title: Pasteurized Akkermansia muciniphila ameliorates preeclampsia via inhibiting mitochondrial dysfunction-mediated placental apoptosis in vivo and in vitro

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

summary: Preeclampsia (PE) is a severe metabolic disorder that occurs during pregnancy and is linked to dysbiosis of the gut microbiota, characterised by a decrease in Akkermansia muciniphila (AKK). Emerging evidence suggests that pasteurised Akkermansia muciniphila (pAKK) is a promising candidate for preventing or treating obesity-related metabolic disorders. Nonetheless, the modulatory function and underlying mechanisms of pAKK as a supplement for PE have yet to be investigated. In this study, we examined the impact of pAKK oral administration on PE and its underlying mechanisms. Our findings demonstrate that pAKK significantly improved PE-like symptoms in mice induced by nitro-L-arginine methylester (L-NAME) in a dose-dependent manner. Importantly, pAKK inhibited L-NAME-induced placental apoptosis, countered apoptosis-related biochemical alterations like the increase in the Bax/Bcl-2 ratio, and the activation of cleaved-Caspase-3, alongside mitigating L-NAME-induced placental mitochondrial dysfunction. Hypoxia-reoxygenation (H/R)-induced HTR8/SVneo cells have been established as an in vitro model to mimic the condition of PE. Interestingly, similar results were also obtained in vitro; mitochondrial dysfunction-mediated apoptosis induced by H/R in HTR-8/SVneo cells was prevented by pAKK. Furthermore, the PI3K inhibitor (LY294002) significantly negated the protective effects of pAKK on mitochondrial dysfunction and apoptosis. Our findings indicate that pAKK improved PE-like symptoms both in vivo and in vitro by activating the PI3K/Akt signalling pathway, highlighting the potential for developing a probiotic therapeutic agent based on AKK for PE.

overall_design: RNA-seq profiling of widetype HTR8/SVneo cells treated with PBS, H/R, or pAKK+H/R

first: Haizhen

last: Wang

first: Yu


title: Cortical bulk RNA sequencing of APOE-TR mice under calorie restriction and normal diet

status: Public on Jun 30 2026

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: The efficacy of calorie restriction (CR) in enhancing cognition, promoting healthy aging, and extending lifespan is well-established. However, the influence of the apolipoprotein E (APOE) genotype, a key modifier of aging and age-related disorder, on the beneficial effects of CR remains unclear. In this study, we utilized humanized APOE mouse models expressing APOE2, APOE3, or APOE4 (referred to as E2, E3, and E4 mice, respectively). These mice were subjected to either standard ad libitum (AL) feeding or 30% CR feeding, starting at 12 months and continuing until 20 months of age (N = 11–20/genotype/group, mixed sex). To investigate how APOE genotype modifies brain transcriptional responses to CR, we performed bulk RNA sequencing on brain cortical tissues including 69 samples from all the groups. The RNA-seq data were adjusted for flow cell, exonic coverage, and extraction batch effects. Using preprocessed gene expression profiles, we conducted weighted gene co-expression network analyses (WGCNA) and differential gene expression analyses. Consistently across both approaches, our results revealed an upregulation of the cholesterol synthesis pathway in E3- and E4-CR mice, but not in E2-CR mice. CR related DEGs also predicted the enhanced myelination, which were further validated through immunofluorescent staining for PDGFRA (an OPC marker), ASPA (an OL marker), and MBP (a myelin sheath protein), as well as electron microscopy of corpus callosum tissues in E3- and E4-CR mice, but not in E2-CR mice. Overall, our study highlights the critical role of APOE genotype in modulating the brain’s response to CR, emphasizing the importance of considering APOE genotype in developing prevention strategies for aging and age-related disorders.

overall_design: A total of 69 samples were used for this project, including 9 from E2-AL (4Female/5Male), 12 from E3-AL (6F/6M), 11 from E4-AL (6F/5M), 11 from E2-CR (5F/6M), 14 from E3-CR (7F/7M), and 12 from E4-CR (6F/6M).

first: Wenhui

last: Qiao

first: Yingxue

last: Ren


title: Tuning BMP-Regulated Cell Differentiation in the Aortic Media by Mutating Matrix Gla Protein

city: Los Angeles

first: Xinjiang

last: Cai

state: CA

department: Medicine/Cardiology

institute: University of California, Los Angeles

summary: The integrity of the vascular wall is crucial for maintaining the normal function of blood vessels. Matrix Gla protein (MGP), originally identified as an inhibitor of bone morphogenetic proteins (BMPs) and vascular calcification, is now recognized as a key vascular morphogen that guides cell differentiation across various tissues. In this study, we employed an MGP Pro64Gly knock-in mouse model alongside single-cell RNA sequencing to explore the role of MGP in mediating vascular cell differentiation. The Pro64Gly mutation specifically impairs MGP's ability to bind to and inhibit BMPs.

overall_design: Aortas were isolated from both wild-type and knock-in mice, followed by enzymatic digestion.  After dead cells wer removed by DAPI staining and FACS, live cells were sent for scRNA-sequencing.

first: Kristina

last: Bostrom


title: Overcoming MET-targeted drug resistance in MET-amplified lung cancer by Aurora Kinase B inhibition

city: Goyang-si

first: Yu-Ra

last: Choi

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: national cancer center

summary: This study investigates the mechanisms of resistance to MET-targeted therapy in MET-amplified lung cancer. Researchers established a lung cancer cell line resistant to MET tyrosine kinase inhibitors (MET-TKI) and found that Aurora kinase B (AURKB) inhibitors significantly inhibited the proliferation of these resistant cells. AURKB knockdown enhanced MET-TKI sensitivity, though the phosphorylation of Histone H3, an AURKB target, remained unchanged. Gene expression analysis revealed an enrichment of STAT3-activated genes, and AURKB influenced the phosphorylation of STAT3. The study also identified an elevated expression of the anti-apoptotic gene BCL2, and AURKB inhibition induced apoptosis by reducing the STAT3/BCL2 axis. The effects of AURKB inhibitors led to G2/M cell cycle arrest and apoptosis in resistant cells. AURKB overexpression was observed in post-treatment tumors from advanced MET-amplified lung cancer patients with MET-TKI resistance. This suggests that targeting AURKB may be a potential therapeutic strategy to overcome resistance to MET-TKIs in MET-amplified lung cancer.

overall_design: The MET-TKI-acquired resistant cell line was established by continuously treating the parental H1993 cell line with increasing concentrations of PHA665752, starting from 1nM to 1uM. The resistant cell line was maintained with 1uM PHA665752 and was cultured in a drug-free medium for 1 week before performing all experiments.

first: Mihwa

last: Hwang

first: Jaemin

last: Kim

first: Seog‑Yun

last: Park

first: Sunshin

first: Jae J

last: Song

first: Youngjoo

last: Lee


title: Histone 3 lysine 36 methylation shapes an epigenetic landscape in intestinal stem cell to orchestrate lipid metabolism and prevent cell senescence [ATAC-seq 2]

city: Shanghai

first: Yue

last: Xu

address: 上海市徐汇区华山路

country: China

institute: 上海交通大学

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The self-renewal capacity and differentiation potential of intestinal stem cells (ISCs) decline with age, leading to a loss of homeostasis and increased susceptibility to intestinal diseases. Despite the established importance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms linking these processes to aging-associated ISC dysfunction remain elusive. Here, we demonstrate that H3K36 methylation, caused by NSD2 or SETD2, is critical to ISC fate. We found that the deficiency of H3K36 methylation results in reduced ISC proliferation and differentiation, disturbs fatty acid metabolism, and induces ISC senescence. This loss leads to increased chromatin accessibility and enhancer activation, impairing the function of the SWI/SNF chromatin remodeling complex and affecting genes expression. Importantly, we find that metabolic intervention can rescue the decline in ISC numbers due to H3K36 methylation deficiency. Our findings reveal a critical role for H3K36 methylation in maintaining epigenetic landscape to orchestrate lipid metabolism and determine intestinal stem cell fate.

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f and Lgr5-EGFP-CreERT2; Nsd2f/f  mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice. We subsequently overlapped the differentially expressed genes and those located near differentially accessible regions.

first: Ziyi


title: Histone 3 lysine 36 methylation shapes an epigenetic landscape in intestinal stem cell to orchestrate lipid metabolism and prevent cell senescence [CUT&Tag]

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f and Lgr5-EGFP-CreERT2; Nsd2f/f  mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice. CUT&Tag was performed according to the instruction of the Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina(TD903-01).We subsequently examined correlation was observed between changes in ATAC-seq and alterations in histone markers.


title: Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning [ChIP-Seq]

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

department: D-BSSE

country: Switzerland

institute: ETHZ

summary: Tissue regeneration requires de novo patterning, which has been proposed to be facilitated by cellular heterogeneity. Yet, how such heterogeneities are integrated with the mechanochemical state of the tissue, and stabilized at the chromatin level into stable and spatially organised fates, remains poorly understood. Using in vivo mouse intestinal regeneration models and organoids, we identify a critical density regime which produces a permissive window of heterogeneity in the mechanosensor YAP1. We show that YAP1 heterogeneity is coupled to lineage-biased chromatin accessibility and is decoded through FOXA1, which integrates the permissive chromatin state to Delta-Notch supra-cellular feedback and lineage commitment. This circuit generates fate bistability and preserves a memory of transient YAP1 activity, maintaining spatial patterning as tissues return to homeostasis after injury. Together, our findings establish a multiscale framework in which tissue-scale mechanics tune single-cell competence and, through FOXA1-mediated bistability, convert transient heterogeneity into stable, reproducible, and self-organised tissue architecture.

overall_design: ChIP-seq and corresponding input samples of FOXA1 in mouse intestinal organoids.

