title: Lipoxin B4 Mitigates TRPV4-Activated Muller Cell Gliosis During Ocular Hypertension

city: BERKELEY

first: Matangi

last: Kumar

state: CA

address: Rm 596, Minor Hall

department: Vision Science

institute: UC Berkeley

summary: Purpose: Müller glia play dual roles in glaucoma, contributing to both retinal homeostasis and neuroinflammation; their activation by elevated intraocular pressure through the mechanosensitive channel TRPV4 promotes a reactive state that drives retinal ganglion cell (RGC) loss. Lipoxin B4 (LXB4), an endogenous lipid mediator produced by retinal astrocytes, has been shown to suppress glial reactivity and directly protect RGCs. This study investigated whether LXB4 modulates TRPV4-driven Müller glial activation and inflammation and whether Müller glia themselves contribute to this retinal lipoxin pathway.  Methods: Ocular hypertension (OHT) was induced in mice via a silicone oil model, and reactive Müller glia were isolated via magnetic sorting for transcriptomic analysis. In vitro, primary and immortalized Müller glia were treated with a TRPV4 agonist with or without LXB4. Glial reactivity was assessed by flow cytometry, immunostaining, qPCR, and western blotting. LC–MS/MS-based lipidomics was used to quantify lipoxin pathway metabolites, and single-cell RNA-seq was used to examine transcriptional responses to LXB4 treatment. GFAP and TRPV4 expression was evaluated via immunohistochemistry in retinal sections.  Results: RNA bulk-sequencing analysis and qPCR revealed that Müller glia express both 5- and 15-lipoxygenase. Lipidomic analysis confirmed that the lipoxin pathway is functional and that Müller glia endogenously produce LXB4, establishing this essential cell type as a source of anti-inflammatory and neuroprotective LXB4 in the retina. TRPV4 activation induced a reactive glial phenotype characterized by increased GFAP and IL6 expression, increased STAT3 phosphorylation, and increased production of lipoxin pathway metabolites, suggesting that biomechanical stress simultaneously triggers both gliosis and lipid signaling. Exogenous LXB4 suppressed TRPV4-induced gliosis in vitro by downregulating IL6 and inhibiting STAT3 activation, and in vivo treatment during OHT reduced the expression of Stat3, Il6, and TNF-α while attenuating TRPV4 upregulation in Müller glia.  Conclusion: These findings identify a self-regulating lipid circuit in Müller glia and support the targeting of the TRPV4–lipoxin pathway to inhibit gliosis and protect against neurodegeneration in glaucoma.

overall_design: RNA seq analysis for magnetically sorted Müller glia from Control (n=3) and Ocular hypertension (n=3) and untreated primary Müller glia (n=3)

first: Shruthi

last: Karnam

first: Shubham

last: Maurya

first: Rama

last: Nagireddy

first: John

last: Flanagan

first: Karsten

last: Gronert


title: Transcript changes in human pericytes exposed to Clostridioides difficile TcdB and an Hippo signaling inhibitor.

status: Public on Feb 11 2026

city: Oklahoma City

first: Jason

last: Larabee

state: OK

address: 940 Stanton L. Young Blvd, BMSB 1035

department: Microbiology and Immunology

country: USA

institute: The University of Oklahoma Health Science Center

type: Expression profiling by high throughput sequencing

summary: These experiments are designed to profile of how TcdB and XMU-MP-1 modify gene expression in pericytes.  TcdB is a bacterial toxin and primary virulence factor produced by the enteric pathogen C. difficile, and pericytes are putative target cells for TcdB in the colon.  XMU-MP-1 is an inhibitor of a core kinase (MST1/2) in the Hippos signaling pathway, and TcdB activates Hippo signaling, which is possibly critical for the pathogenesis of C. difficile disease. RNA-seq was carried out and the resulting gene expression profiles were analyzed focusing on CSPG4 (TcdB receptor) and a panel of genes that are regulated by YAP and TAZ (primary transcriptional regulator in Hippo pathway). We also focused on genes regulated by MTF1, which is another transcription regulator that can be controlled by Hippo signaling.

overall_design: RNA-seq analysis of cultured human pericytes exposed for 24 h to  1 ng/ml of C. difficile TcdB and/or 10 µM XMU-MP-1 (MST1/2 inhibitor).

middle: L

first: Jimmy

middle: D

last: Ballard


title: Amphiregulin and Epiregulin confer radioresistance in esophageal squamous cell carcinoma through oxidative phosphorylation

city: 上海市

first: meilian

last: yao

state: 上海

address: 上海市黄埔区重庆南路

department: 医学院

country: China

institute: 上海交通大学

summary: Neoadjuvant chemoradiotherapy combines surgery has been the standard of care for locally advanced esophageal squamous cell carcinoma (ESCC) patients. However, up to 30-50% of nCRT patients can achieve pathological complete response (pCR) and long-term survival, while a considerable number of patients experience short-term recurrence or even progression disease. Therefore, to find out the biomarkers which can better and accurate predict chemoradiation efficacy and understanding the hidden mechanism is still urgently needed. Herein, we found that mitochondrial oxidative phosphorylation (OXPHOS) was involved in radioresistance of nCRT in ESCC patients. CEBPB/AREG/EREGE axis was responsible to affect radiosensitivity through OXPHOS. Either target mitochondrial OXPHOS or ERBB signal pathway effectively enhanced the radiosensitivity for ESCC cells. This study demonstrated the underlying mechanism for AREG/EREG/ERBB regulated OXPHOS involved in ESCC radiosensitivity and provided more opportunities to target vulnerable processes to improve ESCC radiation efficacy for clinic treatment.

overall_design: RNA-seq profiling of wildtype KYSE410 cells and KYSE410R cells at 24h of irradiation

first: Zhang

last: Lin

first: Meilian

last: Yao

first: Xin

last: Xu

first: Chengkun

last: Chen

first: Dong

last: Zhang

first: Jun

last: Gu

first: Gaoping

last: Cui

first: Yujun

last: Hao

first: Xiumei

last: Ma


title: Effect of knockdown of MED8 on gene expression in bladder carcinoma cell T24.

city: Shenzhen

first: Haiyu

institute: Shenzhen Second People’s Hospital

summary: To explore the function of MED8 in the regulation of gene expression in bladder cancer, we established MED8-knockdown T24 cells.  We then conduct gene expression profiling analysis using data obtained from RNA-seq of MED8-knockdown cells and control cells.

overall_design:
Gene expression profiling analysis of RNA-seq data from T24 MED8-knockdown cells and control cells.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Weisheng

last: Huang

first: Yuhan

last: Liu

first: Yue

first: Qiaolin

last: Mei

first: Hongbing


title: H1299 cells, DLG-41- or DLG-41nc- treated differential gene expression

city: Ann Arbor

first: Alyssa

last: Winkler

state: MI

address: 1150 W Medical Ctr Dr

department: Pathology

institute: University of Michigan Medical School

summary: Gene expression data for H1299 cells treated with DMSO or GAS41 YEATS domain inhibitors 1.5µM DLG-41 (lead compound) or 1.5µM DLG-41nc (chemical negative control) for 7 days.

overall_design: Three biological replicates were analyzed for each of 3 conditions (DMSO, inhibitor DLG-41, inhibitor DLG-41nc treatment)

first: Tomasz

last: Cierpicki


title: Effect of HNF1A-MODY on stem cell islets [S4 bulk rna seq]

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

summary: This project investigates the impact of the hotspot mutation P291fsinsC in HNF1A-MODY (Maturity-Onset Diabetes of the Young) on stem cell-derived islets. RNA sequencing (RNA-seq) was performed on islets differentiated from mutant and control HNF1A-MODY stem cells to study the mutation's effect on gene expression. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms underlying the dysfunction caused by the P291fsinsC mutation during islet development and maturation.

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into the endocrine progentor stage.

first: Simona

last: Chera


title: Single-cell RNA profiling of mammary gland tumours in MMTV-PyMT mouse model of breast cancer upon Prrx1 knock out

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

summary: Disseminated cancer cells rarely succeed in forming macrometastases, yet they continue to be the most life-threatening cause of patient mortality. The determinants driving metastatic competence, however, are still poorly understood. Using data from human breast cancer patients and genetic mouse models, we uncover a non-linear relationship between the expression of the EMT transcription factor Prrx1 in the primary tumor and metastatic outcome. Multi-omics analyses in mouse tumors reveal that Prrx1 functions as a dual regulator, promoting invasive behavior while simultaneously inducing dormancy. Cells with intermediate Prrx1 levels exhibit the highest metastatic fitness, whereas extreme levels (negative or too high) lead to less metastasis, typical of a hormetic behavior, and respectively due to insufficient invasiveness or to dormancy. These findings provide mechanistic insight into the regulation of dormancy and its link to metastatic potential. Additionally, we propose that combined signatures of invasion and proliferation allow robust prognosis prediction in breast cancer patients. Our study further highlights Prrx1-driven heterogeneity, established in the primary tumor, as a key determinant of metastatic competence.

overall_design: Here, we use single cell sequencing to delineate the heterogeneity of tumours from the genetically engineered MMTV-PyMT mouse model of breast cancer (MMTV-PyMT::K14Cre::Rosa-tdTomato mice) upon Prrx1 knock out (both heterozygous and homozygous)

first: Nitin

last: Narwade

first: Raúl

last: Jiménez-Castaño

first: Khalil

middle: K

last: Youssef


title: BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: MECOM rearrangement (r) in AML involves either inv(3)(q21;q26.2) or t(3;3)(q21;q26.2), where the dislocated GATA2 enhancer drives overexpression of the transcriptional regulator EVI1, causes concomitant GATA2 repression, and promotes AML progression, aggressive phenotype and therapy refractoriness. Treatment with BET protein inhibitor (BETi) induces in vitro and in vivo efficacy in 3q26.2-r AML cells (Leukemia 38:545-556,2024). Here, utilizing an unbiased, high-throughput drug screen, focused on mechanistically annotated drugs (NCATS Mechanism Interrogation Plates [MIPE 5.0], we identified BRD4, PIK3CA, mTOR and XIAP as dependencies in the 3q26.2-r AML cells. Monotherapy with mivebresib (BETi), dactolisib (PI3K/mTORi) and LCL161 (IAPi) dose-dependently induced greater lethality in PD 3q26.2-r versus non-3q26.2-r AMLs cells (p < 0.01). RNA-Seq and/or mass spectrometry analyses revealed that treatment with mivebresib or dactolisib downregulated MYC-targets and cell cycle gene-sets whereas CyTOF and Western analyses also demonstrated reduction in the protein levels of EVI1, c-Myb, c-Myc in 3q26.2-r AML cells. Combination of mivebresib with dactolisib or LCL161 synergistically induced apoptosis as well as reduced AML burden and increased survival of the NSG mice engrafted with the luciferized PD 3q26.2-r AML cells (p < 0.05).  In a separate 3q26.2-r AML PDX model, mivebresib-based combination with dactolisib or LCL161, was superior to each agent alone or vehicle control in reducing AML burden and increasing mouse survival (p < 0.05). These findings highlight that combined therapy with a BETi and PIK3CA/mTOR or IAP inhibitor exerts superior in vitro and in vivo efficacy in the 3q26.2-r AML cell models and underscore further evaluation of these BETi-based combinations.

