase (6 Weeks): Papain or papain+CpG, analyzed 6 weeks post-administration (no recall). 3.Long-Term Phase with Recall: Papain or papain+CpG, followed by a secondary papain challenge at 6 weeks.

first: Jaechan

last: Ryu

first: Victoire

last: Baillet

first: Gérard

last: Eberl


title: Decoding the DNA sequence of MAP1S promoter region interacting with HBx

city: beijing

first: yanjun

last: wang

address: Xitoutiao,8#,Youanmenwai Street,Fengtai District, Beijing, 100069, China

institute: Beijing Institute of Hepatology, Beijing You An Hospital, Capital Medical University

summary: Our previous research found that the X protein encoded by the hepatitis B virus (HBx) induces high levels of MAP1S expression. To determine the binding motif and enrichment of HBx in the promoter region of MAP1S gene, we transfected HEK293T cells with pHBx. The chromatin complex was extracted, followed by immunoprecipitation with HBx antibodies, and DNA sequencing. A binding region 1180bp upstream of the MAP1S transcription initiation site (TSS) was found, demonstrating that HBx up-regulated the expression of MAP1S by interacting with the MAP1S gene promoter region.

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) was utilized to investigate the interaction of the HBx protein with the promoter region of the MAP1S gene.

first: Yuanyue

last: Guan

first: Jiaxi

last: Li

first: Yang

last: Zhang

first: Yanjun

last: Wang


title: Tet2 and Tp53 cooperate to promote leukemia and modulate response to inflammation [Bisulfite-Seq]

city: New York

first: Alan

last: Shih

address: 1 Gustave L Levy Place

institute: Icahn School  of Medicine at Mount Sinai

summary: TET2, a regulator of DNA methylation, is amongst the most commonly mutated genes in acute myeloid leukemia (AML) and is linked to enhanced inflammatory responses. The ability to respond to TP53 activation and inflammatory response has been linked to clonal advantage in hematopoietic stem-progenitors. These mutations combine and affect the pyroptosis pathway.

overall_design: LSK cells were sorted from bone marrow of wild-type and Tet2 p53 double mutant transplanted mice. Using RRBS we profiled genome methylation patterns in these hematopoietic stem-progenitor cells

first: Pablo

last: Sanchez-Vela

first: Jonathan

last: Foox

first: Ross L

last: Levine

first: Alan H


title: The long non-coding RNA ELDR suppresses tumorigenicity of AML cell lines with MLL rearrangements by interfering with DNA replication and chromatin accessibility [ATAC-Seq]

city: Montreal

first: Tarik

last: Moroy

state: QC

address: 110, West Pine Avenue, 597

country: Canada

institute: Institut de recherches cliniques de Montréal

summary: ATAC-seq experiments were performed using the C1 and C3 stable ELDR overexpressing THP1 cell lines, an empty vector control cell line (EV) and non-transfected THP-1 cell (NT). The ATAC-seq experiment was done with two replicas for the two ELDR lines C1 and C3, EV- and NT control each.

overall_design: ATAC-seq was carried out with 50,000 cells washed once with 50μl of cold 1X PBS buffer. Spin down at 500g for 5 min, 4 °C. Gently pipetted to resuspend the cell pellet in 50μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Cells were spun down immediately at 500g for 10 min, 4°C and lysed with non-ionic detergent to enrich nuclei. Pellets of 50,000 nuclei were tagmented for 30 minutes at 37°C (TDE1 Transposase, Illumina) and tagmented DNA was purified on column DNA clean-5 (Zymo Research). Illumina UDP Indexes were integrated by PCR-enrichment (11 cycles) and final libraries were purified and size selected (L=1.1; R=0.6) with ampure beads (KAPA, Roche Diagnotics). Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired end reads (PE100), on a Novaseq 6000 system (Illumina), with a S4 flow cell and a coverage of 70M fragments per library. The quality of the raw reads was assessed with FASTQC v0.11.8. After examining the quality of the raw reads, trimming was performed with TRIMMOMATIC v0.36.. The reads were aligned to the GRCh38 reference genome (release 102) with BOWTIE2 v2.2.6 with mean of 77 % of reads uniquely mapped. Alignments were post-processed to remove PCR duplicates (Picard tool v2.4.1) and reads mapping to mitochondrial DNA (samtools v1.8). In order to represent the real Tn5 transposase binding sites of 9bp, the coordinates of the reads were shifted by +4bp for the plus strand and by -5bp for the minus strand, using Deeptools v3.0.1. The former was also used to remove ENCODE's blacklisted regions (signal artefact regions) and convert Bam files to BEDPE format. MACS2 was used to identify significant peaks. Diffbind v2.10.0 R package was used to generate the count matrix of Tn5 insertion site numbers for each consensus peak (peaks that were present in all samples for each condition). Differentially accessibility regions (DARs) were identified between conditions within each cell type and controlling for the effect of gender, using DESeq2 v1.30.0 R package. DARs were annotated with their closest feature and different transcription binding motifs identified with HOMER v4.8.0. A non biaised motif search was also performed with HOMER, in order to identify all known motifs and de novo motifs in these regions.

first: Kaifee

last: Arman

first: Virginie

last: Calderon

first: Gaspard

last: Reulet

last: Möröy


title: Lysosomal control of type I interferon induction via Ragulator-Rag complex

city: Guangzhou

first: Chun-Yan

last: Lim

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

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

overall_design: Refer to individual Series