first: Cornelia

last: Schwayer

first: Silvia

last: Barbiero

first: David

middle: B

last: Brückner

first: Clara

last: Baader

first: Nicole

middle: A

last: Repina

first: Oscar

middle: E

last: Diaz

first: Ludivine

last: Challet Meylan

first: Véronique

last: Kalck

first: Simon

last: Suppinger

first: Qiutan

last: Yang

first: Jakob

last: Schnabl

first: Umut

last: Kilik

first: J. Gray

last: Camp

first: Brigitta

last: Stockinger

first: Marc

last: Bühler

first: Michael

last: Stadler

first: Edouard

last: Hannezo


title: Heparin prevents AKI to CKD transition via HDAC1-mediated anti-inflammatory effect independent from its anticoagulant properties

city: Changsha

first: Lijun

last: Yin

address: No. 139 Renmin Middle Road

institute: The Second Xiangya Hospital of Central South University

summary: Aim: This study aimed to investigate the therapeutic potential of heparin, a traditional anticoagulant, in the acute kidney injury (AKI) to chronic kidney disease (CKD) transition. Main methods: Male C57BL/6 mice were subjected to unilateral ischemia-reperfusion (uIR)-induced and folic acid (FA)-induced AKI to CKD mouse model in vivo. Heparin or chemically modified variant devoid of anticoagulant activity (N-Acetyl heparin sodium salt) was administered subcutaneously. Histological analyses, including H&E staining, Masson’s trichrome staining, immunofluorescence, and immunoblotting, were employed to assess renal tubular cell injury, interstitial fibrosis and inflammatory cell infiltration in the kidneys. RNA sequencing of murine kidney cortex tissues was performed to elucidate the mechanistic actions of heparin. Additionally, drug affinity responsive target stability (DARTS) assays and co-immunoprecipitation were conducted to explore the interaction between HDAC1 and heparin. Key findings: We found that low-dose heparin treatment significantly mitigates the AKI to CKD transition, primarily through the suppression of inflammation responses. Mechanistically, heparin binds to HDAC1 in renal tubular epithelial cells, reducing the acetylation of p65，which in turn downregulates the expression of inflammatory factors. Notably, this anti-inflammatory effect of heparin is independent of its anticoagulant activity, as the interaction between heparin and HDAC1 is unrelated to its anticoagulant domain. Furthermore, the chemically modified variant of heparin (N-Acetyl heparin sodium salt), lacking anticoagulant properties, demonstrated a similar protective effect. Significance: Our findings suggest that low-dose heparin, along with its non-anticoagulant derivatives, holds potential as a novel therapeutic approach to attenuate the progression from AKI to CKD.

overall_design: Renal mRNA profiles of 14-day uIR mouse model treated with or without heparin

first: Lin

last: Ye

first: Baiyu

last: Feng

first: Yu

last: Lu

first: Shaobin

last: Duan

first: Zheng

last: Dong

first: Anqun

last: Chen


title: Genome-scale methylation data from BA8 cortex samples from controls and schizophrenia patients.

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Hyderabad

address: Jawahar nagar

department: Biological Sciences

country: India

institute: Birla Institute of Technology and Science

type: Methylation profiling by genome tiling array

summary: Schizophrenia is a complex disorder with many contributory factors of which evidence for epigenetic mechanisms comes from the observed ~40% discordance rates between monozygotic twins. DNA methylation is one of the epigenetic marks of the genome that influence gene expression in response to developmental and environmental cues. In order to identify DNA methylation differences between frontal cortices of schizophrenia patients and age- and sex-matched controls, genome-scale methylation data was generated. Genomic DNA samples from BA8 samples isolated from 30 controls and 22 schizophrenia patients. The data generated will be useful in identifying patient-associated CpG sites or regions through differential methylation analyses.

overall_design: Genomic DNA samples isolated from 30 control and 22 schizophrenia samples were subjected to Infinium 450 K methylation array analysis

first: Naga

middle: M

last: Kommu


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [RNAseq_MiniBulk]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: In adult tissues, in response to injury or to the acquisition of a mutational landscape, epithelial stem cells leave their homeostatic state and become activated. To identify the epigenetic factors involved in this process we performed pooled genetic screens integrated with two transcriptional read out systems. These revealed a network of factors including Kmt5c (Suv420h2), Ehmt2 and Cbx3. Through a series of omics and cellular functional assays we discovered their functional role at the cellular and molecular level. In particular we identified a multi-layered control of gene expression, dependent by Cbx3, ranging from transcriptional regulation to mRNA localization.

overall_design: Kmt5c (Suv420h2) , Ehmt2 and Cbx3 -dependent transcriptional changes. Mini-bulk RNA-seq profiling of Cbx3, Kmt5c (Suv420h2) and Ehmt2 knockdown (KD) and control mouse keratinocytes.

first: Carlotta

last: Duval

first: Giacomo

last: Donati


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [shRNAseq]

overall_design: Pooled genetic screening to identify epigenetic factor controlling cell viability


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [ReGenTseq]

overall_design: Pooled screening with two reciprocal transcriptional read out systems to identify epigenetic factors controlling epidermal cell activation.


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [RNAseq_FracNuclCyto]

summary: In adult tissues, in response to injury or to the acquisition of a mutational landscape, epithelial stem cells leave their homeostatic state and become activated. To identify the epigenetic factors involved in this process we performed pooled genetic screens integrated with two transcriptional read out systems. These revealed a network of factors including Kmt5c, Ehmt2 and Cbx3. Through a series of omics and cellular functional assays we discovered their functional role at the cellular and molecular level. In particular we identified a multi-layered control of gene expression, dependent by Cbx3, ranging from transcriptional regulation to mRNA localization.

overall_design: Cytoplasmic RNA localisation controlled by Cbx3. Subcellular RNA-seq profiling of nuclear and cytoplasmic polyA+ RNA in Cbx3 knock-down (KD) (sh-Cbx3) and control (sh-Scramble) mouse keratinocytes.


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [ChIP-Seq]

overall_design: Cbx3-dependent, Kmt5c-dependent and Ehmt2-dependent chromatin states. ChIP-seq profiling of H3K27ac in Cbx3, Kmt5c (Suv420h2) and Ehmt2 knockdown (KD) and control mouse keratinocytes. ChIP-seq profiling of Cbx3 binding in mouse keratinocytes.


title: The risk SNP rs11067228 promotes prostate cancer drug resistance and neuroendocrine differentiation through 3D chromatin interactions (4C-seq data set)

city: Tianjin Shi

first: Yuan

last: Jiang

state: Tianjin Shi

address: No. 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

summary: Neuroendocrine prostate cancer is an aggressive disease characterized by early metastasis, drug resistance and poor prognosis. Genome-wide association studies (GWAS) previously identified the single nucleotide polymorphism (SNP) rs11067228 as a significant variant associated with castration-resistant metastasis (CM) in prostate cancer (PCa). However, mechanisms underlying activity of the rs11067228 risk variant remain unclear. Here, we demonstrated that risk SNP rs11067228 is located in an active H3K27ac-enriched enhancer, and show that activity of that region affects castration-resistance and neuroendocrine differentiation in PCa cells. We identified 5 functional target genes (UGT2B15, NFASC, TBX3, SRRM4, and HSPA1A) regulated by the risk enhancer and overexpression of the RNA-splicing factor SRRM4 alone was sufficient to induce PCa cell drug resistance and neuroendocrine differentiation. Moreover, site-directed mutation of the rs11067228 non-risk G to the risk A allele enabled binding of the transcription factor SOX4, activating candidate target gene expression. Taken together, our findings indicated that the rs11067228-associated enhancer modulates expression of multiple genes via allele-specific long-range chromatin interactions, thereby governing PCa drug resistance and neuroendocrine differentiation.

overall_design: 4C-seq of rs11067228-related enhancer in 22Rv1.


title: the role of NOTCH agonist and inhibitor on CC fibroblasts

city: Zhuhai

first: Biao

last: Liu

address: meihuadong road

institute: The Fifth Affiliated Hospital, Sun Yat-sen University

summary: Fibroblasts are the most abundant cell population in human corpus cavernosum. Previously, they are regarded as static and homogeneous cells, however, recent study reported fibroblasts are a dynamic and heterogeneous cell population. An article published in ‘Science’ discovered that CC fibroblasts act as key blood flow regulators, shifting the balance between vasodilators and the vasoconstrictor norepinephrine toward vasodilation. Notch signaling serves as a central hub coordinating fibroblast turnover, norepinephrine sensitivity, and, ultimately, the erectile process.  We treated CC fibroblasts with NOTCH agonist and inhibitor and performed transcriptome to find out the mechanism of Notch signaling on CC fibroblasts.

first: Liangyu

last: Zhao

first: Zhitao

last: Han


title: Degenerate long-range interactions drive phase transition of heterochromatin [Hi-C]

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

summary: Despite intensive efforts, the molecular mechanisms that organize genomes into A and B compartments are still not understood. This is largely due to experimental challenges in targeted manipulation of the molecular components involved. We made use of C. elegans as elementary model system to unveil fundamental concepts of genome compartmentalization. Simultaneous deletion of the H3 lysine 9 methylation-binding proteins HPL-2, a heterochromatin protein 1- type factor, and LIN-61, a malignant brain tudor-domain factor, expression of a dominant negative HPL-2 mutant, or abolishment of H3 lysine 9 methylation resulted in near-complete loss of A/B compartmentalization. Compartmentless genomes follow an equilibrium model of organization with transitions of compartment identity having only moderate effects on local contact domains or on gene expression. We identify degenerate long-range interactions that scalewith the high combined genomic density of HPL-2, LIN-61 and H3 lysine 9 methylation to drive heterochromatin segregation. Using simulations of a minimal polymer system, we show that such interactions are sufficient for the establishment of B compartments and for the phase transition that drives the spatial segregation of heterochromatin from euchromatin. Our findings define genomic, molecular, and mechanistic determinants that are essential for comprehending the role of genome compartmentalization and 3D organization in health and disease.

overall_design: Hi-C was performed as described with minor modifications (Crane et al., 2015). Freshly isolated nuclei were distributed into 6 x 1.5 mL Eppendorf tubes and resuspended in 300 µL 1.25X DpnII buffer. After adding 38 µL of 1% (w/v) SDS, nuclei were incubated at 65 °C and shaking at 600 rpm for 10 min on a thermomixer (Eppendorf, Germany). 34 µL of 20% (v/v) Triton X-100 wereadded and samples were incubated at 37 °C and 600 rpm for 1 hour. 12.5 µL of DpnII (NEB, USA) were added before incubation overnight at 37 °C and 2,000 xg. Following this, 52 µL of 10% (w/v) SDS were added (65 °C for 20 minutes, shaking at 1,000 rpm). Reactions were then added to 7.6 mL of ligation master mix (10% (v/v) Triton X-100, 10X T4 ligation buffer (500 mM Tris-HCl, pH7.5; 100 mM MgCl2; 100 mM DTT), 80 µL of 10 mg/mL BSA, 80 µL of 100 mM ATP, and 5.96 mL nuclease free water). 100 µL T4 DNA ligase (Invitrogen, USA) were added and the reactions were incubated for 4 hours on a rotator at 16 °C. 50 µL of 10 mg/mL proteinase K were added (65 °C, overnight). The following day, an additional 50 µL of 10 mg/mL proteinase K was added (65 °C, 2 hours) followed by 2 µL of 1 mg/mL RNaseA (Sigma, Germany) (37 °C, 30 minutes). The ligated DNA was extracted using a Midi prep kit (Macherey- Nagel™ , Germany; elution in 200 µL of nuclease free water) and stored at -20 °C. 2 µg of the eluted DNA in a total volume of 130 µL water were sheared using a Covaris E220 Focused- ultrasonicator (Covaris, USA) in micro tubes (microTUBE AFA Fiber Snap-Cap) with the following settings: duty factor, 10%; peak incident power 140 W; cycles/burst, 200; time, 55 seconds. The sheared DNA was then size selected for fragments of average size of 400 bp using SPRI beads (SPRIselect, USA). DNA was quantified using Qubit Fluorometric Quantification and libraries were prepared for sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s protocol. Libraries were sequenced on Novaseq 6000 PE150 S4 flowcells. All Hi-C experiments were conducted as biologically independent duplicates.