overall_design: Paired end RNA Seq of MECOM rearranged AML191 and AML194 cells treated with 500 nM of BET inhibitor mivebresib for 16 hours.

first: Warren

last: Fiskus

first: Kapil

last: Bhalla


title: Spatial transcriptomics profile of mammary gland tumours in MMTV-PyMT mouse model of breast cancer [MERFISH]

overall_design: We designed a MERSCOPE panel targeting 265 genes using the Vizgen Gene Panel Design Portal. Formalin-fixed paraffin-embedded (FFPE) samples from three distinct MMTV-PyMT tumors were processed according to Vizgen MERSCOPE protocols. The resulting data were utilized to analyze transcriptional heterogeneity at the spatial level within the tumors.


title: Sepsis–induced skeletal muscle wasting is ameliorated by the pharmacological inhibition of STAT3 signaling in mice [16S-Metagenome]

city: Kobe

first: Yuko

last: Ono

state: Hyogo

address: Kusunoki-cho 7-5-2

department: Department of Disaster and Emergency Medicine

country: Japan

institute: Kobe University

summary: Septic patients frequently develop skeletal muscle wasting and weakness, which adversely affects survival and functional outcomes. Currently, no drugs are available for the treatment of sepsis-associated skeletal muscle wasting. Here, we tested the effects of C188-9, a STAT3-specific signaling inhibitor, on muscle wasting in vivo and myotube atrophy in vitro induced by sepsis. In mice, sepsis severity-dependently phosphorylated STAT3, which subsequently activated the ubiquitin–proteasome and autophagy proteolytic pathways, resulting in skeletal muscle atrophy. Similar dose-dependent responses were observed in lipopolysaccharide-treated C2C12 myotubes. In human septic patients, plasma interleukin-6 levels positively correlated with the extent of sepsis-associated skeletal muscle wasting. STAT3 inhibition in mice or cells treated with C188-9 suppressed activation of the ubiquitin–proteasome degradation pathway—but not autophagy pathways—and alleviated sepsis-associated skeletal muscle wasting. Overall, our results indicate that pharmacological inhibition of STAT3 signaling may represent a novel therapeutic strategy for sepsis-associated skeletal muscle wasting.

overall_design: Tibialis anterior muscle, blood, liver, and spleen were collected from septic C57BL/6 mice (8–10 weeks old, weighing 22–26 g) 24 hours after cecal slurry injection. Total cDNA from these samples and CS stock was obtained as described in extract protocol. The extracted cDNA samples were subjected to microbiota analysis using 16S rRNA gene sequencing on the MiSeq (Illumina, San Diego, CA, USA).

first: Masafumi

last: Saito

first: Ikumi

last: Yoshihara

first: Yutaka

last: Kondo

first: Kazuho

last: Sakamoto

first: Jun

last: Sugiyama

first: Nobuto

last: Nakanishi

first: Shigeaki

last: Inoue

first: Joji

last: Kotani


title: Muribaculum intestinale negatively impacts glioma growth in mice through the toll-like receptor 2

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

summary: Glioblastoma (GBM) is the most common and malignant brain tumor in adult humans. Recent studies have demonstrated a link between the composition of the gut microbiota and glioma progression. Here, we describe that the growth of glioma in mice is inversely correlated with the relative abundance of the anaerobic bacterium Muribaculum intestinale in the feces. We found that M. intestinale administration: 1) induced an inflammatory environment in the gut; 2) reduced glioma growth; 3) increased the pro-inflammatory profile of tumor-associated microglial cells and the frequency of CD8+ T cells; and 4) increased the peripheral TNF-α levels. The effects induced by M. intestinale administration were significantly reduced upon toll-like receptor 2 (TLR2) silencing using siRNA targeting TLR2. These receptors recognise microbial patterns and control immune responses to infection. Collectively, these data demonstrate that M. intestinale induces a pro-inflammatory response in glioma bearing mice, inhibiting tumor growth via TLR2-dependent signaling.

overall_design: To investigate the effects of M. intestinale treatment on the gut tissue of  glioma beraring mice, bulk mRNA sequencing was performed in the distal colon tissues of vehicle and M. intestinale glioma mice.

first: Francesco

last: Marrocco

first: Giuseppina

last: D'Alessandro

first: Cristina

last: Limatola

first: Giuseppe

last: Sciumé

first: Silvano

last: Sozzani

last: Pietropaolo


title: Prevention of cholestatic liver disease through BCL6-FXR enterohepatic crosstalk

city: Chicago

first: Ellen

last: Fruzyna

address: 1349 E Washington St

institute: Northwestern University

summary: Bile acid (BA) metabolism must be tightly regulated because BAs serve as metabolic signaling molecules but become cytotoxic at high levels. The farnesoid X receptor (FXR) is a crucial bile acid sensor, but our understanding of its regulation and coordination with other transcription factors is limited. Here, we found that B cell lymphoma 6 (Bcl6) functions along with FXR to control bile acid levels. We found that mice lacking hepatic BCL6 (Bcl6LKO) had increased BA synthesis and serum levels. In line with this, Bcl6LKO mice had elevated serum cholesterol, the upstream substrate for BA synthesis, as well as reduced expression of the hepatic BA re-uptake transporter sodium-taurocholate cotransporting polypeptide (NTCP).  Furthermore, loss of BCL6 reduced hepatic fibroblast growth factor 4 (FGFR4) expression, causing dysregulated entero-hepatic BA feedback signaling. To better understand the relative contribution of BCL6 and FXR in regulating BA homeostasis, we generated mice with a combined deletion of hepatic BCL6 and FXR (Bcl6LKOFxrKO). Critically, combined deletion of FXR and hepatic BCL6 caused massive elevations in BA synthesis/levels compared to loss of Fxr or Bcl6 alone, which resulted in cholestatic liver damage. Mechanistically, we found that Bcl6LKO FxrKO mice had an almost complete loss of hepatic Shp expression, causing high levels of the rate-limiting BA synthesis enzyme CYP7A1. Together, these findings demonstrate that BCL6 and FXR function together to limit BA synthesis and protect the liver from cholestatic injury.

overall_design: RNA-seq of liver from FXRKO and BCL6LKOFXRKO males

first: Barish

last: Grant

first: Christopher

last: Futtner


title: Prevention of cholestatic liver disease through BCL6-FXR enterohepatic crosstalk [RNA-seq]

overall_design: RNA-seq of ileum from Bcl6fl/fl (WT) and Bcl6LKO (LKO) male and female mice

first: Grant

last: Barish


title: Structural and biochemical insights into RNA unfolding by a chaperone machine

city: Frederick

first: Sandra

last: Wolin

state: Maryland

address: 1050 Boyles Street, BLDG 560 Room 11-39

department: NCI

institute: NIH

summary: Although ATP-independent chaperones assist RNA folding, the mechanisms by which they function remain elusive. Here, we demonstrate how two chaperones collaborate to unfold misfolded noncoding RNAs (ncRNAs). Ro60 is a ring that binds the ends of misfolded ncRNAs in its cavity, while La binds many nascent ncRNAs, stabilizing them and assisting correct folding. Using cryoelectron microscopy to resolve the structure of a misfolded RNA complexed with Ro60 and La, we show that La cradles the Ro60 RNP, with its N-terminal domain binding the RNA 3' end after it passes through the Ro60 cavity, while its C-terminal domain interacts with the RNA body. Using SHAPE-MaP, we show that La and Ro60 function synergistically to disrupt weak structural elements. As the RNAs bound by Ro60 and La include both ncRNA precursors and RNAs with oligouridine tails, La- and Ro60-mediated RNA unfolding may both promote correct folding and assist misfolded RNA degradation.

overall_design: From RO60-/- human HaCaT cells expressing Ro60 fused to twin-strep-tag, Ro60/La RNP bound RNAs were purified by strep-tactin pulldown followed by immunoprecipitation of La. cDNAs were made after Ro60/La RNP bound RNAs were extracted and ligated to 3' adapter, followed by library construction and sequencing.

first: Hyeyeon

last: Nam

first: Justin

middle: C

last: Deme

first: Soyeong

last: Sim

first: Marco

last: Boccitto

first: Susan

middle: M

last: Lea


title: Protein-interaction network reveals a role of Prp19 splicing factor in transcription of both intron-containing and intron-less genes

city: Warren

first: Katherine

last: Dwyer

address: 29529 Cunningham Drive

institute: Wayne State University

summary: We have previously demonstrated that the transcription-dependent interaction of the promoter and terminator ends of a gene, which results in the formation of a gene loop, is facilitated by the interaction of the general transcription factor TFIIB with the CF1, CPF and Rat1 termination complexes. To further elucidate the protein-protein interactions that stabilize gene loop, we performed mass spectrometry of affinity purified termination complexes from chromatin fraction. Quantitative proteomic analysis revealed additional interactions of termination factors with TFIID and SAGA complex. Since gene looping of intron-containing genes involves additional contacts of the promoter and terminator with the intron, we examined if termination factors interact with the splicing factors as well. All three termination complexes displayed statistically significant interactions with Prp19, Prp43, Sub2, Snu114, Brr2 and Smb1 splicing factors. Since Prp43 and Prp19 consistently emerged as the interactor of both initiation and termination factors, we affinity-purified both and performed mass spectrometry. Prp19 exhibited interactions with subunits of TFIID, CPF complex, and the RSC chromatin remodeling complex. These interactions were observed exclusively in the chromatin context, thereby implicating the factor in transcription of protein coding genes. Since fewer than 4% of yeast genes contain introns, we hypothesized that Prp19 might have a broader role in RNAPII transcription cycle. Auxin-mediated depletion of Prp19 resulted in about two-fold decrease in transcription of a subset of both intron-containing and intron-less genes. Specifically, the promoter recruitment of TBP registered a significant decline in the absence of Prp19. Chromatin immunoprecipitation (ChIP) analysis revealed crosslinking of Prp19 to the promoter proximal as well as downstream regions of both intronic and non-intronic genes. These findings demonstrate that Prp19 has a novel role in the initiation step of transcription in budding yeast.