first: Yogesh

last: Ostwal

first: Fernando

last: Muzzopappa

first: Alexandre

last: Heurteau

first: Raoul

last: Raffel

first: Alaguraj

last: Veluchamy

first: Karthik

last: Eswara

first: Shakila

last: Ali

first: Reema

last: Kumari

first: Ahlem

last: Boudellioua

first: David

last: Depierre

first: Satya

last: Vadlamani

first: Nicolas

last: Chanard

first: Stephane

last: Schaak

first: Fabian

last: Erdel

first: Wolfgang

last: Fischle


title: Single-cell RNA sequencing of miALI epithelial cells derived from UHOMi002-A cell line

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

institute: IRMB, Hôpital Saint Eloi

summary: The goal of this study was to characterise the cells obtained after differentiation of NKX2.1+ bronchial progenitors derived from iPSCs (UHOMi002-A cell line) deposited on a collagen-chitosan matrix (miALI) pre-seeded with primary bronchial fibroblasts. The transcriptomic profiles were assessed by single-cell RNA-sequencing (10x Genomics Chromium).

overall_design: Global transcriptomic profiling at single cell resolution of iPSC-derived cells. Cell epithelial clusters were analysed on Seurat based on literature specific markers and then visualized by Uniform Manifold Approximation and Projection (UMAP).

first: John

last: De Vos

first: Arnaud

last: Bourdin

first: Florent

last: Foisset

first: Nelly

last: Frossard


title: Effect of topical application of propionic acid on gene expression in the skin lesions of AD mice

city: Guangzhou

first: Lan

last: Yang

state: Guangdong

address: 1838 North Guangzhou Street

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

summary: Secondary metabolites such as short chain fatty acids (SCFAs) are primarily responsible for skin microbiota to modulate skin homeostasis. We here report propionic acid can relieve AD in mice. To further explore the mechanism underlying the modulation of skin microbiota-derived propionic acid on AD, we performed RNA-seq analysis on the skin lesions of ctrl or propionic acid-treated MC903 induced AD mice.

overall_design: To get differentially expressed genes (DEGs) in the skin lesions of the control and propionic acid-treated AD mice,  we first generated an AD mice model by topically applying 5 nmol of MC903 on the back skin of the C57BL/6 mice (6 weeks of age, female) for 10 consecutive days. After 1 h of MC903 treatment, control or propionic acid (1 mM) was topically applied on the skin of these mice. At day 11, the skin lesions were harvested for RNA-seq

first: Gaofeng

last: Wang


title: High-resolution transcriptomic profiles of kidney distal convoluted tubules in male and female mice

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary: Sexual dimorphic responses to physiological factors in the kidney have been emerging as important considerations for understanding kidney physiology and pathophysiology. Here, we report high-resolution transcriptome profiles of distal convoluted tubules isolated from the kidneys of male and female mice. Transcriptomic analysis based on RNA-Seq cooupled with tubule microdissection was carried out in male and female mice. To accurately isolate the early DCT (DCT1) segments, microdissection was performed in a Pvalb-cre tdTomato transgenic mouse model. Transcript profiles in male and female DCT1 segments revealed comprehensive sex differences in the molecular features of the early DCT segments. Our data provide a high-resolution DCT1 (early DCT) transcriptome and serve as a reference resource for DCT research.

overall_design: RNA-Seq analysis in distal convoluted tubules isolated from the kidneys of female and male mouse mice

first: Ebrahim

last: Taheai

first: Paul

middle: R

last: Grimm

last: Welling

first: Hyun

middle: J


title: Arid1a mediates cell recovery upon gastric injury to prevent tumorigenesis [Multiome]

city: TORONTO

first: Adrian

middle: Kwan Ho

last: Loe

state: ON

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

summary: When tissues and organs are damaged, they undergo a reversible regenerative response. Since it often activates oncogenic signaling pathways, recovery after regeneration must be precisely regulated. However, its underlying mechanisms and relationship with cancer remain unclear. The stomach is constantly exposed to environmental damages such as H. pylori infection and ulcer, and undergoes an evolutionally conserved, regenerative response called spasmolytic polypeptide-expressing metaplasia (SPEM). Although this process is highly reversible, occurring in precancerous lesions, the epigenetic regulation underlying SPEM is unknown. Our single-cell chromatin and gene expression analysis defines cell fate and state dynamics in homeostasis, regeneration and recovery. Upon injury, gastric epithelial cells rapidly induce SPEM gene expression under accessible chromatin, while losing the expression and accessibility of differentiation genes. Strikingly, when Arid1a, the second most mutated gastric cancer gene, is deleted in regeneration, it abolishes cell recovery. By analyzing histone modification and chromatin accessibility, as well as mapping the binding sites of ARID1A and BRG1, we demonstrate they promote recovery through the regulation of enhancer activity. Notably, failed recovery by Arid1a loss in combination with Trp53 deletion is sufficient to induce cancer initiation and invasion, providing key insight into the mechanistic relationship between tissue recovery after regeneration and cancer.

overall_design: Wildtype or CluCreERT2;Arid1a mice were treated with 5mg/20g tamoxifen for 3 consecutive days. Stomachs glands were isolated after 0, 7 or 35 days after first dose.

middle: K

first: Alyssa

last: Ialongo

first: Yan

last: Qin

first: Ho-Sung

last: Rhee

first: Tae-Hee

last: Kim


title: Profile of mineralocorticoid receptor-dependent transcriptome from the mouse aldosterone-sensitive distal nephron

summary: The mineralocorticoid receptor (MR, Nr3c2) is responsible for aldosterone-regulation of Na+ and K+ balance and blood pressure. We apply RNA-Seq and bioinformatic approaches in isolated tubule segments of MR KO vs. Control mice to understand how aldosterone activates electrogenic Na+- K+ exchange in the aldosterone sensitive distal nephron (ASDN), including connecting tubule and cortical collecting duct tubule. MR-flox/Pax8‐rtTA/LC1 mice were used as a doxycycline (DOX)-inducible Nr3c2 gene KO model. After DOX treatment, four groups were prepared to distinguish between K+ and MR effects: 1) control mice on normal K+ diet (CT-NK) or 2) high K+ diet (CT-HK) and 3) MR knockout mice on normal K+ diet (KO-NK) or 4) low K+ diet (KO-LK). RNA-Seq analysis was carried out in the microdissected connecting tubule and cortical collecting duct tubule segments (5-6 mice per group and ~10 fresh ASDN tubules per mouse). Differential expression (DE) genes were identified (FDR< 0.05) and used for further bioinformatic analyses. DE genes were identified from comparisons of MR KO-NK vs. CT-NK and MR KO-LK vs. CT-HK, respectively. Absence of transcripts on the third exon of Nr3c2 gene confirmed complete disruption of Nr3c2 gene in the MR KO. All known aldosterone-response genes were significantly decreased in MR KO-LK compared to CT-HK. Our data provide a comprehensive MR-dependent transcriptomic profile of the ASDN isolated from the kidney.

overall_design: RNA-Seq analysis in connecting tubule and cortical collecting ducts isolated from the mouse kidneys after induction of Nr3c2 knockout.

first: Xiao-Tong

last: Su

first: David

middle: H

last: Ellison


title: B-Domain deleted Factor VIII exhibits notable differences in intracellular processing and cellular responses when compared to full length Factor VIII

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

country: Germany

institute: University Clinic Bonn

summary: Background: Gene therapy for the treatment of hemophilia A have achieved good results. However, major problem is the lack of sustainability of FVIII blood levels; also no data on the cellular response of the targeted cells is available. Hepatocytes targeting and use of B-domain-deleted F8, are two non-natural phenomena that could be linked to the decrease of FVIII-blood-levels over time, this strongly demand a thorough investigation of the suspected mechanisms at the cellular level. Aim: The aims of this study are to compare the cellular trafficking and response to different forms (FL vs BDD) and to levels of expression and secretion of FVIII in the cells. Method: we established single cells HEK293 clones expressing various levels of full-length or B-domain-deleted-FVIII. We studied the correlations between FVIII copy number and levels of expression, secretion and storage as well as homeostatic cellular parameters like ATPs level, cellular proliferation, intracellular markers co-segregation and co-localization with FVIII. Effect of cells treatment with Chloroquine, Cyclohexamid, glucose deficiency and BFA were determined. In addition, we performed 3´RNA-seq for expression profiling. Results: Our results show differences in expression/copy (higher in BDD), secretion (higher in BDD) and intracellular storage (higher in FL) between BDD and FL clones. The cellular proliferation rate was higher in FL while ATP was higher in BDD clones. Chloroquine treatment lowered secretion in FL clones but not in BDDs, while starvation, Cyclohexamid and BFA had similar effect. The co-localisations of cellular markers with FVIII show reduced presence of FVIII BDD in ER/ERGIC/GABARAP and GAPARAPL1/Lysosome while higher at GABARAPL2 and LC3B vesicles is observed. Bioinformatic analysis confirmed the cellular phenotype as differentially activated pathways and processes include organization of cytoplasm, energy, stress and proliferation related. Finally, expression association with level of secretion potentials showed clear dose effect but absence of overlaps between BDD and FL clones, indicating clear divergence of response to overexpression of BDD and FL-FVIII. Conclusions: Our data indicate intrinsic differences/effects in cellular response between BDD and FL FVIII expression/secretion.

overall_design: To investigate the effect of FVIII B-Domain deletion on FVIII secretion compared to FVIII full length

first: Muhammad

first: Osman

last: El-Maarri


title: Genome-wide distribution of REC8 cohesin is correlated with active transcription and regulated by transcription suppressor BEND2 during early meiosis [CUT&Tag]

city: Beijing

first: Chunsheng

last: Han

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To characterize REC8-binding sites on the genome, we conducted CUT&Tag analyses by using testicular cells of the Rec8-3×FLAG-2×HA knock-in (Rec8 KI) mice whose spermatogenesis was synchronized to  preleptotene, leptotene or zygotene spermatocytes. We found that REC8 preferentially binds to open promoter regions of actively transcribed genes. Futhermore, we found the dynamic changes in REC8 binding sites during meiosis are correlated with gene transcriptional status. To describe the changes of REC8 binding sites in Bend2 knockout (Bend2 KO) mice, we conducted CUT&Tag analyses by using zygotene spermatocytes from Bend2 WT and KO mice in Rec8 KI background with HA antibodies. We found both up- and down-regulated REC8 peaks were observed despite of more down-regulated ones. Moreover, we found that these changed peaks were also located in open chromatin regions which was further increased in zygotene spermatocytes of Bend2 KO mice.

overall_design: To characterize REC8-binding sites on the genome, testicular tissues from Rec8 KI mice whose spermatogenesis was synchronized to generate  preleptotene, leptotene or zygotene spermatocytes were performed in experiment. CUT&Tag data analyses were based on two independent replications. To describe the changes of REC8 binding sites in Bend2 KO mice, zygotene spermatocytes isolated by FACS from Bend2 WT and KO mice in Rec8 KI background whose spermatogenesis were synchronized to zygotene stages were performed in each experiment. CUT&Tag data analyses were based on three independent replications.