overall_design: Global run-on (GRO)-seq profiling of wildtype W303 cells that have Prp19 tagged with the auxin-inducible degron (AID) treated with DMSO (control) and auxin (Prp19-depletion). The cells were treated with DMSO or auxin (500 uM) for 90 minutes.

first: Mary-Ann

last: Essak

first: Ahlam

last: Awada

first: Zuzer

last: Dhoondia

first: Athar

last: Ansari


title: Single-cell RNA-seq of E14.5 mouse ventricular tissue from ETS1 endothelial-specific knockout and control embryos

city: San Diego

first: Zeyu

last: Chen

address: 9500 Gilman Drive, BFRII 1217

department: School of Medicine

institute: UCSD

summary: This study investigates the role of endothelial ETS1 in regulating cardiomyocyte proliferation and ventricular compact myocardium development. Using ETS1 conditional knockout mice, single-cell RNA sequencing (scRNA-seq) was performed on embryonic day 14.5 (E14.5) ventricles from ETS1 endothelial knockout (eKO) and control mice.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on embryonic day 14.5 (E14.5) mouse ventricular tissues to investigate the role of endothelial ETS1 in regulating cardiomyocyte proliferation and compact myocardium development. Two ETS1 endothelial knockout samples (Tie2Cre;ETS1^fl/fl) and two control samples (Tie2Cre;ETS1^fl/+) were collected, with each biological replicate consisting of pooled ventricles from three embryos. Single-cell suspensions were prepared by enzymatic dissociation, and libraries were constructed using the Chromium Next GEM Single Cell 3' v3.1 kit (10X Genomics). Libraries were sequenced on the Illumina NextSeq S4 platform.

first: Lu

last: Wang

first: Ju

first: Grossfeld

last: Paul


title: Gene expression levels of Acidithiobacillus ferrooxidans with varying intracellular c-di-GMP concentrations during bioleaching

city: BeiJing

first: Xi

last: Han

address: 5 Yiheyuan Road, Haidian District, Beijing, China   Postal Code: 100871

institute: Peking University

summary: Bioleaching, a sustainable and environmentally friendly emerging technology, relies on Acidithiobacillus ferrooxidans as a model microorganism for extracting metals from ores. This study investigated how intracellular cyclic diguanylate (c-di-GMP) concentrations regulate biofilm composition and bioleaching performance in A. ferrooxidans. By constructing strains with varying c-di-GMP levels, it was found that moderate c-di-GMP concentrations enhance bioleaching efficiency by upregulating genes associated with extracellular electron transfer (e.g., omcB and cyc2) in biofilms, a mechanism linked to optimized iron oxidation pathways. In contrast, high c-di-GMP levels improve arsenic resistance by promoting exopolysaccharide (EPS) synthesis in biofilms, likely through activation of pel-like operons (e.g., pelD), which strengthen biofilm structural integrity under toxic conditions. These findings reveal a dual regulatory role of c-di-GMP: prioritizing leaching efficiency via electron transport in low-arsenic environments and enhancing stress resistance through EPS production in high-arsenic scenarios. This study provides a theoretical foundation for tailoring A. ferrooxidans to diverse industrial bioleaching environments, leveraging its metabolic versatility and biofilm adaptability. The integration of synthetic biology approaches (e.g., genetic engineering of c-di-GMP pathways) further highlights potential applications for optimizing bioleaching strains.

overall_design: Cell transcriptome data of Acidithiobacillus ferrooxidans strains with varying intracellular cyclic diguanylate (c-di-GMP) concentrations during bioleaching under arsenic stress.


title: Plasticity of epigenomic aging creates vulnerabilities to early-life environmental exposures, reshaping adult cell- and direction-specific trajectories

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To understand how early-life exposures shape health and disease trajectories across the lifecourse, the TaRGET II Consortium exposed mice from pre-conception through weaning to diverse environmental toxicants, followed by longitudinal epigenomic and transcriptomic profiling into adulthood.  These studies revealed that early-life exposures caused persistent epigenomic reprogramming and correlative disruption of the transcriptome.  Notably, for the xenoestrogen BPA, obesogen TBT, dioxin TCDD, and air pollutant PM2.5, 40–60% of the genes disrupted in their exposure signatures overlapped with genes differentially expressed during liver aging.  Epigenetic histone modifications at enhancers—and, to a lesser extent, promoters—emerged as key targets for this reprogramming.  Despite differing mechanisms of action, these 4 toxicants induced a polarized signature in the liver, characterized by cell- and direction-specific disruption of the aging transcriptome.  In hepatocytes, genes that typically increase with age, particularly those in metabolic pathways, were downregulated.  Conversely, in non-parenchymal cells, genes typically downregulated with age, including those involved in extracellular matrix production, were upregulated.  This polarized aging signature correlated strongly with liver transcriptomes from patients with liver disease and hepatocellular carcinoma (HCC), effectively distinguishing healthy from diseased human livers.  These findings demonstrate that the plasticity of epigenomic aging is vulnerable to early life environmental exposures, which can reprogram the epigenome, with lasting impacts on the transcriptome, and disease risk, later in life.

overall_design: This dataset consists of ChIP-Seq data generated from the livers of 3-week, 5-month, or 10-month-old male mice in response to maternal exposure to vehicle (control) through weaning

first: Cheryl

last: Walker

first: Cristian

last: Coarfa

first: Rahul

last: Jangid

last: Grimm

first: Tia

last: Talley


title: GmMYB331 regulates seed traits of soybean

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No 2

institute: Chinese Academy of Science

summary: Seed traits, including seed size, weight, and quality, are among the most important characteristics in the crop cultivation process. We conducted a comparative analysis of the transcriptome data between high-oil and high-protein soybeans. By constructing a co-expression network of oil-related genes, we identified an MYB-type transcription factor，GmMYB331. Overexpression of the GmMYB331 gene in soybeans results in a series of gradient phenotypes corresponding to its varying expression levels. When GmMYB331 gene is moderately overexpressed (about 10-fold increase compared to wild type plants), the plant morphology remains similar to the wild type, with slightly larger seed size and marginally higher yield per plant, alongside a significant increase in seed fatty acid content. However, when the gene is excessively overexpressed (tens of thousands of times higher than wild type plants), the plant stems exhibit noticeable curling, there is a greater tendency towards increased seed size rather than fatty acid content, and the yield per plant significantly decreases. To reveal the molecular mechanism of GmMYB331, RNA-sequencing was performed to identify downstream genes and the pathway that GmMYB331 is invovled.

overall_design: For leaf analysis, young leaves of wild-type and two transgenic plants (overexpression of GmMYB331-3 and overexpression of GmMYB331-4) were chosen for RNA sequencing. For seed analysis, middle stage seeds of wild-type and two transgenic plants were chosen for RNA sequencing.


title: Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: Regeneration of amputated salamander limbs or fish fins restores pre-injury size, illustrating positional memory. Although appreciated for centuries, the identity of position-dependent cues and how they control tissue growth are not resolved. Here, we quantify Erk signaling events in populations of osteoblasts during zebrafish fin regeneration. We find osteoblast Erk activity depends on Fgf receptor signaling and organizes into millimeter-long gradients spanning the distal tip to the amputation site. Erk activity scales with amount of tissue amputated, predicts likelihood of osteoblast cycling, and predicts size of regenerated skeletal structures. Mathematical modeling suggests gradients are established by transient deposition of long-lived ligands that are transported by tissue growth. This is supported by the observed scaling of expression of the essential epidermal ligand fgf20a with extents of amputation. Our work provides evidence that localized, scaled expression of pro-regenerative ligands instructs long-range signaling and cycling to control size in regenerating appendages.

overall_design: To isolate RNA from the amputation plane, a region spanning one bone segment above and below the amputation plane was collected from fish at 0, 3.5, 7, 14, and 21 dpa. For each time point, tissue samples from 10 animals were pooled for each of 3 biological replicates. Bulk RNAseq libraries were prepared to identify gene expression profiles at the distal tip of regenerates.

first: Ashley

last: Rich

first: Ziqi

last: Lu

first: Alessandro

last: De Simone

first: Lucas

last: Garcia

first: Jacqueline

last: Janssen

first: Kazunori

last: Ando

first: Jianhong

last: Ou

first: Massimo

last: Vergassola

first: Kenneth D

last: Poss

first: Stefano

last: Di Talia


title: Loss of H3K9me3 maintenance leads in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons [Bulk RNA-seq]

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: We used CRISPRi-mediated deletion of the H3K9me3 methyltransferase SETDB1 in a human neural epithelial-like stem cell line with the characteristics of human neural progenitor cells (hNPCs) to model disruption of heterochromatin maintenance. We found that a key event following the loss of H3K9me3 maintenance was the expression of evolutionary young full-length L1 elements. Transcriptional activation of L1s was associated with a loss of CpG DNA methylation at their promoters, suggesting that deposition of H3K9me3 at the L1 promoter is required to maintain DNA methylation.

overall_design: Expression levels of genes and transposable elements in human neural pluripotent stem cells (hNPCs) was examined by Bulk-RNA sequencing in two different conditions: LacZ - CRISPRi (a control targetting a bacterial gene which is not present in the human genome) and SETDB1 - CRISPRi.


title: Targeting PKMYT1 enhances antitumor immune responses in castration-resistant prostate cancer [scRNA-seq]

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

institute: shandong university

summary: Although immunotherapy has been successful in various tumors, its efficacy in castration resistant prostate cancer (CRPC) is minimal, due to reduced presence of intratumoral immune effector cells in CRPC. How CRPC cells escape immune surveillance is not fully defined. Here we demonstrate that PKMYT1 expression is elevated in CRPC cases, which related to low immune infiltration in these patients. Patients with high PKMYT1 expression exhibit low CD8+ T cells signature and resistance to ICB therapy. Targeting PKMYT1 can suppress CRPC progression, accompanied with increased intratumoral CD8+ T cells. Selective PKMYT1 inhibitor, RP-6306, augmented ICB in a manner dependent on CD8+ T cells. PKMYT1 inhibitors alone or in combination with PD-L1 blockade causes CD8+ T cell infiltration and remarkable tumor suppression, which suggests a promising immunotherapeutic approach in CRPC. Mechanically, targeting PKMYT1 activated the cGAS-STING pathway, which increases expression of type I and II interferon response genes and led to upregulation of key immune regulators. These findings highlight a key role of PKMYT1 in CRPC progression and rationalize PKMYT1 as a potential therapeutic target.

overall_design: In this research, RM-1 cells were injected subcutaneously into C57BL/6 mice.Tumor tissues were collected from two RM-1 tumor-grafted mice on 10d post-treatment with either vehicle control or RP-6306. scRNA-seq profiling of RM-1 tumors treated with vehicle or RP-6306.

first: Bo

last: Han

first: Jing

last: Hu


title: Meningioma microenvironment harbors a rich immune landscape with therapeutic implications (Bulk RNA-seq part)

city: Boston

first: Wenya Linda

last: Bi

state: MA

address: 60 Fenwood Road

department: Neurosurgery

institute: Mass General Brigham

summary: Effective therapeutic targets are urgently needed for aggressive meningiomas. Given the pivotal role of immune microenvironment in tumor progression, we developed a comprehensive atlas of the meningioma microenvironment. Using single-cell and bulk techniques, we revealed a rich immune infiltrate in 2,610 meningiomas, among the highest observed across 34 human cancer types. Macrophages predominated in meningioma, contrasting with the lymphoid dominance of peripheral blood, with meninges exhibiting an intermediate immune profile. Cellular states and phenotypes of both immune and tumor cells shift during tumor progression toward an earlier-stage immune-suppressive and proliferative profile in aggressive meningiomas. Using ex vivo patient-derived tumor organoids, we demonstrated inducible responses to STING activation, marked by elevated cytokine release, which were synergistic when combined with PD-1 blockade. Together, these findings provide an extensive resource on the cellular heterogeneity of the meningioma microenvironment and provide a framework for rational therapeutic modeling and strategy development.

overall_design: A total of 47 human meningiomas (fresh frozen tumor tissues) resected at Brigham and Women's Neurosurgery were sent for bulk RNA-seq at the Broad Institute of MIT and Harvard.

first: Xiaopeng

last: Guo

first: Joseph

last: Driver


title: RIPseq of AtMKIP1-YFP and AtBE3-YFP in Arabidopsis thaliana

city: Potsdam

first: Yang

state: Brandenburg

address: Am Mühlenberg 1

department: Organelle Biology, Biotechnology and Molecular Ecophysiology

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

summary: Chloroplast group IIA introns derive from bacterial ribozymes. Their splicing likely requires Maturase K (MatK), which has been largely inaccessible to functional analyses being itself a chloroplast intron-encoded protein. We show that MatK physically interacts with a conserved, essential plastid-localized homolog of starch branching enzymes (BEs), dubbed MATURASE K INTERACTING PROTEIN1 (MKIP1). We demonstrate that MKIP1 proteins have lost BE activity and acquired an insertion enabling direct interaction with the N-terminal region of MatK. Arabidopsis MKIP1 specifically co-precipitates all known intron targets of MatK. Induced MKIP1 silencing results in pale newly emerging leaves, in which the splicing of these intron targets is strongly reduced. Our data suggest that MKIP1 functionally diverged from canonical BEs to facilitate splicing in conjunction with MatK. We propose that the N-terminus of MatK, in turn, has evolved from an RNA-binding domain into a platform for protein interaction, helping its transition towards a general splicing factor.

overall_design: To identify RNA regions specifically associated with AtMKIP1 or its complex in vivo, we performed RNA co-immunoprecipitation (co-IP) followed by RNA sequencing (RIP-seq) on 10-days old Arabidopsis thaliana seedlings (Col-0 ecotype) stably expressing PUBQ10::AtMKIP1-YFP in the mkip1 mutant background. An Arabidopsis thaliana line stably expressing PUBQ10::AtBE3-YFP (in the wild-type background) served as control. The input RNA and immunoprecipitated RNA associated with either bait (AtMKIP1-YFP or AtBE3-YFP) in Arabidopsis seedlings were subjected to RNA sequencing. Three replicates, each consisting of ~10 g (fresh weight) of pooled 10-day old seedlings, were analyzed per line.

first: Yuanyuan

last: Liang

first: Reimo

last: Zoschke

first: Barbara

last: Pfister


title: Incorporating histone H2B variants into chromatin modifies chromatin accessibility to induce the epithelial-to-mesenchymal transition in breast cancer

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

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

overall_design: Refer to individual Series


title: Nonsense mutations in USH2A exon-13 activate the innate immune response in Müller glial cells

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Pathological USH2A mutations cause Usher Syndrome type II, characterized by progressive retinitis pigmentosa and hearing and balance impairment. This study aims to investigate the cellular mechanisms underlying USH2A-related retinal degeneration using human induced pluripotent stem cell (hiPSC)-derived retinal organoids. The introduction of a homozygous nonsense mutation in the USH2A hotspot exon-13 resulted in normal photoreceptor development, but alterations in ciliary length, and loss of ciliary localization of usherin long form B and its interacting proteins, ADGRV1 and whirlin. Notably, single-cell RNA sequencing revealed unexpected significant changes in Müller glial cells (MGCs), with disruptions in the translation, innate immune response, and endolysosomal system. These findings suggest that, while photoreceptor cells are mildly affected by the exon-13 USH2A mutation, MGCs exhibit major dysfunction, potentially contributing to the disease progression and therefore shedding light on potential alternative therapeutic targets.

overall_design: Isogenic control (ISO-CTRL) and USH2A KO (13KO) hiPSC-derived retinal organoids were analyzed by scRNAseq at differentiation day 225 in a single run. Samples were multiplexed using cell hashing oligonucleotide (HTO). The run contained 14 HTO. Number of organoids used: ISO-CTRL n=4, 13KO subclone E11 n=4, 13KO subclone G8 n=3, 13KO subclone B7 n=3.

first: Rossella

last: Valenzano

first: Ioannis

last: Moustakas

first: Jan

last: Wijnholds


title: Prevention of cholestatic liver disease through BCL6-FXR enterohepatic crosstalk [ChIP-seq]

first: Ellen

last: Fruzyna

overall_design: FXR ChIP-seq from Bcl6fl/fl (WT) and Bcl6LKO (LKO) male liver

first: Grant

last: Barish


title: Targeting PKMYT1 enhances antitumor immune responses in castration-resistant prostate cancer

first: Lin

overall_design: In this research, RNA-seq profiling of C4-2B control cells (DMSO) and C4-2B with 500nM RP-6306 treatment for 24h.


title: Timosaponin AIII enhances CAR-T cell potency and prevents relapse through impairing CAR-Tregs

city: Hefei

first: Mingqi

last: Hou

institute: USTC

summary: Chimeric antigen receptor (CAR)-T cell therapy has become the standard treatment for refractory and relapsed (r/r) DLBCL in recent years. However, more than half of these patients develop primary or secondary resistance. Given that CAR Tregs are crucial in driving resistant and relapse to CAR-T therapy, but the strategies to overcome are limited. Here, we established a Treg functional high-throughput screening system and identified a natural product, currently in clinical trials, Timosaponin AIII (TAIII), impairs Treg function while activating T cell immune response during CAR-T therapy. Mechanistically, TAIII recruits and blocks the A2AR signaling in CAR-T cells as a novel allosteric inhibitor of A2AR, thereby eliminating CAR-Tregs by suppressing CREB-mediated FoxP3 transcription. Furthermore, TAIII suppresses tumor growth and improves the efficacy of PD-1 immunotherapy by reducing intratumoral Tregs in solid tumor models. Importantly, TAIII increases the Tcm percentage and enhances cytotoxic cytokine secretion of CAR-T cells post-infusion, improving their function. Combining or pretreating CAR-T cells with TAIII enhances their antitumor activity, thereby overcoming late relapses in lymphoma models. These results identify TAIII as a potent adjuvant for CAR-T cell function and manufacturing through eliminating CAR-Tregs proportion, thereby enabling CAR-T therapy to be applied with a broader perspective.

overall_design: PBMC or CAR-T cells were co-cultured with Dynabeads or target cells at a ratio of 1:1 and treated with DMSO or 1 μM TAIII in the presence of 5 μM NECA. After 16 hours of treatment, the cells were collected for RNA sequencing.

last: Yang

first: Wenjun

last: Zhang

first: Xiaochen

last: Tang

first: Rui

last: Jin

first: Husheng


title: Single-cell ATAC profiling of mammary gland tumours in MMTV-PyMT mouse model of breast cancer

city: San Juan de Alicante

first: Angela

last: Nieto

address: Av. Ramón y Cajal s/n

institute: Instituto de Neurociencias (CSIC-UMH)

summary: Disseminated cancer cells rarely succeed in forming macrometastases, yet they continue to be the most life-threatening cause of patient mortality. The determinants driving metastatic competence, however, are still poorly understood. Using data from human breast cancer patients and genetic mouse models, we uncover a non-linear relationship between the expression of the EMT transcription factor Prrx1 in the primary tumor and metastatic outcome. Multi-omics analyses in mouse tumors reveal that Prrx1 functions as a dual regulator, promoting invasive behavior while simultaneously inducing dormancy. Cells with intermediate Prrx1 levels exhibit the highest metastatic fitness, whereas extreme levels (negative or too high) lead to less metastasis, typical of a hormetic behavior, and respectively due to insufficient invasiveness or to dormancy. These findings provide mechanistic insight into the regulation of dormancy and its link to metastatic potential. Additionally, we propose that combined signatures of invasion and proliferation allow robust prognosis prediction in breast cancer patients. Our study further highlights Prrx1-driven heterogeneity, established in the primary tumor, as a key determinant of metastatic competence.

overall_design: Here, we use single cell sequencing to delineate the chromatin heterogeneity of tumours from the genetically engineered MMTV-PyMT mouse model of breast cancer (MMTV-PyMT::K14Cre::Rosa-tdTomato mice)

first: Nitin

last: Narwade

first: Raúl

last: Jiménez-Castaño


title: Meningioma microenvironment harbors a rich immune landscape with therapeutic implications (Single-cell RNA-seq part)

first: Wenya Linda

last: Bi

address: 60 Fenwood Rd

overall_design: A total of 9 human samples (1 arachnoid and 8 meningioma samples) resected at BWH were sent for single-cell RNA-seq at the BWH Single-cell Genomics Core.

first: Xiaopeng

last: Guo

first: Joseph

last: Driver


title: Formyl peptide receptor 2 determines sex differences in pulmonary hypertension-associated right ventricular dysfunction

city: Wenzhou

first: jiafei

last: lu

state: Zhejiang

address: The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, 109 Xueyuan Road, Lucheng District, Wenzhou, Zhejiang 325027, China.

institute: wenzhou medical university

summary: Aims Pulmonary hypertension (PH) involves structural and functional changes in pulmonary vessels due to various diseases, leading to increased vascular resistance and arterial pressure. Prolonged high load gradually enlarges the right ventricle, potentially leading to right heart failure. Female patients exhibit a more favorable prognosis due to the cardioprotective effect. Formyl peptide receptor 2 (FPR2) appears to be crucial in these processes. Methods and results Here we show that FPR2 mediates sex-specific responses to SuHx（sugen5416 combined hypoxia）-induced PH in mice. Elevated RVSP and pulmonary artery remodeling were induced in both sexes during SuHx exposure, but compared with females, male mice had more severe right ventricular dysfunction (RVD). FPR2 was more highly expressed in healthy right heart from females than males, and Fpr2 deletion exacerbated RVD in SuHx-induced PH in female mice. We also found that FPR2 mediates the cardioprotective effect of estradiol in mice with PH. Data from our transcriptomics experiment further demonstrated FPR2 mediates these effects by affecting mitochondrial function and cytokines secretion from cardiomyocytes. Conclusion We demonstrate that FPR2 play an important role in mediating sex-specific responses to SuHx, thereby identifying a potential novel therapeutic target for optimizing treatment of PH and associated right heart failure.