first: Dan

last: Xie

first: Longfei

last: Ma


title: Impaired vitamin D signaling in VDRgem mutants reveals novel targets in tooth and alveolar bone

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

summary: Teeth are established as targets for vitamin D metabolites but have retained less attention than the well-defined bone cell metabolism. Here we report that VDRgem mice, which bear a point-mutated vitamin D receptor unresponsive to the endogenous bioactive vitamin D, are more severely affected and have a greater severity of tooth and alveolar bone defects than VDR-null mice. Micro computed tomography (µCT) and histological analysis of adult VDRgem mice unravels severely reduced alveolar bone density, with abnormal root and pulp morphology. VDRgem mutants had severely hypocalcified alveolar bone and dentin- comparatively worse than VDR-null mice- as confirmed by scanning electron microscopy and mineral analysis. This genetically confirmed that vitamin D, acting through its receptor, enables bone and tooth to accumulate enough calcium and phosphorous for structural integrity. In addition, enamel structure was defective in VDRgem mice, displaying hypomineralized areas. Transcriptional profiling of postnatal day 5 VDRgem and VDR-null mutant incisors revealed vitamin D ligand signaling targets which promote mineralization, induce alveolar bone growth, assure dentin integrity, and regulate ribosomal protein synthesis. RNA sequencing analysis of VDRgem mutants uniquely showed defects in developmental targets- notably fibroblast growth factor and sonic hedgehog signaling reductions. Collectively, the severe defects in VDRgem tooth and alveolar bone demonstrate the importance of vitamin D actions during odontogenesis.

overall_design: To investigate the role of Vitamin D Receptor (VDR), we analyzed 2 mouse mutants (VDRgem and VDR-null). Independent lower incisors of PN5 male VDRgem, VDR-null and WT controls were analyzed by high throughput RNA sequencing (RNA-seq). Bioinformatic analysis were performed selecting significant genes using p-value < 0.05 and absolute value of log2 Fold-Change > 0.3.

first: Alexandra

last: Jimenez-Armijo

first: Agnès

last: Bloch-Zupan


title: Free fatty acid induced Nlrp3 inflammasome activation in mouse BMDMs

first: An

last: Lao

state: Shanghai

address: Xin Hua Hospital

institute: Xin Hua Hospital, Shanghai Jiao Tong University 9 School of Medicine

summary: In this manuscript, we focused on solving systemic inflammation in T2D. Chronic inflammation, is a well-established contributor to metabolic disorders such as type 2 diabetes (T2D). The Nlrp3 inflammasome appears substantial role in participating in the mechanism of T2D-induced inflammation. In the context of metabolic-inflammatory diseases like T2D, free fatty acid (FFAs) may serve as more pertinent activators of the Nlrp3 inflammasome compared to Nlrp3 regular activators like ATP. While limited works explored further mechanisms and therapy of Nlrp3 inflammasome dependent post–translational processing of proinflammatory cytokines in response to T2D-associated metabolic danger signals in the development of inflammatory-metabolic impairments.

overall_design: In this experiment, we used free fatty acid (PA-BSA) as seconed activation signals for Nlrp3 inflammasome other than the regular signals ATP. We used LPS as the first activation signals and then induced mouse BMDMs by PA-BSA.

first: Jiaqiang

last: Liu

first: Yuting

last: Cao

first: Weiqi

last: Li


title: Canonical and non-Canonical Target-directed microRNA degradation controls cell fitness and transcriptional plasticity in breast cancer

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

summary: MicroRNAs (miRNAs) play pivotal roles in cancer biology and hold promise as therapeutic targets. A recently discovered mechanism, termed target-directed miRNA degradation (TDMD), involves certain RNA transcripts ("triggers") inducing the degradation of miRNAs ("substrates"). The extent of TDMD regulation in human cancer and its implications in cancer phenotypes remain poorly understood.  Here, we fill this gap identifying miRNA substrates that accumulate post-transcriptionally upon TDMD blockade in a panel of breast cancer cell lines. Our approach identified 31 high-confidence miRNA substrates, with a few miRNAs - including miR-7, miR-29b and miR-33a/b - controlled by degradation in multiple cell types.  Combining transcriptome-wide mapping of miRNA:mRNA interactions by eCLIP with single cell RNA sequencing analysis of intratumor heterogeneity, we found that NREP limits the expression and activity of miR-29b in triple-negative breast cancer (TNBC) cell lines, fine tuning the transcriptional and phenotypic plasticity of cells along the epithelial-to-mesenchymal trajectory.   Lastly, we demonstrated the existence of a non-canonical TDMD mechanism. Specifically, SERPINE1 triggers miR-30c-5p degradation in a ZSWIM8-independent manner in TNBC cell lines, contributing to aggressive cancer phenotypes such as cancer stem cell behavior, drug resistance, and cancer heterogeneity. In conclusion, our findings support a direct role for the TDMD mechanism in cancer biology and suggest a broader involvement of miRNA decay in human physiopathology.

overall_design: HMLE cells were infected with a doxycycline inducible construct (pLVX-TetOne-Puro) expressing the TWIST protein tagged with V5 at the N-term (V5-TWIST) or C-term (TWIST-VT) . After 3 days of doxycycline, cells were fixed and ChIP performed with an anti V5 antibody.

first: Matteo

last: Marzi


summary: MicroRNAs (miRNAs) play pivotal roles in cancer biology and hold promise as therapeutic targets. A recently discovered mechanism, termed target-directed miRNA degradation (TDMD), involves certain RNA transcripts ("triggers") inducing the degradation of miRNAs ("substrates"). The extent of TDMD regulation in human cancer and its implications in cancer phenotypes remain poorly understood.  Here, we fill this gap identifying miRNA substrates that accumulate post-transcriptionally upon TDMD blockade in a panel of breast cancer cell lines. Our approach identified 31 high-confidence miRNA substrates, with a few miRNAs - including miR-7, miR-29b and miR-33a/b - controlled by degradation in multiple cell types. Combining transcriptome-wide mapping of miRNA:mRNA interactions by eCLIP with single cell RNA sequencing analysis of intratumor heterogeneity, we found that NREP limits the expression and activity of miR-29b in triple-negative breast cancer (TNBC) cell lines, fine tuning the transcriptional and phenotypic plasticity of cells along the epithelial-to-mesenchymal trajectory.  Lastly, we demonstrated the existence of a non-canonical TDMD mechanism. Specifically, SERPINE1 triggers miR-30c-5p degradation in a ZSWIM8-independent manner in TNBC cell lines, contributing to aggressive cancer phenotypes such as cancer stem cell behavior, drug resistance, and cancer heterogeneity. In conclusion, our findings support a direct role for the TDMD mechanism in cancer biology and suggest a broader involvement of miRNA decay in human physiopathology.

overall_design: SUM159PT cells were enginereed with a doxycycline inducible dCAS9-KRAB protein (CRISPRi) and infected with sgRNA targeting ZSWIM8 (n=2, sg34 and sg42) or control regions (n=2; sg118 and sg119). After 10 days, cells were fixed and miR-eCLIP protocol was performed by ECLIPSEBIO.


title: Synthetic lethal therapy reveals precision therapeutic strategy for MSH2-mutated bladder cancer

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

summary: hMSH2 (human mutS homolog 2) is the most frequently mutated gene in the DNA mismatch repair (MMR) system in bladder cancer (BCa). The majority of hMSH2 mutations result in a reduction of expression and a consequent promote cisplatin (CDDP) chemoresistance. However, precision therapeutic strategy based on hMSH2 mutations is not available clinically. Herein, we reported that knockout of hMSH2 mediated by CRISPR/cas9 technology reduced the sensitivity of BCa to CDDP. Importantly, GK921, a TGM2-specific inhibitor, increased tumor cell killing by CDDP in hMSH2-deficient BCa in a synthetic lethal manner. GK921 also promoted the chemosensitivity of Msh2-knockout mice to CDDP. Hi-C analysis indicated that hMSH2 deficiency rewired chromatin accessibility of the TGM2 promoter region, which recruits more transcription factors. The enrichment levels of transcription factor AP-1 in TGM2 promoter region were increased in hMSH2-knockout BCa cells, thereby promoting the expression of TGM2 transcriptionally. This study shows that CDDP effectiveness depends on TGM2 levels in hMSH2-mutated BCa and that combining CDDP with TGM2 inhibition may provide a promising personalized therapeutic strategy for hMSH2-mutated BCa patients.

overall_design:
Hi-C analysis indicated that hMSH2 deficiency rewired chromatin accessibility of the TGM2 promoter region, which recruits more transcription factors.
5×105 cells was collected in the 1.5 ml tube with 1mL culture medium(Gibco,11965092),and formaldehyde solution was added to achieve a final concertration of 1%. Then, the tube was placed in a Rotator for 15minuters at RT. After cross-linking, the remaining formaldehyde was sequestered by adding 27.9 μL of 2 M glycine (Sigma, G7126) and continued to rotate for 10 minutes at RT. Then, the restriction enzyme HaeIII was used for digestion. Biotin-labeled bridge linkers was used to ligate DNA fragments. Purify labled DNA fragments with Dynabeads(Invitrogen, 11047 ).Quantify the recovered DNA.The purified DNA is used directly for cluster generation and sequencing analysis using the Illumina novaseq6000 following the manufacturer’s protocols.

first: xiuyu

last: jiang


title: Characterization of leukemic stem cells in FLT3-ITD-positive acute myeloid leukemia

city: Roma

first: Serena

last: Travaglini

address: Via Montpellier 1

institute: Università di Roma Tor Vergata

summary: Despite major treatment advances, FLT3-ITD mutated acute myeloid leukemia (FLT3-ITDmut AML) still remains an unmet clinical need. We previously showed that rare CD34/CD123/CD25/CD99+ FLT3-ITDmut leukemic progenitor cells (LPCs), may persist after induction treatment and be responsible for drug resistance and disease progression.  We aimed at the functional characterization of FLT3-ITDmut LPCs, also using a NSG mouse model. The transcriptomic profile of paired blasts and LPCs, purified from 13 FLT3-ITDmut AML using RNAseq showed significant upregulation of receptor tyrosine kinases pathway, primarily lymphocyte-specific protein tyrosine kinase (LCK), which also cooperates with STAT5. Interestingly, LCK upregulation was confirmed in 28 additional FLT3-ITDmut samples, suggesting a specific therapeutic vulnerability. Indeed, a clear anti-proliferative effect of the LCK inhibitor Dasatinib was detected on the FLT3-ITDmut MV4-11 cell line and 3 primary AML LPCs, together with inhibition of FLT3 and STAT5 signalling, further potentiated by the addition of Gilteritinib. Dasatinib also induced significant downregulation of ABC transporters, a well-known cause of LSCs multi-drug resistance. Sorted LPCs were then injected into conditioned NSG mice, demonstrating their potential to engraft and induce leukemia. Interestingly, after sequential passages in mice, the LPCs compartment expanded, indicating unveil of the ancestral leukemic precursor cells.  In conclusions, we deeply characterized the FLT3-ITDmut LSCs compartment in AML, providing the first evidence that FLT3-ITDmut progenitors may engraft NSG mice, while maintaining the stem cell potential. Dasatinib/Gilteritinib combinations are able to target FLT3-ITDmut LSCs and may support eradication of residual leukemic cells harbinger of relapse.