overall_design: RNA-Seq analysis of right ventricles from 8-week-old female WT and Fpr2-KO mice under baseline conditions and after 3 weeks of SuHx exposure.

first: Jiafei

last: Lu

first: Yu

last: Hao

first: Xiaoyan

last: Chen

first: Xinyu

last: Li

first: Huating

last: Xie

first: Jialin

last: Wang

first: Man


title: Combined Effects of Mesenchymal Stromal Cells and Antibiotic Therapy on Enterobacter Ventilator-Associated Pneumonia in Rabbits

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

summary: Mesenchymal stromal cells (MSCs) enhance outcomes and attenuate the inflammatory response in preclinical models of community-acquired pneumosepsis. Ventilator-associated pneumonia (VAP), a major cause of mortality in intensive care units, is closely linked to immune dysfunction. This study aimed to evaluate whether MSCs combined with an antibiotic (cefepime) could improve outcomes and restore immune and metabolic cellular homeostasis in a preclinical model of VAP, compared to cefepime alone.

overall_design: Male rabbits underwent protective mechanical ventilation and received an injection of LPS (3 ng/kg) to mimic the effects of an initial infectious challenge and associated immune alterations. Twenty-four hours later, they were inoculated intratracheally with an Enterobacter aerogenes strain to induce VAP. Rabbits (10/group) were randomly assigned to receive either human umbilical cord-derived MSCs (3.10^6/kg, intravenous) or sodium chloride, 4 hours after the Enterobacter challenge. All animales were treated with an antibiotic (cefepime). Lung bacterial concentrations (primary outcome), systemic bacterial burden, 24-hour survival post-bacterial challenge, lung injury, immune and mitochondrial dysfunctions were evaluated.

first: Marine

last: Jacquier

first: Mathieu

last: Blot

first: Corentin

last: Richard


title: FAM20A Deficiency Drives Transcriptomic Dysregulation and Functional Impairment in Gingival Fibroblasts

city: Dindaeng

first: Kanokwan

last: Sriwattanapong

state: กรุงเทพมหานคร

address: 558/392, Lumpini suite dindaeng-ratchaprarop

country: Thailand

institute: Chulalongkorn University, Faculty of Dentistry

summary: Amelogenesis imperfecta type 1G (AI1G), also known as Enamel-Renal-Gingival Syndrome (ERGS), is an autosomal recessive disorder caused by variants in FAM20A, encoding a Golgi apparatus protein crucial for protein processing and secretion. AI1G presents with enamel defects, nephrocalcinosis, and gingival overgrowth. Building upon our previous findings demonstrating the impact of FAM20A insufficiency on deciduous dental pulp cells, this study investigated the molecular mechanisms underlying gingival fibromatosis in AI1G. RNA sequencing of gingival fibroblasts from an AI1G patient revealed widespread differential gene expression (DEG). Gene Ontology (GO) analysis demonstrated enrichment of DEGs in biological processes related to cell adhesion, differentiation, proliferation (including positive regulation and cell division), cell cycle regulation, apoptosis, and signal transduction. Furthermore, enriched molecular functions included protein, ATP, and calcium ion binding, protein homodimerization and kinase activity, and receptor binding. Pathway analysis (Reactome and KEGG) further highlighted the dysregulation of signaling pathways, including Wnt, TGF-β, cell cycle, DNA replication, Rho GTPase signaling, and extracellular matrix organization. Functional assays confirmed these findings, revealing delayed initial attachment and spreading, impaired osteogenic differentiation (evidenced by reduced mineralization and downregulation of DLX5, OCN, RUNX2, and OPN), enhanced cell cycle progression and proliferation (increased colony size and proliferation rates, along with a shift from G0/G1 to G2/M phase), and suppressed apoptosis in FAM20A-insufficient fibroblasts. These results suggest that FAM20A plays a critical role in regulating fundamental processes in gingival fibroblasts, and its insufficiency contributes to the gingival fibromatosis phenotype observed in AI1G through the disruption of cell adhesion, differentiation, proliferation, and apoptosis. This study proposes novel insights into the pathogenesis of AI1G and highlights potential therapeutic targets for this complex disorder.

overall_design:
Gingival fibroblast cells from AI1G patient and healthy individuals were performed an RNA extraction. The total RNA libraries were constructed using Illumina TruSeq Stranded mRNA LT Sample Prep Kit and sequenced using Illumina NovaSeq platform.
The RNA differential expression compared between FAM20A gingival fibroblast cells and four individual control cells  was analyzed using RNA-Seq Differential Expression program (Illumina Inc., San Diego, CA, USA).

first: Sriwattanapong

last: Kanokwan


title: Effect of HNF1A-MODY on stem cell islets [II]

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

institute: University of bergen

summary: This project investigates the impact of the hotspot mutation P291fsinsC in HNF1A-MODY (Maturity-Onset Diabetes of the Young) on stem cell-derived islets. RNA sequencing (RNA-seq) was performed on islets differentiated from mutant and control HNF1A-MODY stem cells to study the mutation's effect on gene expression. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms underlying the dysfunction caused by the P291fsinsC mutation during islet development and maturation.

overall_design: HNF1A-MODY stem cells with the P291fsinsC hotspot mutation and wild-type controls were differentiated into the posterior foregut. The Sonic Hedgehog (SHH) pathway was manipulated by removing SANT1 of the differenciation protocol at the start of the stage to assess its effect on the differentiation process and evaluate the impact of the mutation on this developmental stage. Samples where taken at different timpoint along the differentation.

first: Simona

last: Chera


title: H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment [CUT&Tag]

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Gene expression heterogeneity creates subpopulations of tumor cells with increased resistance, posing a challenge to effective cancer treatment. This non-genetic variability stems from the stochastic nature of transcription, where gene activation occurs in bursts of RNA synthesis. The estrogen-responsive TFF1 gene is heterogeneously expressed due to periods of inactivity lasting several days. Here we uncover the mechanism driving heterogeneous TFF1 activity by examining cells sorted based on TFF1 activity levels (High vs Low TFF1 expressing cells). In both populations, genome-wide assays and live cell imaging were performed to assess chromatin state, ERα occupancy, allele activation and transcriptional bursting behavior.

overall_design: Nascent and total RNA levels measured in MCF7 cells treated with 1nM of Estrogen to evaluate the transcriptome. NUN refers to Nascent RNA sequencing and pA-RNA refers to total RNA sequencing. All experiments have been performed in triplicates (referred as Rep 1, 2, 3 or A, B, C)

first: Fleur

last: Chapus

first: Christopher

last: Day

first: Laura

last: Kammel

first: Pelin

last: Yasar

first: Erica

last: Scappini

first: Charles

last: Tucker

first: Maria

last: Sifre

first: Celyn

last: Bregio

first: Alyson

last: Palia

first: Joseph

last: Rodriguez


title: The METTL3-YTHDC1 axis mediates architectural RNA m6A modification to modulate the integrity of chromatin TADs in MLLr+ AML genome

city: Hangzhou

first: Huacheng

last: Luo

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

summary: Methyltransferase-like protein 3 (METTL3) as a key regulator of leukemia-associated gene expression in acute myeloid leukemia (AML) contributes to malignant transformation. Chromatin topologically associating domains (TADs) are essential for maintaining the structural integrity and activity of the AML genome. However, the regulatory mechanism by which METTL3 facilitates the integrity and activity of chromatin TADs leading to AML progression remains unknown. Our findings demonstrate that METTL3 has a specific interaction with YTHDC1, METTL3 and CCCTC-binding factor (CTCF) by METTL3 immunoprecipitation-mass spectrometry (IP-MS) analysis in MLLr+ AML cells. METTL3 colocalizes with CTCF at the promoters and enhancers of the MLLr+ AML genome by analysis of METTL3 ChIP-seq and CTCF ChIP-seq. Notably, METTL3 is highly upregulated in MLLr+ AML cells. Depletion of METTL3 significantly impacts CTCT binding sites (CBSs) and chromatin accessibility at the promoters and enhancers of key leukemia genes, such as MYB and RUNX1, resulting in reduced leukemia gene expression and impaired cell proliferation. Critically, high-resolution chromatin conformation capture (Hi-C) data indicates that YTHDC1 loss substantially disrupts CTCF-dependent 3D genome organization. Furthermore, disruption of chromatin architectural RNAs (arcRNAs) mediated R-loops influences the chromatin TAD structures at specific leukemia signature gene loci. YTHDC1 recognizes m6A-modified arcRNAs, enhancing their formation of R-loops to maintain the CTCF-dependent TADs in MLLr+ AML genome. This interaction is crucial for regulating oncogenic TAD boundary activity and integrity to modulate the transcription of leukemia signature genes. In conclusion, the METTL3-YTHDC1-CTCF axis plays a critical role in regulating the expression of AML signature genes through facilitating AML genome organization. These findings provide a valuable theoretical insight for identifying new therapeutic targets in AML treatment.

overall_design: We have finished the RNA-seq, ATAC-seq, DRIP-seq, DRIPc-seq, RIP-seq, MeRIP-seq, ChIP-seq, 4C-seq, sgAPEX-seq, ChIRP-seq, and Hi-C-seq in Control, shMETTL3, shYTHDC1 and RNase treated MOLM13 leukemia cells.


title: Neuregulin-1β treatment augments compensatory remodeling and ameliorates cardiac function during pressure overload

city: Basel

first: Parisa

last: Aghagolzadeh

address: Hebelstrasse 20

country: Switzerland

institute: Basel university

summary: Purpose: This study investigates the impact of NRG1 on the cardiac adaptation to pressure overload and analyzes the underlying mechanisms. Methods: Male C57BL/6NRj mice underwent sham or transverse aortic constriction (TAC) surgery, received minipumps with either saline or NRG1 and were followed by echocardiography and BRB-seq analysis. Results: NRG1-induced functional improvement of the heart after TAC.

overall_design: mRNA of LV heart tissue was isolated from male C57BL/6NRj mice underwent sham or transverse aortic constriction (TAC) surgery, received minipumps with either saline or NRG1 and were followed by echocardiography and BRB-seq analysis.

first: Lifen

last: Xu

first: Marijke

last: Brink


title: AMPK promotes TFEB transcriptional activity through dephosphorylation at both mTORC1-dependent and -independent sites [dataset 2]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: TFEB (transcription factor EB) is a critical regulator of lysosomal biogenesis, macroautophagy/autophagy and energy homeostasis through controlling expression of genes belonging to the coordinated lysosomal expression and regulation network. AMP-activated protein kinase (AMPK) has been reported to phosphorylate TFEB at three conserved C-terminal serine residues (S466, S467, S469) and these phosphorylation events were reported to be essential for transcriptional activation of TFEB. In sharp contrast to this proposition, we demonstrate that AMPK activation leads to the dephosphorylation of the C-terminal sites. We show that a synthetic peptide encompassing the C-terminal serine residues of TFEB is a poor substrate of AMPK in vitro. Treatment of cells with an AMPK activator (MK-8722), glucose deprivation or MTOR inhibitor (torin1) robustly dephosphorylated TFEB not only at the MTORC1-targeted N-terminal serine sites, but also at the C-terminal sites. Loss of function of AMPK abrogated MK-8722- but not torin1-induced dephosphorylation and induction of the TFEB target genes.

overall_design: mRNA-seq of Mouse Embyonic Fibroblasts comparing the interaction between AMPK knock-out and treatment with Torin-1 and MK8722

first: Florentina

last: Negoita

first: Conchita

middle: F

last: Bringas

first: Kristina

last: Hellberg

first: Katarzyna

last: Luda

first: Hongling

last: Liu

first: Zhiyuan

last: Li

first: Joyceline

last: Cuenco

first: Jin-Feng

last: Zhao

first: Gajanan

last: Sathe

first: Ian

last: Ganley

first: Gopal

last: Sapkota

first: Kei

last: Sakamoto


title: Differential Expression and Bioinformatics Analysis of miRNAs in the Sp5C of  Migraine Mouse Models

city: Beijing

first: Lu

address: No. 23, Hutong Street, Art Gallery, Dongcheng District

institute: Beijing Hospital of Traditional Chinese Medicine, Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Migraine is a prevalent neurological disorder that affects a significant portion of the global population. Previous studies have suggested that microRNAs (miRNAs) may play a crucial role in the pathogenesis of migraine. This study aims to explore the potential functions of miRNAs through sequencing analysis of the Sp5C in a migraine mouse model. Method: Migraine mouse models were established through repeated inflammatory soup dural injections. Total RNA was extracted from the Sp5C of both the migraine and control groups. High-throughput sequencing technology was employed to analyze the miRNA expression profiles, followed by differential expression analysis using bioinformatics tools. Pathway enrichment analysis was performed based on differential expressed miRNAs, and literature review was conducted to identify target genes for subsequent animal experiments. Results: Compared to the control group, we identified four miRNAs with differential expression (fold change ≥1.5, P < 0.05), all of which were upregulated in the migraine model group. These miRNAs included miR-12179-5p, miR-23b-5p, miR-214-5p, and miR-6239. We employed online miRNA prediction tools (Targetscan, miRWalk, and miRDB) and obtained 7,909 predicted target genes. Bioinformatics analysis of these target genes identified several enriched signaling pathways, with particular interest in chemotaxis, immune receptor activity, immune system development, and the MAPK signaling pathway. These pathways play important roles in mediating pain and neuroinflammation. Based on a literature review and bioinformatics analysis, we identified Cxcr5 as a potential key gene for further research. Conclusion: Our results indicated that four upregulated miRNAs (miR-12179-5p, miR-23b-5p, miR-214-5p, and miR-6239) were identified in the migraine model compared to the control group. Whether Cxcr5 can serve as a key regulatory gene for migraine treatment requires further experimental validation.

overall_design: We obtained Sp5C region brain tissue samples from three mice in the migraine model group and three mice in the control group. .

first: Yine

last: Song

first: Shaoru

first: Chengcheng

last: Zhang


title: AMPK promotes TFEB transcriptional activity through dephosphorylation at both mTORC1-dependent and -independent sites

first: Lars


title: Effect of EDC exposure on differentiation of iPSC derived stem cell islets

first: Simona

last: Chera

address: Haukelandsbakken 15

institute: University of Bergen

summary: This project investigates the impact enodcrine disrupting chemicals (EDCs) on differentiation toward stem cell derived islets. RNA sequencing (RNA-seq) was performed on EDCs treated and non-treated islets differentiated from iPSCs to SC-islets. By comparing the transcriptomic profiles of these islets, the study aims to uncover molecular mechanisms affected by EDCs treatment, and the impact on SC-islet fate.

overall_design: iPSCs were differenitated toward ST-islet fate using a 7 stage step wise protocol. At Endocrine progenitor stage the each well of aggreagtes were split in 2 wells, one for treatment and one for control. For 14 days the treatment were treated with a 1 mM mix of bisphenol A, bisphenol S and trans-nonachlor. The SC-islets were harvested at day 38 of the protocol, 7 days after end of treatment.

first: Legøy

last: Thomas

first: Lucas

last: Unger


title: Incorporating histone H2B variants into chromatin modifies chromatin accessibility to induce the epithelial-to-mesenchymal transition in breast cancer [CUT&RUN]

first: Yvonne

last: Fondufe-Mittendorf

summary: Histones scaffold genomic DNA  and regulate access to the transcriptional machinery. However, naturally occurring histone variants can alter histone-DNA interactions, DNA and histone modifications, and the chromatin interactome.  Hence, alterations in histone variant deposition can disrupt chromatin, and are increasingly recognized as a way to trigger various disease (including cancer). While significant attention has been placed on the biochemical and functional roles of H2A and H3 variants, H2B variants remain largely understudied. Here, we show that H2B variants are dysregulated in breast cancer and that certain variants are associated with specific breast cancer subtypes. HIST1H2BO overexpression (in particular) is more common in Asian, African American/Black, and young female populations and is associated with a worse prognosis. In vitro, H2B1O compacts chromatin, and incorporating H2B1O into chromatin activates pro-inflammatory and oncogenic pathways and the epithelial-to-mesenchymal transition (EMT), and generates resistance to first-line chemotherapeutic agents. Thus, H2B1O acts much like an onco-histone, with H2B variant expression being a prognostic biomarker for breast cancer and a potential new target for drug therapies to enhance treatment efficacy.

overall_design: To investigate the genomic localization of histone H2B variants, MCF10A cells were transfected with mRNA encoding HA-tagged H2B variants or an empty vector control. CUT&RUN experiments were performed using an anti-HA tag antibody to target the HA-tagged variants. Additionally, activating and repressing histone markers were employed to assess the activation or repression status of gene promoters.

first: Hejer

last: Dhahri

first: Kin

last: Lau


title: Incorporating histone H2B variants into chromatin modifies chromatin accessibility to induce the epithelial-to-mesenchymal transition in breast cancer [RNA]

summary: Histones scaffold genomic DNA and regulate access to the transcriptional machinery. However, naturally occurring histone variants can alter histone-DNA interactions, DNA and histone modifications, and the chromatin interactome. Hence, alterations in histone variant deposition can disrupt chromatin, and are increasingly recognized as a way to trigger various disease (including cancer). While significant attention has been placed on the biochemical and functional roles of H2A and H3 variants, H2B variants remain largely understudied. Here, we show that H2B variants are dysregulated in breast cancer and that certain variants are associated with specific breast cancer subtypes. HIST1H2BO overexpression (in particular) is more common in Asian, African American/Black, and young female populations and is associated with a worse prognosis. In vitro, H2B1O compacts chromatin, and incorporating H2B1O into chromatin activates pro-inflammatory and oncogenic pathways and the epithelial-to-mesenchymal transition (EMT), and generates resistance to first-line chemotherapeutic agents. Thus, H2B1O acts much like an onco-histone, with H2B variant expression being a prognostic biomarker for breast cancer and a potential new target for drug therapies to enhance treatment efficacy.

overall_design: To determine the impact of histone H2B variants incorporation or ctokine inducing-EMT on oncogenic pathway activation in human breast epithelial cells (MCF10A), cells were either transfected with H2B variants mRNA, or empty vector control, or treated with TNFɑ and TGFB.


title: Compartmentalization of mRNA and translation by cell adhesions

first: Terry

last: Lechler

address: 307 Research Dr

institute: Duke University

summary: Subcellular compartmentalization allows cells to concentrate and locally regulate functions. Here we identify translational compartmentalization in epidermal cells, with ribosomes, a subset of mRNAs, and the RNA-Induced Silencing Complex (RISC) being enriched at the cell cortex. We identify a crucial role for the desmosomal protein, desmoplakin, in directing ribosome localization and translation to the cortex. Transcript localization is also desmoplakin-dependent, but molecularly separable from ribosome recruitment. Analysis of local translation reveals that most of the cortical transcripts are translationally inhibited, while mRNAs for cell adhesion and the cytoskeleton are translationally active at the cortex under homeostatic conditions. Wounding induces translational changes, characterized by loss of RISC cortical localization and an increase in translation of RISC-associated transcripts, including cell adhesion mRNAs. Together our data demonstrate a desmosome-dependent cortical compartmentalization of mRNAs and translation that dynamically responds to barrier perturbations including wounding.

overall_design: Comparison of total and cortical translatome in unwounded and wounded keratinocytes.

first: D'Alessandro

last: Alec


title: H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment

first: Brian

last: Bennett

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

overall_design: Refer to individual Series


title: KAT8 Cut&Tag profiling of Bone Marrow Derived macrophage stimulated with R848

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: Purpose: Genome-wide identification of genes binding by KAT8, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type BMDMs. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT BMDMs were stimulated with R848 (100ng/ml) for 2 hours or not. Results: We carried out the CUT&Tag assay using antibodies against KAT8, and found the global binding prefernece of KAT8 in activated macrophages.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for KAT8-binding gene peaks in WT BMDMs stimulated with R848 for 2h or not.

first: Yan

last: Xiang

first: Yunkai


title: RNA-seq of ear skins from KAT8 cKO and WT mice in IMQ-induced psoriatic model

summary: To investigate whether KAT8 is involved in the development of psoriasis,we performed gene expression profiling analysis using data obtained from RNA-seq of ear skins from KAT8f/f（WT） and KAT8f/f Lyz2-cre+(KAT8-cKO )psoriatic mice

overall_design: A daily topical dose of 30 mg IMQ cream (5%) (Shichuan MedShine Pharmaceuticals Co.) per ear for three consecutive days. At day 4, ears were collected for RNA isolation.