overall_design: To functionally characterize FLT3-ITDmut LPCs and identify survival signatures and potential vulnerabilities, we investigated the transcriptome profile of sorted LPCs and paired blasts by RNA sequencing.

first: Barbieri

last: Caterina

first: Travaglini

last: Serena

first: Antonelli

last: Silvia

first: Silvestrini

last: Giorgia


title: Ectopic expression of wheat TOR coordinates a balance between photosynthetic performance and water use efficiency

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: Drought is one of the most severe environmental stresses affecting wheat production worldwide, addressing this challenge requires the development of drought-resistance wheat varieties. Target of Rapamycin (TOR) signaling is a central regulator that integrates diverse nutrient, energy, hormone, and environmental stress response signals to coordinate plants growth and development. Recent studies have uncovered the functions of TOR in plant responses to abiotic stresses. In this study, with the aim to investigate TOR functions in response to drought stress in wheat, we generated wheat transgenic plants expressing TaTOR under the control of constitutive and drought inducible promoters. We found that enhancing the expression of TaTOR, expressed by either a constitutive promoter (UBQ) or drought-induced promoters (DREM/DEH2), significantly improved drought resistance and effectively alleviated the yield loss caused by drought stress in wheat. Our findings through transcriptome analysis of TaTOR transgenic plants highlight the role of TaTOR in wheat drought resistance, thus providing a valuable new target for developing wheat cultivars with improved drought resistance to address the drought and climate change challenges threatening the wheat crop performance and productivity.

overall_design: We investigate the transcriptome of 27 samples from the three treatments (well-watered, drought-treated and re-watered) of the three genotypes (WT, GC, OE), with three replicates for each condition and genotype.

first: Sheng

last: Huajin

first: Raju

last: Datla

first: Leon

middle: V

last: Kochian


title: Genome-wide maps in breast cancer MCF-7 cells with or without the overexpression of RNPC1.

city: Nanjing

first: Huilong

address: China Pharmaceutical University

institute: China Pharmaceutical University

summary: Analysis of MCF-7 cells following RNPC1 overexpression or not. RNPC1 regulates various RNA metabolic process in MCF-7 cells.Results provide insight into the role of RNPC1-involved mechanisms underlying RNPC1-mediated effects on breast cancer stemness.

overall_design: mRNA profiles of MCF-7 cells with or without RNPC1 overexpression were generated by deep sequencing, in 3 repeats, using Illumina NovaSeq 6000.

first: Lufeng

last: Zheng


title: Transcriptom modulated by LDOC1 / H2Bub1 axis

city: Zhunan Town, Miaoli County

first: Pin

middle: Feng

last: Hung

state: Taiwan, ROC

address: 35, Keyan Road

department: Cancer research

country: Taiwan

institute: National Health Research Institutes

summary: Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is one of the prominent epigenetic marks that regulates multiple cellular processes, including immunity, stem cell differentiation, tumorigenesis, and DNA damage response, mainly through affecting transcription of specific gene sets. The Ring Finger Protein 40 (RNF40) and its paralog RNF20 forms a stable E3 ligase heterodimer is the major enzymatic complex responsible for H2B monoubiquitylation. Dysregulation of H2Bub1 was observed in early stage of non-small cell lung carcinoma (NSCLC). However, the underlying regulatory mechanism and the impact of aberrant H2Bub1 level in the metastasis and chemotherapy response of NSCLC patients remains unelucidated. We found LDOC1 associated with RNF40 in NSCLC A549 cells. In this study, we investigate the role of LDOC1 in epigenome and aggressiveness of NSCLC involving H2Bub1.

overall_design: LDOC1 depletion (shLDOC1 increased the levels of H2Bub1 in A549, ectopic expression of H2BK120R (a monoubiquitylation defected H2B) decreased the levels of H2Bub1 in A549-shLDOC1

first: Chia-Huei

last: Lee

first: Huang

last: Hsien-Neng


title: HSD17B13 Deficiency Modulates Interferon Signaling to Ameliorate Metabolic Dysfunction-Associated Steatohepatitis Fibrosis

city: Bethesda

first: Yaron

last: Rotman

address: 10 Center Drive, 10/10N248C

department: Liver Diseases Branch

institute: NIDDK

summary: The discovery that loss-of-function variants in HSD17B13 are associated with protection from Metabolic dysfunction-associated steatohepatitis (MASH, previously known as NASH) and fibrosis led to the use of HSD17B13-targeting agents in clinical trials but the underlying mechanism remains unknown. We were able to phenocopy the human findings in Hsd17b13-knockout (KO) mice fed choline-deficient amino acid-defined high fat diet (CDAA-HFD). Metabolomic and lipidomic analysis identified a beneficial shift in Hsd17b13-KO from lipotoxic cholesterol and ceramides to neutral lipids and sphingomyelins. Hepatic interferon signaling was upregulated in Hsd17b13-KO in parallel with the decrease in fibrosis. We confirmed in vitro that medium from Hsd17b13-depleted hepatocytes decreases hepatic stellate cell (HSC) activation. Hsd17b13 depletion was sufficient to induce hepatocyte interferon signaling, and induction of this pathway was sufficient to inhibit medium-exposed HSCs. We show that DiHOMEs, lipokines derived from linoleic acid, are likely the mediator by which HSD17B13 affects interferon signaling. Finally, we find a similar upregulation of hepatic interferon signaling in human subjects who carry the HSD17B13 rs72613567 loss-of-function variant. Collectively, our data suggest that loss of HSD17B13 attenuates MASH fibrosis through augmentation of protective hepatocyte interferon signaling to mitigate HSC activation. These findings shed new light on potential strategies to treat MASH-associated fibrosis.

overall_design: Total RNA isolated from livers of WT and Hsd17b13-KO mice fed with CDAA-HFD for 12 weeks. Comparative gene expression analysis of RNA-seq data obtained from CDAA-HFD fed WT and KO mouse livers were performed. Experimental groups are CDAA-WT and CDAA-KO (n=6).

first: Wenqi

last: Cui


title: N6-methyladenosine methylation landscape of human normal skin and middle ear cholesteatoma

city: Changsha

first: Wei

last: Liu

state: Hunan

address: 139 Renmin central road,Furong district

department: Otolaryngology

institute: the second xiangya hospital of central south university

summary: To determine the lncRNA and mRNA m6A quantity and expression profile in middle ear cholesteatoma and normal skin tissues, we used lncRNA and mRNA epitranscriptome microArray analysis from Arraystar to examine the RNA m6A and expression levels in middle ear cholesteatoma and normal skin tissues.

overall_design: Surgical specimen were distributed into two experimental groups: normal tissue group and cholesteatoma tissue group, then performed by Arraystar Human epitranscriptomic array (Arraystar).

first: Jun

last: He


title: miRNA-seq and RNA-seq profiles of breast cancer cell lines

first: Francesco

last: Nicassio

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Endometrial mesenchymal stem cell derived exosomal miR-4669 promotes EMT by inducing M2 macrophage polarization via the DUSP6/ERK pathway in adenomyosis

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

summary: Adenomyosis-associated macrophage (AAM) polarization-induced epithelial‐mesenchymal transition (EMT) has been implicated as a key driver in AM progression. Mechanistic studies revealed that miR-4669 induces M2 macrophage polarization by directly downregulating DUSP6 expression and activating the MAPK/ERK pathway. In turn, the polarized M2 macrophages promote EMT in ISK cells via TGF-β1 secretion. In vivo studies demonstrated that miR-4669 depletion inhibits EECs invasion and migration by targeting the DUSP6/ERK1/2 pathway in macrophages.

overall_design: RNA-seq profiling of  Negative control siRNA (NC-siRNA)  and DUSP6 siRNA (DUSP6-siRNA)

first: Yingying

last: Qiu


title: Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

institute: ETHZ


title: Histone 3 lysine 36 methylation shapes an epigenetic landscape in intestinal stem cell to orchestrate lipid metabolism and prevent cell senescence [ATAC-seq 1]

city: Shanghai

first: Yue

last: Xu

address: 上海市徐汇区华山路

institute: 上海交通大学

summary: The self-renewal capacity and differentiation potential of intestinal stem cells (ISCs) decline with age, leading to a loss of homeostasis and increased susceptibility to intestinal diseases. Despite the established importance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms linking these processes to aging-associated ISC dysfunction remain elusive. Here, we demonstrate that H3K36 methylation, caused by NSD2 or SETD2, is critical to ISC fate. We found that the deficiency of H3K36 methylation results in reduced ISC proliferation and differentiation, disturbs fatty acid metabolism, and induces ISC senescence. This loss leads to increased chromatin accessibility and enhancer activation, impairing the function of the SWI/SNF chromatin remodeling complex and affecting genes expression. Importantly, we find that metabolic intervention can rescue the decline in ISC numbers due to H3K36 methylation deficiency. Our findings reveal a critical role for H3K36 methylation in maintaining epigenetic landscape to orchestrate lipid metabolism and determine intestinal stem cell fate.

overall_design: adult  Lgr5-EGFP-CreERT2; Setd2f/f and Lgr5-EGFP-CreERT2; Nsd2f/f  mice were intraperitoneal (i.p.) injected with tamoxifen daily for five days. Control mice were intraperitoneal (i.p.) injected with corn oil. The crypts single cells isolated from Lgr5-EGFP mice. We subsequently examined correlation was observed between changes in ATAC-seq and alterations in histone markers.

first: Ziyi

last: Wang


title: Histone 3 lysine 36 methylation shapes an epigenetic landscape in intestinal stem cell to orchestrate lipid metabolism and prevent cell senescence


title: small RNA-seq gene expression profile of the SUM159PT breast cancer cell line, upon overexpression of the microRNA responsive elements of candidate TDMD triggers (ABCA1, HADHB, TRAF6)

summary: We investigate the potential of candidate microRNA responsive elements (MRE, contained in the 3'UTR of candidate transcripts) to trigger target-dependent microRNA degradation (TDMD). To this purpose, we  over-expressed the MRE by delivering a lentiviral construct in SUM159PT cells and we profiled microRNAs by small RNA sequencing 7 days after the infection.

overall_design: Lentiviral constructs (Addgene #107253), expressing a reporter gene (GFP) fused with a portion of the 3'UTR containing the MRE to be tested, was used to infect SUM159PT cells. After 7 days, RNA was collected and microRNA profiled by small RNA sequencing

first: Matteo

last: Marzi


title: Bcr1 as a negative regulator of filamentation in Candida albicans

city: ATHENS

first: Aaron

middle: P

last: Mitchell

state: GA

address: 120 EAST GREEN STREET

department: Microbiology

institute: University of Georgia

summary: Purpose: Study the impact of bcr1 mutation on the gene expression at 30°C

overall_design: Transcriptome of bcr1 mutant vs. Transcriptome of the wild-type, Transcriptome of TDH3-HGC1 mutant vs. Transcriptome of the wild-type, Transcriptome of TDH3-HGC1 bcr1 mutant vs. Transcriptome of the wild-type

first: Anupam

last: Sharma


title: RNA-Seq analysis TMAO effect on vascular smooth muscle cells

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

summary: Thoracic aneurysm/dissection (TAAD) is a life-threatening condition that lacks effective pharmacotherapeutic treatment. Vascular smooth muscle cells (VSMCs) phenotype switch and extracellular matrix (ECM) degradation has been thought to be critical to the development of TAAD. Trimethylamine N-oxide (TMAO), a metabolite produced by gut microorganisms, is tied with various risk factors for cardiovascular disease, however direct correlation with TAAD remains elusive.  RNA-seq analysis TMAO targets identified a cohort of genes, critically involved in the ECM signaling.

overall_design: VSMCs isolated and cultured from mouse aorta were treated with TMAO or control (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: Wenqian

last: Yu


title: Extensive antisense transcription in Azoarcus olearius strain BH72

city: Bremen

first: Shanmugam

last: Solaiyappan Mani

address: Leobner strasse

department: Department of Microbe-Plant Interactions

institute: University of Bremen

summary: Azoarcus olearius strain BH72 is a plant endophyte that can fix atmospheric nitrogen for plant assimilation. Our recent directional RNA-Seq analysis detected widespread presence of reads mapping in the antisense orientation to the annotated genes. Although this has been discovered for several bacteria, the stable expression and functional relevance of such antisense RNAs (asRNAs) are still being debated. In this study we ventured to confirm the single-cell expression and unravel the functionality of antisense transcription in strain BH72. First, from the directional RNA-Seq data we predicted 798 asRNAs that were encoded against 709 genes (18 % of the annotated genome). Using a cassette encoding for two fluorescent reporters (GFP and TdTomato), in convergent orientation with transcriptional terminators in between, we were able to confirm the single-cell co-expression of both the sense and the antisense transcripts within azo1349 in at least 90 % of the bacterial population. By modifying the above experimental setup, we observed the interference exhibited by these overlapping transcripts. Further, decreasing the ribosomal occupancy on one of the overlapping transcripts increased its repression of the complimentary transcript. However, RNA-Seq analysis of a RNase III deficient mutant indicated a minimal effect of the endoribonuclease on the regulation of sense-antisense pairs in strain BH72.  Lastly, we elucidated the control mediated by RNase III and asRNA on the expression of genes in the type six secretion system-1 cluster.

overall_design: Directional RNA-Seq analysis to compare the transcriptome of diazotrophic Azoarcus olearius strain BHΔrnc grown microaerobically under N2-fixing and ammonium-based growth (with ammonium chloride as nitrogen source). Samples 1-3: Samples from ammonium-based growth. Samples 4 and 5: Samples grown under N2-fixing conditions.

middle: S

last: Mani

first: Thomas

last: Hurek

first: Barbara

last: Reinhold-Hurek


title: Pattern of variation in DNA methylation

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

institute: National institute of Biomedical Genomics

summary: Genome-wide DNA methylation profiling of peripheral blood DNA. The Illumina Infinium EPIC Human DNA methylation BeadChip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs.

overall_design: Bisulphite converted DNA from the 136 samples were hybridised to the Illumina Infinium EPIC Human Methylation BeadChip v1.2.8.

first: Jagyashila

last: Das

first: Soumi

last: Sarkar

first: Indranil

last: Bagchi

first: Shekhar

last: Ghosh

first: Nitya

last: Wadhwa

first: Uma

middle: C

last: Nachu

first: Ramachandran

last: Thiruvengadam

first: Pallavi

last: Kshetrapal

first: Shinjini

last: Bhatnagar

first: Partha

last: Majumder


title: 冷冻化处理和通道依赖性恢复下HeLa细胞的RNA序列分析

status: Public on Jun 29 2026

city: Guangzhou

first: Jiangfan

last: Cao

address: Xiaoguwei Street

institute: South China University of Technology

summary: This study performed RNA sequencing to investigate transcriptional changes in HeLa cells under cryosilicification treatment (Si20 and Si30) and in untreated controls. Cells were profiled at early response stage (P0, 0 h and 6 h) and during passage-dependent recovery (P1–P3). Differential gene expression and pathway analyses were conducted to characterize cellular responses to cryosilicification and to evaluate the persistence of transcriptional changes across cell passages. All samples were sequenced using Illumina NovaSeq platforms (NovaSeq 6000 and NovaSeq X Plus), and both raw sequencing data and processed expression matrices are provided.

overall_design: HeLa cells were subjected to cryosilicification treatment using Si20 and Si30 conditions, with untreated cells serving as controls. Transcriptomic profiles were generated at early response stage (0 h and 6 h, P0) and during subsequent passages (P1–P3) to assess both immediate and long-term transcriptional effects. Samples were grouped by treatment condition and passage number, and RNA-seq was performed using paired-end sequencing on Illumina platforms.

first: 江凡

last: 曹

first: 魏

last: 朱


title: Smarcc1 drives optic stalk patterning and optic nerve head astrocyte differentiation

city: Tel aviv

first: Nitay

last: Zuk-Bar

address: Chaim Levanon St 55

country: Israel

institute: Tel aviv university

summary: The optic nerve develops from the neuroectodermal optic stalk, which undergoes coordinated morphogenesis and gives rise to optic nerve astrocytes that support retinal ganglion cell (RGC) axons. Here, we define the progression of astrocyte formation from the optic stalk and identify stage‑specific functions of the SWI/SNF scaffolding subunits Smarcc1 (Baf155) and Smarcc2 (Baf170). Both factors are co‑expressed in retinal pigment epithelium (RPE) and optic stalk progenitors, with Smarcc2 persisting in differentiated RPE and astrocytes. Conditional deletion using Dct‑Cre revealed compensatory activity in pigmented lineages, whereas Smarcc1 loss uniquely disrupted optic nerve head (ONH) morphogenesis, resulting in glial lamina collapse, RGC degeneration, and progressive visual decline. Spatial transcriptomics and functional assays show that Smarcc1 enables dorsal optic stalk progenitors to transition from a pigmented, RPE‑like state to astrocyte progenitors by repressing pigment gene programs and permitting Pax2/Sox2 activity. After specification, Smarcc1 is also required for glial lamina assembly and astrocyte migration into the inner retina. These findings demonstrate that Smarcc1‑dependent chromatin remodeling coordinates astrocyte specification with ONH morphogenesis to maintain long‑term retinal function.

overall_design: The spatial transcriptome of the developing RPE and OS was obtained according to the Geo-seq (Chen et al. 2017) protocol with minor modifications. Briefly, E12 and E14 mouse embryonic heads were fresh frozen embedded in OCT and cryosectioned at a thickness of 12 μm. Sections were transferred onto LCM PEN membrane slides, immediately fixed in ethanol, and stained with 1% (v/v) Cresyl Violet acetate in 75% ethanol solution. From the selected sections, using LCM, we isolated four RPE sections and six OS sections of the E12 embryos (four controls and six Smarcc1-DCT-cKO ), or three sections of the transverse OS from the E14 embryos (four controls and five Smarcc1-DCT-cKO ).

first: Shai

last: Ovadia

first: Guizhong

last: Cui

first: Naihe

last: Jing

first: Ruth

last: Ashery-Padan


title: Time-resolved transcriptomic responses of kidney distal convoluted tubules induced by furosemide

city: Baltimore

first: Hyun Jun

last: Jung

address: 720 Rutland Ave, Ross Research Building 1165B

institute: Johns Hopkins University School of Medicine

summary: The distal convoluted tubule (DCT) of the kidney undergoes tubule remodeling in response to physiologic stresses. This process has been implicated in physiological mechanisms resistant to loop diuretics. However, the molecular mechanisms underlying DCT cell state transitioning in the development of diuretic resistance are unknown. Here, we investigated early cellular responses in the high-resolution transcriptome of the early DCT (DCT1) and an initial activation of cellular regulatory programs after furosemide administration. Time-resolved transcriptomic changes of the DCT1 at four different time points (12h, 24h, 48h, and 96 h) after furosemide administration were identified RNA-Seq analysis in the microdissected DCT1 segments. This study provides comprehensive resource for the early DCT transcriptome and a novel insight into a cellular process of the distal tubule remodeling in the development of loop diuretic resistance.

overall_design: Time-course RNA-Seq analysis in distal convoluted tubules isolated from female and male mice fed with furosemide-containing diet or control diet

first: Ebrahim

last: Taheai

first: Paul

last: Grimm

last: Welling

first: Hyun


title: Role of the catalytic beta subunit of calcineurin (Ppp3cb) in angiotensin II induced vascular changes

city: Halle

first: Alexander

last: Nolze

address: Magdeburger Strasse 6

institute: MLU Halle-Wittenberg

summary: Cardiovascular diseases are common causes of death and often coincide with vascular remodeling induced by pathological activation of the renin-angiotensin-aldosterone system (RAAS). angiotensin II (angII), a key effector of the RAAS, is an important mediator of pathological vascular changes by contributing to altered vascular tone, inflammatory processes and structural remodeling with fibrosis. Several studies showed sex differences in the cardiovascular angII response. Calcineurin (PPP3), a serine/threonine phosphatase consisting of an enzymatic and a catalytic subunit, is known for its role in inflammatory processes and cellular hypertrophy. Hence, we investigated the role of calcineurin for angII-induced vascular remodeling with the help of a mouse model lacking the catalytic beta subunit of calcineurin (Ppp3cb KO).

overall_design: Mice were purchased from Jackson laboratory (JAX; B6,129S6-Ppp3cbtm1Jmk/J; stock #009066) and kept under SPF conditions 25. Mice were kept under a 12h/12h light/dark cycle with a room temperature of 20 ± 1 °C. Genotyping was performed according to JAX. Mouse experiments were performed with 5 month old male and female mice and were approved by the local government (Landesverwaltungsamt Sachsen-Anhalt, Halle, Germany, permit number 42502-2-1164 MLU and 42502-2-1602 MLU). All animal procedures performed conformed to the guidelines from Directive 2010/63/EU. The study was blinded and randomized. AngII-releasing osmotic minipumps (500 ng/kg bodyweight/min) were implanted after isoflurane narcotizing (2 % in 100 % O2, 1 L/min) for a time period of four weeks. During that time period systolic blood pressure was measured via tailcuff method after a 2 week training period. Animals were then sacrified, organ weights were determined and aortae as well as mesenteric arteries were used for myography measurements , histological stainings and RNA isolation.