title: H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment [RNA-seq]

first: Fleur

last: Chapus

first: Christopher

last: Day

first: Laura

last: Kammel

first: Pelin

last: Yasar

first: Erica

last: Scappini

first: Charles

last: Tucker

first: Maria

last: Sifre

first: Celyn

last: Bregio

first: Alyson

last: Palia

first: Joseph

last: Rodriguez


title: scRNA-SEQ analysis of SW620 xenografts tumor in nude mice

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

summary: In order to illustrate the change of SW620 xenografts in nude mice, we collected SW620 xenografts at Week5 after the tumor cells were injected subcutaneously in nude mouse. Tumor tissues were collected and disocciated  to single cells and subjected to scRNA-SEQ.

overall_design: There were four mice with subcutaneous tumor.  All of these mice were injected with SW620 subcutaneously and fed for 5 weeks. Then mice were sacrificed and tumor tissues were collected and subject to single cell dissociation. Live cells were enriched and subjected to scRNA-SEQ analysis.

first: Hui

last: Zheng

first: Changpeng

last: Li

first: Fei

last: Meng


title: Incorporating histone H2B variants into chromatin modifies chromatin accessibility to induce the epithelial-to-mesenchymal transition in breast cancer [ATAC-seq]

first: Yvonne

last: Fondufe-Mittendorf

address: 333 Bostwick Ave NE

institute: Van Andel Institute

overall_design: To determine the impact of histone H2B variants incorporation or ctokine inducing-EMT on chromatin accessibility changes in human breast epithelial cells (MCF10A), cells were either transfected with H2B variants mRNA, or empty vector control, or treated with TNFɑ and TGFB.

first: Hejer

last: Dhahri

first: Kin

last: Lau


title: Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow Derived macrophage administrated with KAT8 inhibitor

first: Xingguang

last: Liu

summary: Purpose: The purpose of this study is to detect activated or silenced genes following pretreatment with KAT8-inhibitor in bone marrow derived macrophages (BMDMs). Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80,and the use of BMDMs with purity greater than 97.5% for subsequent experiments.BMDMs pretreated with DMSO or KAT8 inhibitor were stimulated with R848 (100ng/ml) for 2 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA between DMSO or KAT8 inhibitor-treated BMDMs.

overall_design: mRNA profiles of  BMDMs pretreatment with DMSO and KAT8 inhibitor were generated by deep sequencing.

first: Yan

last: Xiang

first: Yunkai

last: Zhang


title: Transcriptomic analysis of renal cell carcinoma and cysts in a patient affected by von Hippel Lindau disease

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

institute: Fondazione Human Technopole

summary: Patients with von Hippel-Lindau (VHL) disease have a high probability to develop multiple primary clear cell renal cell carcinomas (ccRCCs) and kidney cysts throughout their lifetime. Therefore, VHL disease constrained setting provides a ready-made in vivo model to study the development of multiple independent ccRCCs and kidney cysts from the same patient, thus keeping a constant genetic background and systemic and local environment. This offers unique opportunities to comprehensively understand the drivers of cancer evolution while providing distinctions from benign lesions. In order to perform a characterization of concomitant and independent ccRCC lesions and kidney cysts in the same individual, we conducted a transcriptomic profiling on multiple kidney lesions from one VHL patient.

overall_design: Six ccRCC primary tumor lesions (i.e., L1, L2, L4, L5.1, L7 and R10), three renal cysts (i.e., LC1, LC2, and LC4) and one normal renal parenchyma sample (i.e. LN) from the same VHL-disease patient were processed with bulk RNA-sequencing.

first: Isaline

last: Rowe

first: Giovanni

last: Pipitone

first: Andrea

last: Salonia


title: H4K16ac Cut&Tag profiling of Bone Marrow Derived macrophage stimulated with R848

summary: Purpose: Genome-wide identification of genes with H4K16ac, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT)and KAT8-deficient BMDMs. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. BMDMs were stimulated with R848 (100ng/ml) for 2 hours. Results: We carried out a CUT&Tag assay using antibodies against H4K16ac（CST）, and found the global influence of H4K16ac in regulating genes of transcription regulatory regions of key genes for psoriasis.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for H4K16ac peaks in WT and KAT8-deficient BMDMs stimulated with R848.


title: Shielding Retinal Ganglion Cells: Suppression of the PAX6-JNK3 Axis Protects Against NMDA-Induced Excitotoxicity in a Glaucoma Model [RNA-seq]

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary: Retinal degenerative diseases frequently cause visual impairment due to a lack of regeneration systems and self-renewable cells. Glaucoma is characterized by the progressive degeneration of retinal ganglion cells (RGCs), yet the underlying mechanisms remain poorly understood. Here, our study investigated the role of the transcription factor PAX6 in RGC death during NMDA excitotoxicity, a model for glaucoma. Using public single-cell RNA sequencing data, we found that PAX6 is consistently expressed in RGCs across both mouse and human retinas. Notably, we demonstrated that PAX6 phosphorylation was enhanced following NMDA exposure, and JNK3 was identified as a key kinase responsible for PAX6 phosphorylation. Epigenome-wide analysis revealed co-occupancy of PAX6 and JNK3 at key apoptotic gene promoters, with PAX6 acting as a recruitment factor for JNK3. Furthermore, suppressing PAX6 and JNK3 significantly protected against NMDA-induced RGC death, highlighting PAX6-JNK3 contribution to excitotoxicity-mediated apoptosis. Collectively, our findings elucidate a novel mechanism of RGC death in glaucoma, implicating the PAX6-JNK3 signaling axis as a critical mediator of retinal cell fate under excitotoxic conditions, suggesting potential therapeutic targets for preserving RGCs in glaucoma.

overall_design: We administered NMDA (40 mM, 1 µL; n = 4) and phosphate-buffered saline (PBS, used as a control, 1 µL; n = 4) by intravitreal injection into wild-type (WT) mice. ChIP-seq for PAX6 were performed in PBS- or NMDA-injected mouse retinas.


title: LOXL2 protects temporomandibular joint from mitochondrial dysfunction, apoptosis and osteoarthritis like progression

city: Boston

first: Manish

middle: V.

last: Bais

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

summary: Temporomandibular joint (TMJ) osteoarthritis (OA) affects a significant population, and there are no FDA-approved drugs for its treatment. Our previous studies showed that lysyl oxidase-like-2 (LOXL2) has anabolic effects on cartilage; however, whether LOXL2 plays a role in relieving TMJ-OA remains unknown. The goal of this study was to comprehensively investigate LOXL2 mechanism in TMJ protection, with an emphasis on transcriptomic network analysis, mitochondria, and apoptosis during TMJ-OA. We showed that the TMJ is transcriptionally unique compared to the knee, with elevated Loxl2 expression and cartilage-degenerative genes, potentially indicating its different mechanisms of action. Aggrecan promoter-specific homozygous deletion of Loxl2 in mice resulted in a cartilage-degeneration phenotype, mitochondrial dysfunction, NF-κβ-mediated chondrocyte apoptosis, and inflammatory immune response leading to TMJ-OA-like conditions. IL-1β is known to induce osteoarthritis via NF-κβ. With regard to translation, adenoviral-Loxl2 transduction in ex-vivo goat cartilage reduced the IL-1β-mediated degenerative effects. Importantly, LOXL2 preserved IL-1β–induced mitochondrial dysfunction, p62-mediated mitophagy, apoptosis, and  extracellular matrix degeneration. Overall, we identified the protective role of LOXL2 during natural TMJ-OA-like progression and established LOXL2 as a potential candidate gene therapy candidate for future therapeutics.

overall_design: A total of 20 temporomandibular joint (TMJ) tissue samples from Acan-Cre;Loxl2^fl/fl mice (Jax #019148) were subjected to RNA sequencing using the Illumina NovaSeq 6000 platform. Among these, 8 samples were vehicle-treated controls, and 12 were LOXL2 conditional knockouts. Raw fastq files were processed by aligning the reads to the Mus musculus mm10 genome assembly. Gene expression levels were quantified using featureCounts to generate a count matrix. Differential gene expression analysis was performed using the DESeq2 package in R, where standard normalization and filtering were applied to identify significant changes in gene expression between the control and knockout groups.

middle: V

first: Rajnikant

last: Raut

first: Chumki

last: Choudhury

first: Faiza

last: Ali

first: Amit

last: Chakraborty


title: ATAC-seq to profile the chromatin accessibility of BMDMs stimulated with R848

summary: To identify chromatic alterations in BMDMs stimulated by R848, we performed ATAC-sequencing. We identified regions of chromatin that were altered in BMDMs stimulated with R848(2 Hours) or not.

overall_design: ATAC-seq to profile the chromatin accessibility in BMDMs stimulated with R848 or not.


title: Imaging spatial transcriptomics in a transgenic mouse model of α-synucleinopathy

city: Bethesda

first: Mark

last: Cookson

state: MD

address: Building 35, Room 1A116, MSC3707 35, Convent Drive

institute: National Institute on Aging

summary: One of the unifying pathological hallmarks of the age-related neurodegenerative disorders Parkinson’s disease (PD) and dementia with Lewy bodies (DLB) is the presence of misfolded, aggregated, and often phosphorylated forms of the protein α-synuclein (α-syn) in neurons. α-syn pathology appears in select populations of neurons throughout various cortical and subcortical regions, and little is currently known about why some neurons develop pathology while others are spared. Here, we utilized subcellular-resolution imaging-based spatial transcriptomics (IST) in a transgenic mouse model which overexpresses wild-type human α-syn (α-syn-tg) to evaluate patterns of selective neuronal vulnerability to α-syn pathology. By performing post-run immunofluorescence for α-syn phosphorylated at Ser129 (pSyn), we identified cell types in the cortex and hippocampus of these mice which were vulnerable or resistant to developing pSyn pathology. Next, using a set of custom probes to detect genes involved in α-syn processing and toxicity, we investigated the transcriptional underpinnings of the observed selective vulnerability; this pointed to expression of the kinase-substrate pair Plk2, which phosphorylates α-syn at Ser129, and human SNCA (hSNCA), as a driving mechanistic force behind these neurons’ selective vulnerability to pSyn pathology in this model. Finally, we performed differential gene expression analysis, comparing non-transgenic cells to pSyn- and pSyn+ α-syn-tg cells; this revealed gene expression changes downstream of hSNCA overexpression and pSyn pathology which were conserved across cell types, including some genes which were differentially expressed in a pSyn-specific manner. This study provides one of the most comprehensive use cases of newly developed IST to date, yielding new biological insights into the formation of α-syn pathology and its downstream effects in a PD/DLB mouse model.

overall_design: 8 samples, 4 non-transgenic and 4 α-synuclein transgenic, 2M/2F each

first: Liam

last: Horan-Portelance

first: Michiyo

last: Iba

first: Dominic

middle: J

last: Acri

first: J

middle: R

last: Gibbs


title: Shielding Retinal Ganglion Cells: Suppression of the PAX6-JNK3 Axis Protects Against NMDA-Induced Excitotoxicity in a Glaucoma Model [ChIP-seq]


title: The intrinsically disordered region of the E3 ubiquitin ligase TRIP12 induces the formation of chromatin condensates and interferes with DNA damage response.