first: Nolze

last: Alexander

first: Ruhs

last: Stefanie

first: Quarch

last: Katja

first: Straetz

last: Nicole

first: Koehler

last: Conny

first: Gekle

last: Michael

first: Grossmann

last: Claudia


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [RNAseq_FracNuclCytoProtr]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

institute: University of Turin

summary: In adult tissues, in response to injury or to the acquisition of a mutational landscape, epithelial stem cells leave their homeostatic state and become activated. To identify the epigenetic factors involved in this process we performed pooled genetic screens integrated with two transcriptional read out systems. These revealed a network of factors including Kmt5c (Suv420h2), Ehmt2 and Cbx3. Through a series of omics and cellular functional assays we discovered their functional role at the cellular and molecular level. In particular we identified a multi-layered control of gene expression, dependent by Cbx3, ranging from transcriptional regulation to mRNA localization.

overall_design: Cell protrusions RNA localisation controlled by Cbx3. Subcellular RNA-seq profiling of cell body, nuclear, cytoplasmic and cell protrusions polyA+ RNA in Cbx3 knock-down (KD) (sh-Cbx3) and control (sh-Scramble) mouse keratinocytes.

first: Carlotta

last: Duval

first: Giacomo

last: Donati


title: Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [RNAseq_Deep]

summary: In adult tissues, in response to injury or to the acquisition of a mutational landscape, epithelial stem cells leave their homeostatic state and become activated. To identify the epigenetic factors involved in this process we performed pooled genetic screens integrated with two transcriptional read out systems. These revealed a network of factors including Kmt5c, Ehmt2 and Cbx3. Through a series of omics and cellular functional assays we discovered their functional role at the cellular and molecular level. In particular we identified a multi-layered control of gene expression, dependent by Cbx3, ranging from transcriptional regulation to mRNA localization.

overall_design: Cbx3-dependent regulation of RNA splicing. Deep RNA-seq profiling of Cbx3 knock-down (KD) (sh-Cbx3) and control (sh-Scramble) mouse keratinocytes.


title: GABARAPs proteins modulate FVIII secretion in molecule-specific manner via energy related pathways

city: Bonn

first: Muhammad Ahmer

last: Jamil

address: Sigmund-Freud Str. 25

institute: University Clinic Bonn

summary: Little is known about the biogenesis of Factor VIII (FVIII), its control of expression, intracellular trafficking, secretion, and associated cellular energy requirements. In this project, we employed a Y2H approach in to identify new interacting proteins that may play a role in the above mentioned processes. As a result, we successfully isolated GABARAP, an ATG8 protein, as a potential interactor with the FVIII-B domain. While GABARAP did not co-immunoprecipitate with FVIII, we observed a weak interaction with full-length FVIII (FL-FVIII) but not with the B-domain-deleted FVIII (BDD-FVIII) using the BLITZ system. Additionally, there was a significant increase in the co-localization of GABARAP with FL-FVIII compared to BDD-FVIII. Furthermore, both transient knockdown of GABARAP through siRNA and stable knockout using CRISPR resulted in a decrease in FVIII secretion. Similar effects on FVIII secretion were observed for knockouts of MCFD2, LMAN1, and Calreticulin, while a contrasting effect, increasing secretion, was seen for knockouts of Calnexin, GABARAPL1, GABARAPL2, and ATG7. To explain the differential effects on FVIII secretion, we examined the expression profiles of the knockouts and the wild-type clones, revealing differences in several pathways, notably energy related oxidative phosphorylation and mitochondrial function. The residual cellular ATP content and cellular mitochondrial function showed a strong correlation with FVIII secretion levels. These findings establish a link between GABARAP proteins, the cellular energy status, and FVIII secretion.

overall_design: To investigate the effect of individual knockouts on F8 secretion/activity, we perform a knockout of CALR, CANX, LMAN1, MCFD2, GABARAP, GABARAPL1, GABARAPL2, and ATG7 in specialized cell line of HEK28. It is HEK293 cell line with a specific function of secreting significant amount of F8

first: Muhammad

first: Osman

last: El-Maarri


title: EV-mediated Monocytes Reprogramming in Mycobacterium tuberculosis Infection

city: New Orleans

first: Tony

last: Hu

state: LA

address: 333 S Liberty St

department: Biochemistry and Molecular Biology

institute: Tulane University

summary: Extracellular vesicles (EVs) secreted by Mtb-infected macrophages (MΦEVMtb) may influence the host innate immune response to Mtb-infection, but specific EV-induced mechanisms that regulate such cell phenotype changes are not yet known. We report that PMBCs cultured with MΦEVMtb exhibit a marked classical to intermediate monocyte polarization effect, as detected by single-cell RNA sequencing and flow cytometry results. Moreover, this effect appears to correspond with the activation of the alternative NF-κB pathway, and can be partially recapitulated by treating PBMCs with EV derived from recombinant cell line that overexpresses TRAF1, a direct regulator of this pathway. Collectively, we depict an EV-mediated monocyte reprogram landscape in the context of Mtb infection and highlight a potential link between EV and pathogenesis of tuberculosis.

overall_design:
PBMCs isolated from individuals with and without evidence of Mtb infection, were cultured for 48 h with MΦEVMtb and MΦEVMock fractions, and then analyzed by single cell RNA sequencing (scRNA-seq)
Please note that each sample record represents pooled-sample, and that the information for the 13 individual samples, (e.g. attributes/characteristics, processed data files, raw data files, etc.) is provided in the 'Supplemental file_sample_metadata.xlsx' file.

first: Lin

last: Li

middle: Y

first: Xiaojiang

last: Xu

first: Haoyang

last: Liang

first: Bo

last: Ning

first: Christopher

last: Lyon


title: Degenerate long-range interactions drive phase transition of heterochromatin [RNA-Seq]

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

institute: CNRS

summary: Despite intensive efforts, the molecular mechanisms that organize genomes into A and B compartments are still not understood. This is largely due to experimental challenges in targeted manipulation of the molecular components involved. We made use of C. elegans as elementary model system to unveil fundamental concepts of genome compartmentalization. Simultaneous deletion of the H3 lysine 9 methylation-binding proteins HPL-2, a heterochromatin protein 1- type factor, and LIN-61, a malignant brain tudor-domain factor, expression of a dominant negative HPL-2 mutant, or abolishment of H3 lysine 9 methylation resulted in near-complete loss of A/B compartmentalization. Compartmentless genomes follow an equilibrium model of organization with transitions of compartment identity having only moderate effects on local contact domains or on gene expression. We identify degenerate long-range interactions that scalewith the high combined genomic density of HPL-2, LIN-61 and H3 lysine 9 methylation to drive heterochromatin segregation. Using simulations of a minimal polymer system, we show that such interactions are sufficient for the establishment of B compartments and for the phase transition that drives the spatial segregation of heterochromatin from euchromatin. Our findings define genomic, molecular, and mechanistic determinants that are essential for comprehending the role of genome compartmentalization and 3D organization in health and disease.

overall_design: C. elegans RNA was extracted as described (Green and Sambrook, 2020). Briefly, late stage embryos were collected from worms grown on five NGM plates and flash frozen in liquid N2. The frozen pellet was grinded to a fine powder and dissolved in ten volumes of TRIzol™ (Invitrogen, USA). Total RNA was isolated according to the manufacturer’s protocol, flash frozen in liquid N2 and stored at -80 °C. For RNA-seq, library preparation and sequencing were performed by Novogene (Novogene Co, Hong Kong).

first: Yogesh

last: Ostwal

first: Fernando

last: Muzzopappa

first: Alexandre

last: Heurteau

first: Raoul

last: Raffel

first: Alaguraj

last: Veluchamy

first: Karthik

last: Eswara

first: Shakila

last: Ali

first: Reema

last: Kumari

first: Ahlem

last: Boudellioua

first: David

last: Depierre

first: Satya

last: Vadlamani

first: Nicolas

last: Chanard

first: Stephane

last: Schaak

first: Fabian

last: Erdel

first: Wolfgang

last: Fischle


title: Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning [scATAC-Seq]

first: Prisca

last: Liberali

summary: Tissue regeneration requires de novo patterning, which has been proposed to be facilitated by cellular heterogeneity. Yet, how such heterogeneities are integrated with the mechanochemical state of the tissue, and stabilized at the chromatin level into stable and spatially organised fates, remains poorly understood. Using in vivo mouse intestinal regeneration models and organoids, we identify a critical density regime which produces a permissive window of heterogeneity in the mechanosensor YAP1. We show that YAP1 heterogeneity is coupled to lineage-biased chromatin accessibility and is decoded through FOXA1, which integrates the permissive chromatin state to Delta-Notch supra-cellular feedback and lineage commitment. This circuit generates fate bistability and preserves a memory of transient YAP1 activity, maintaining spatial patterning as tissues return to homeostasis after injury. Together, our findings establish a multiscale framework in which tissue-scale mechanics tune single-cell competence and, through FOXA1-mediated bistability, convert transient heterogeneity into stable, reproducible, and self-organised tissue architecture.

overall_design: Single cell ATAC-seq timecourse of mouse intestinal organoid regeneration at 12h intervals from 24h until 84h after seeding.

first: Cornelia

last: Schwayer

first: Silvia

last: Barbiero

last: Brückner

first: Clara

last: Baader

first: Nicole

last: Repina

first: Oscar

last: Diaz

first: Ludivine

last: Challet Meylan

first: Véronique

last: Kalck

first: Simon

last: Suppinger

first: Qiutan

last: Yang

first: Jakob

last: Schnabl

first: Umut

last: Kilik

first: J. Gray

last: Camp

first: Brigitta

last: Stockinger

first: Marc

last: Bühler

first: Michael

last: Stadler

first: Edouard

last: Hannezo


title: Genome-wide distribution of REC8 cohesin is correlated with active transcription and regulated by transcription suppressor BEND2 during early meiosis [ATAC-seq]

city: Beijing

first: Chunsheng

last: Han

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To characterize REC8-binding sites on the genome in leptotene spermatocytes, we conducted ATAC-seq analyses by using leptotene spermatocytes isolated from wildtype mice through Hoechst 33342 staining and FACS. We found that REC8 preferentially binds to open promoter regions in leptotene spermatocytes.

overall_design: Leptotene spermatocytes isolated by FACS from adult wildtype mice were performed in each experiment. ATAC-seq data analyses were based on two independent replications.

first: Dan

last: Xie

first: Longfei

last: Ma


title: The risk SNP rs11067228 promotes prostate cancer drug resistance and neuroendocrine differentiation through 3D chromatin interactions (RNA-seq data set)

city: Tianjin Shi

first: Yuan

last: Jiang

address: No. 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

summary: Neuroendocrine prostate cancer is an aggressive disease characterized by early metastasis, drug resistance and poor prognosis. Genome-wide association studies (GWAS) previously identified the single nucleotide polymorphism (SNP) rs11067228 as a significant variant associated with castration-resistant metastasis (CM) in prostate cancer (PCa). However, mechanisms underlying activity of the rs11067228 risk variant remain unclear. Here, we demonstrated that risk SNP rs11067228 is located in an active H3K27ac-enriched enhancer, and show that activity of that region affects castration-resistance and neuroendocrine differentiation in PCa cells. We identified 5 functional target genes (UGT2B15, NFASC, TBX3, SRRM4, and HSPA1A) regulated by the risk enhancer and overexpression of the RNA-splicing factor SRRM4 alone was sufficient to induce PCa cell drug resistance and neuroendocrine differentiation. Moreover, site-directed mutation of the rs11067228 non-risk G to the risk A allele enabled binding of the transcription factor SOX4, activating candidate target gene expression. Taken together, our findings indicated that the rs11067228-associated enhancer modulates expression of multiple genes via allele-specific long-range chromatin interactions, thereby governing PCa drug resistance and neuroendocrine differentiation.

overall_design: 22Rv1 mRNA profiles of wild type (WT), rs11067228 knockout (KO) and rs11067228 mutation (MUT).


title: Methyglyoxal reshapes the transcriptional network of human retinal endothelial cells [miRNA-seq]

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

summary: Diabetic retinopathy (DR) is a complex microvascular complication of diabetes and a leading cause of vision impairment. A primary event of DR is the functional impairment of microvascular cells (i.e., pericytes and endothelial cells) and pathological changes in the retinal neurovascular unit. In diabetes-related complications, advanced glycation end products (AGEs) play a pivotal role in oxidative damage induced by chronic hyperglycemia particularly in damaging retinal endothelial cells. Methylglyoxal (MGO) is the most reactive AGE precursor, able to induce vascular damage, neuroretinal dysfunction and retinal lesions. Here, we demonstrate that sublethal doses of MGO induce protein glycation adduct formation in human retinal endothelial cells (hRECs), impairing the migratory and tube-forming capabilities. Moreover, transcriptome and miRNome analyses highlighted extensive perturbations in gene expression and microRNA profiles, especially related to gene expression regulation, cell cycle, cell death and vasculature development.

overall_design: To assess, at the molecul level, the pathological changes in the retinal neurovascular unit caused by methylglyoxal (MGO), we expsoed primary human retinal endothelial cells (hRECs) to a fixed sublethal dose of MGO. Then, we analyzed the gene expression changes by transcriptome analysis (bulk RNA-Sequencing) and miRNome analyses.

first: Alfredo

last: Ciccodicola

first: Marianna

last: Aprile

first: Claudia

last: Miele

first: Cecilia

last: Nigro


title: Ly6Chi and Ly6Clow blood monocytes from naïve and Heligmosomoides polygyrus bakeri infected mice

city: Manchester

first: Kelly

last: Wemyss

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary: Alterations to monocyte output and function occur during infections that drive classical Th1-type inflammation. The degree to which the circulating monocyte compartment responds to infections that initiate alternative types of response is poorly understood. Here we describe a unique state of the monocyte compartment associated with type 2-favouring intestinal helminths. The adapted monocyte state in a type 2 setting was associated with an interferon-signature. Acquisition of this interferon-induced state provided helminth-infected animals with unappreciated systemic protection against secondary bacterial infection, but still allowed for the development of effective type-2 immunity. This pathway of monocyte education was completely distinct from that described in Th1-settings and involved an endogenous-bacteria-mediated induction of type I IFN that led to adaptive lymphocyte-dependent IFN- priming of monocytes. These findings reveal an IFN-driven mechanism of monocytes education that enables the host to be simultaneously protected against type-2 infections at barrier sites and type-1 infections in the circulation.

overall_design: Bulk RNA-seq profiling of Ly6hi and Ly6Clow blood monocytes, sorted by FACS (from n=3 mice), from wild-type (sex) C57BL/6J, male, 8-12 weeks, that were naïve or at day 7 post-infection with 200 Heligmosomoides polygyrus bakeri L3 larvae that had been orally administered.

first: Ian

last: Prise

first: John

last: Grainger


title: Expression of the transcription factor ZBTB16 in porcine testes and molecular mechanisms for its regulation in porcine immature spermatogonia self-renewal

city: 咸阳市

first: YouJie

last: Cui

state: 陕西省

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院

summary: ZBTB16, a transcription factor, plays a critical role in the self-renewal and differentiation of mouse primordial germ cells. However, the subcellular localization of ZBTB16 in the porcine testis and its molecular mechanism in regulating the self-renewal of immature porcine germ cells remain unclear. Using immunofluorescence co-staining, we examined the subcellular localization of ZBTB16 and its co-localization with molecular markers for immature porcine germ cells (DBA, ZBTB16, UCHL1) and the proliferation marker Ki67 in the testes of pigs at 7, 30, 70, and 90 days of age. The results showed that ZBTB16-positive cells in the four age groups of pig testes highly overlapped with SALL4/UCHL1-positive cells and partially overlapped with DBA-positive cells, indicating that ZBTB16 is predominantly expressed in immature porcine germ cells, including pig primordial germ cells, spermatogonial stem cells, and undifferentiated spermatogonia. Furthermore, the immunofluorescence co-staining of ZBTB16 and Ki67 revealed that ZBTB16-positive cells in pig testes at different developmental stages exhibited proliferative activity, but with significant fluctuations. RNA-seq analysis identified 5931 differentially expressed genes in ZBTB16-knockdown immature porcine germ cells, while CUT&Tag analysis identified 5409 ZBTB16 target genes, with 2084 of them overlapping with the differentially expressed genes. ZBTB16 preferentially bound to gene promoters. Knockdown of ZBTB16 expression resulted in the suppression of mRNA levels of target genes involved in the self-renewal of immature germ cells. Additionally, we found that ZBTB16 regulates the self-renewal of immature porcine germ cells through the PI3K/AKT/mTOR pathway. These findings reveal the expression pattern of ZBTB16 in the porcine testis and its regulation of target genes and pathways involved in the self-renewal of immature germ cells. This contributes to the understanding of the function and regulatory network of the transcription factor ZBTB16 in porcine germ cell development and spermatogenesis, and holds significant implications for unraveling the molecular mechanisms underlying porcine germ cell development and sperm production.

overall_design: Firstly, we plan to select porcine testicular tissues at 7, 30, 70, and 90 days of age for paraffin embedding. Immunofluorescence double staining will be conducted using molecular markers for undifferentiated germ cells, such as ZBTB16, SALL4, UCHL1, and DBA, to investigate the expression and localization of ZBTB16 in different age groups of porcine testes. Qualitative and quantitative analysis will be performed to determine the co-localization of ZBTB16 with other germ cell molecular markers.Next, primary porcine immature spermatogonia will be collected, and a library of ZBTB16-bound target genes in porcine immature spermatogonia will be established using ZBTB16 antibodies and CUT&Tag technology. Through systematic analysis of the sequencing results, ZBTB16-bound target genes in porcine immature spermatogonia will be identified, and their associated pathways will be predicted using bioinformatics software.Subsequently, siRNA sequences targeting the porcine Zbtb16 gene will be designed and synthesized. The efficiency of Zbtb16 knockdown will be evaluated by transfecting immortalized porcine immature spermatogonia lines and performing qPCR. The siRNA with the highest knockdown efficiency will be selected. The designed oligos will be packaged into lentiviruses, and primary porcine immature spermatogonia will be transduced with Zbtb16-shRNA using lentiviral transduction. RNA-seq analysis will then be performed. Finally, the CUT&Tag data will be combined with the RNA-seq data for integrated analysis. Key genes and pathways related to the regulation of porcine immature spermatogonia self-renewal by ZBTB16 will be identified and experimentally validated. In addition, cross-species analysis will be conducted by downloading mouse ZBTB16 ChIP-seq and RNA-seq data to identify conserved and differential target genes and associated pathways regulated by ZBTB16 in mouse and porcine immature spermatogonia self-renewal.


title: Evolution of transcriptomic profiles in relapsed inv(16) acute myeloid leukemia

city: Roma

first: Serena

last: Travaglini

address: Via Montpellier 1

institute: Università di Roma Tor Vergata

summary: Acute myeloid leukemia (AML) with inv(16) is typically associated to a favourable prognosis. However, up to 40% of patients will eventually experience disease relapse. Herein, we dissected the transcriptomic profile of AML with inv(16) to identify potential prognostic markers and devise novel therapeutic vulnerabilities. Sequencing data from 222 diagnostic samples, including 44 relapse/refractory patients, revealed the presence of a median of 1 concomitant additional mutation, cooperating with inv(16) in leukemogenesis. Notably, the mutational landscape at diagnosis did not significantly differ between patients experiencing primary induction failure or relapse when compared to the rest of the cohort, except for an increase in the mutational burden in the relapse/refractory group. RNA-Seq of unpaired diagnostic and relapse) samples allowed the identification of oxidative phosphorylation (OXPHOS) as one of the most significantly downregulated pathways at relapse. Considering that OXPHOS could be targeted by Venetoclax/Azacitidine combination, we explored its biological effects on ME-1 inv(16) cell-line, but there was no additional advantage in terms of proliferation suppression over Azacitidine alone. To enhance Venetoclax efficacy, we tested the in vitro effects of Metformin as a potential drug able to enhance chemosensitivity of AML cells by inhibiting the mitochondrial transfer. By challenging ME-1 with this combination, we observed a significant synergistic interaction at least similar to that of Venetoclax/Azacitidine. In conclusion, the study of transcriptomic features of inv(16) at relapse unveiled OXPHOS as a potential target in this subset. The use of specific metabolic-oriented and synthetic lethal approaches (e.g., Venetoclax/Metformin) provided a rationale for its future clinical use.

overall_design: To better understand the behaviur of leukemic cells and to eventually identify potential markers of disease relapse in AML patients with inv(16) at the time of relapse, we exploited the transcriptome profile of diagnostic and relapsing samples by RNA sequencing.

first: Caterina

last: Barbieri

first: Giorgia

last: Silvestrini


title: Patients who received abatacept for graft versus host disease prophylaxis have lower peri-engraftment NETosis and less endothelial injury

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

summary: Abatacept decreases risk of aGVHD in adult and pediatric patient populations, but its effect on other clinical outcomes of HSCT has not been well studied. Abatacept’s effect in reducing GVHD has been linked to T-cell dependent mechanisms, but it’s effect on neutrophils and completement activation is largely unknown. In this study we analyzed the effect of abatacept prophylaxis in clinical outcomes of HSCT and explored other potential mechanisms.

overall_design: We analyzed RNA expression in neutrophils isolated from day 14 blood in a subset of patients. We compared 3 patients who received calcineurin inhibitors (CNI) based regimen to 3 patients who received abatacept in addition to CNI based regimen

first: Azada

last: Ibrahimova

first: Nathan

last: Luebbering

first: Lauren

last: Strecker

first: Lucy

last: Langenberg

first: Sheyar

last: Abdullah

last: Lake

first: Adam

last: Lane

first: Jane

last: Koo

first: Christopher

last: Towe

first: Kasiani

last: Myers

last: Dandoy

first: Kristin

last: Hudock

first: Pooja

last: Khandelwal

first: Sonata

last: Jodele