city: Toulouse

first: Claire

last: Vargas

address: 2 Avenue Hubert Curien

institute: Centre de Recherches en Cancérologie de Toulouse

summary: Chromatin compaction is crucial for the expression and the integrity of the genome. We previously showed that the nuclear HECT-type E3 ubiquitin ligase TRIP12 (Thyroid hormone Receptor Interacting Protein 12) is tightly associated to chromatin. Overexpressed in several types of cancers, we explored herein the consequences of TRIP12 overexpression on chromatin homeostasis. First, we established the proxisome of TRIP12 by BioID and unveiled its pleiotropic role in chromatin regulation. Second, we demonstrated that an overexpression of TRIP12, via its intrinsically disordered region, leads to the formation of chromatin condensates enriched in heterochromatin epigenetic marks. We further discovered that the formation of TRIP12 mediated-chromatin condensates is highly dynamic and driven by a mechanism of polymer-polymer phase separation (PPPS). Chromatin condensates formation is dependent not only on the concentration, the length of TRIP12-IDR but also electrostatic interactions. Chromatin compaction is a determinant parameter in several biological processes. Indeed, we measured that the formation of TRIP12 mediated-chromatin condensates alters cell cycle progression, genome accessibility, transcription as well as DNA damage response (DDR) by inhibiting the accumulation of Mediator DNA Damage Checkpoint (MDC1). Altogether, this study reveals a novel dynamic role for TRIP12 in chromatin compaction independently of its ubiquitin ligase activity with important consequences on cellular processes.

overall_design: Comparative gene expression analysis of RNA-seq data from two experiments of HeLaS3 cells transfected with TRIP12-IDR-GFP versus non transfected HeLaS3 cells.

first: Jérôme

last: Torrisani

first: Marlène

last: Dufresne


title: AMPK promotes TFEB transcriptional activity through dephosphorylation at both mTORC1-dependent and -independent sites [dataset 1]

first: Lars

last: Ingerslev

summary: TFEB (transcription factor EB) is a critical regulator of lysosomal biogenesis, macroautophagy/autophagy and energy homeostasis through controlling expression of genes belonging to the coordinated lysosomal expression and regulation network. AMP-activated protein kinase (AMPK) has been reported to phosphorylate TFEB at three conserved C-terminal serine residues (S466, S467, S469) and these phosphorylation events were reported to be essential for transcriptional activation of TFEB. In sharp contrast to this proposition, we demonstrate that AMPK activation leads to the dephosphorylation of the C-terminal sites. We show that a synthetic peptide encompassing the C-terminal serine residues of TFEB is a poor substrate of AMPK in vitro. Treatment of cells with an AMPK activator (MK-8722), glucose deprivation or MTOR inhibitor (torin1) robustly dephosphorylated TFEB not only at the MTORC1-targeted N-terminal serine sites, but also at the C-terminal sites. Loss of function of AMPK abrogated MK-8722- but not torin1-induced dephosphorylation and induction of the TFEB target genes.

overall_design: mRNA-seq of Mouse Embyonic Fibroblasts comparing the interaction between Tfeb/Tfe3 knock-out and treatment with Torin-1 and MK8722

first: Florentina

last: Negoita

first: Conchita

last: Bringas

first: Kristina

last: Hellberg

first: Katarzyna

last: Luda

first: Hongling

last: Liu

first: Zhiyuan

last: Li

first: Joyceline

last: Cuenco

first: Jin-Feng

last: Zhao

first: Gajanan

last: Sathe

first: Ian

last: Ganley

first: Gopal

last: Sapkota

first: Kei

last: Sakamoto


title: LOXL2 protects temporomandibular joint from mitochondrial dysfunction, apoptosis and osteoarthritis like progression [RNA-Seq]

first: Manish

last: Bais

overall_design: Total 12 temporomandibular joint (TMJ) cell samples derived from the goat superficial layer cartilage (SLC) and middle layer cartilage (MLC) and subjected to RNA sequencing using the Illumina NovaSeq 6000 platform. Each group (SLC and MLC) contained 6 samples, with 3 treated with IL-1β and 3 treated with IL-1β+LOXL2. Raw fastq files were aligned to the Capra hircus reference genome (ncbi_capra_hircus_gcf_001704415.2_ars1.2), and gene expression levels were quantified using featureCounts to generate a count matrix. The differential gene expression analysis was conducted using the DESeq2 package in R, comparing the treatment conditions within each cell group.

first: Rajnikant

last: Raut

first: Chumki

last: Choudhury

first: Amit

last: Chakraborty


title: Plasma extracellular vesicle sampling from high grade gliomas demonstrates a small RNA signature indicative of disease and identifies lncRNA RPPH1 as a high grade glioma biomarker.

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

country: Canada

institute: Vitalité Health Network

summary: Background: High grade gliomas (HGGs) and cells of the tumour microenvironment (TME) secrete extracellular vesicles (EVs) into the plasma that contain genetic and protein cargo which function in paracrine signaling. Isolation of these EVs and their cargo from plasma could lead to a simplistic tool that can inform on diagnosis and disease course of HGG.Methods: In the present study, plasma EVs were captured utilizing a peptide affinity method (Vn96 peptide) from HGG patients and normal controls followed by next generation sequencing (NovaSeq6000) to define a small RNA (sRNA) signature unique to HGG.Results: Over 750 differentially expressed sRNA (miRNA, snoRNA, lncRNA, tRNA, mRNA fragments and non-annotated regions) were identified between HGG and controls. MiEAA 2.0 pathway analysis of the miRNA in the sRNA signature revealed miRNA highly enriched in both EV and HGG pathways demonstrating the validity of results in capturing a signal from the TME. Also revealed were several novel HGG plasma EV sRNA biomarkers including lncRNA RPPH1 (Ribonuclease P Component H1), RNY4 (Ro60-Associated Y4) and RNY5 (Ro60-Associated Y5). Furthermore, in paired longitudinal patient plasma sampling, RPPH1 informed on surgical resection (decreased on resection) and importantly RPPH1 increased again on clinically defined progression.Conclusions: The present study supports the role of plasma EV sRNA sampling (and particularly RPPH1) as part of a multi-pronged approach to HGG diagnosis and disease course surveillance.

overall_design: Extracellular vesicles were captured by peptide affinity captured methods (Vn96 peptide), extracted with miRVana Total RNA kit (Thermo Fisher) and small RNA sequencing was performed using NEXTFLEX small RNA sequencing (v3; Perkin Elmer).

first: Jae

last: Han

first: Gabriel

last: Wajnberg

first: Kathleen

last: Attwood

first: Lindsay

last: Noiles

first: Brandon

last: Hannay

first: Robert

last: Cormier

first: Simi

last: Chacko

first: Maya

last: Willms

first: Andrea

last: Hebb

first: Mary

last: MacNeil

first: Matthias

middle: H

last: Schmidt

first: Sidney

middle: E

last: Croul

first: Adrienne

last: Weeks

first: Jeremy

middle: W

last: Roy


title: Cryptic Last Exon splicing is a conserved tuning mechanism during neural development

status: Public on Feb 10 2026

city: London

first: Matthew

middle: Paul

last: Bostock

address: New Hunt's House, Guy's Campus

department: CDN

country: United Kingdom

institute: King's College London

summary: Cryptic Last Exons (CLEs) are unannotated terminal exons that arise from intronic regions and their inclusion results in shorter mRNA that can be translated into truncated proteins. CLE-mRNAs have been described predominantly in neurodegenerative disease, where they are widely interpreted as pathological and a consequence of splicing dysfunction. Whether CLE-mRNAs are expressed under physiological conditions or contribute to normal gene regulation remains unknown. Here, we show that CLEs are indeed used in normal cellular events. Large scale analysis of public RNA sequencing datasets revealed thousands of CLE mRNAs expressed in wild-type tissues. While CLE sequences were not conserved, CLE usage repeatedly occurred in homologous genes across species. This indicates a selection for CLE usage in specific genes and a conservation at the level of gene architecture rather than primary sequence. CLE-mRNAs display defined spatio-temporal expression patterns across development where they are associated with ribosomes. Using a CLE-mRNA previously described as abundant in ALS models (ephA4b-CLE), we demonstrate that, although initially described as pathogenic, it is temporally expressed in a tissue specific manner, translated, and essential for correct retinal ganglion cell axon growth and connectivity. Together, these findings redefine cryptic last exons as regulated transcript elements that contribute to cellular processes instead of splicing errors only relevant to disease settings.

overall_design: RNA-seq profiling of wildtype zebrafish embryos at 24hpf and Translating Ribosome Affinity Purification (TRAP) mRNA-injected embryo experiment both flow through and pulldown samples (pooled embryos at 24hpf, 48hpf, and 72hpf).

first: Bostock

last: Matthew

first: Houart

last: Corinne


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type and KAT8-deficient Bone Marrow Derived macrophage Transcriptomes

first: Xingguang

last: Liu

summary: Purpose: The purpose of this study is to detect activated or silenced genes during wild type (WT) and KAT8-deficient bone marrow derived macrophages (BMDMs). Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and KAT8-deficient BMDMs were stimulated with R848 (100ng/ml) for 0 and 2 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA  between WT and KAT8-deficient BMDMs.

overall_design: mRNA profiles of WT and KAT8-deficient BMDMs were generated by deep sequencing.

first: Yan

last: Xiang

first: Yunkai

last: Zhang


title: AT2-specific knockout of SLC39A1 in murine model of acute lung injury

city: ChongQing

first: Zhen

last: Zou

address: Medical College Road, Yuzhong District

department: Institute of Life Sciences

institute: ChongQing Medical University

summary: Acute lung injury (ALI) is a common severe respiratory syndrome, with nearly 3 million new ARDS patients worldwide every year. There is no clear effective treatment for ALI.The zinc ion transporters that mediate the change of zinc ion content in target cells during pathophysiology are very different and exert very different biological effects.We identified key zinc ion transporters in ALI and found that SLC39A1 may play an important role in transporting zinc ions during ALI and mediate zinc uptake in AT2 cells.

overall_design:
To explore the role of zinc ion transporter SLC39A1 in ALI, We constructed tamoxifen-induced AT2-specific SLC39A1 knockout mice (Slc9a1 icKO)  and stimulate the day with lipopolysaccharide to complete the molding.
We then performed gene expression profiling analysis using data obtained from RNA-seg of 4 sets of lung tissues treated and without treatment of control and knockout mice.
Comparative gene expression profiling analysis of RNA-seq data for Control+vehicle, Control+LPS, icKO+vehicle, icKO+LPS