title: High burden of premature ventricular contractions upregulates transcriptional markers of inflammation linked with adverse cardiac remodeling and cardiomyopathy.

city: Cincinnati

first: Jose

last: Gomez-Arroyo

state: Ohio

address: 3333 Burnet Ave

department: Pulmonary and Critical Care Medicine

institute: University of Cincinnati

summary: Premature ventricular contractions (PVCs) are the most prevalent ventricular arrhythmia in adults. High PVC burden can lead to left ventricular (LV) systolic dysfunction, eccentric hypertrophy, and an increased risk of heart failure (HF) and sudden cardiac death (SCD). Deficient angiogenesis is a key determinant in the transition from adaptive to maladaptive cardiac hypertrophy and fibrosis is a risk factor for arrhythmias and SCD. Here,  the primary objective was to quantitatively assess the structural remodeling and transcriptional alterations associated with PVC-induced cardiomyopathy (PVC-CM). Canines were implanted with modified pacemakers to reproduce bigeminal PVCs (200-220 ms coupling interval) for 12 weeks. Collagen deposition and interstitial ultrastructure were visualized using light and transmission electron microscopy, respectively, in LV samples. Morphometric studies of pericytes, fibroblasts, myocytes, smooth muscle and endothelial cells were performed using confocal microscopy and quantified with an artificial intelligence-based segmentation analysis and compared using hierarchical statistics. Transcriptional changes were assessed via RNAseq. Although the cardiomyocytes were hypertrophied in PVC-CM LV samples, capillary rarefaction was not observed due to an increase in capillary-to-myocyte ratio. Additionally, thicker blood vessels were more abundant in PVC-CM. Fibroblast-to-myocyte ratio more than doubled, interstitial collagen fibers increased, and the interstitial space thickened in PVC-CM. Transcripts involved in interstitial remodeling, inflammatory response, and alarmins were strongly elevated in PVC-CM. While the angiogenic response meets the metabolic demands of cardiac hypertrophy, upregulated markers of inflammation and cardiomyopathy linked to reactive fibrosis collectively represent an adverse remodeling that heightens the risk of HF and SCD in PVC-CM.

overall_design: Female mongrel canines (>10 months old, ~21 Kg) were implanted with a modified dual-chamber epicardial pacemaker. After a 2-week surgical recovery, animals were randomized into 2 groups: 1) PVC-CM group, receiving bigeminal PVCs (50% burden) with a 200-220 ms coupling interval for 12 weeks, and 2) sham group where PVCs were not enabled. Echocardiographic recordings were obtained at baseline and at 12-weeks of chronic PVCs to evaluate the development of cardiomyopathy. Euthanasia was performed at week 12, via exsanguination during final left thoracotomy surgery under general anesthesia. The harvested heart was immediately rinsed with ice-cold phosphate-buffered saline (PBS), which was injected directly through the left main coronary artery to remove blood. Segments of the anterior LV were snap frozen and snap-frozen myocardial tissue from randomly selected regions of the left ventricular (LV) free wall was used for RNA extraction and downstream analysis.

first: Juana

last: Medina-Contreras

first: Jaime

last: Balderas-Villalobos

middle: F

last: Huizar

last: Eltit


title: RSK1 modulates the translatome of glioblastoma cells in an isoform-specific manner

status: Public on Jun 25 2025

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Institute

summary: The p90 ribosomal S6 kinase (RSK) family, downstream targets of Ras/ERK signaling, encompass four human isoforms (RSK1-4). Glioblastoma (GBM) predominantly expresses RSK1 and RSK2. Notably, RSK1 is markedly upregulated in a subset of GBMs associated with dismal prognosis and immune infiltration, whereas RSK2 expression remains consistent across cases. We verified that GBM-derived cell lines recapitulate RSK isoform expression profiles and estimated their stoichiometry. Through the generation of RSK1 and RSK2 knockout (RSK1KO and RSK2KO) as well as double knockout (DKO) GBM cells, we investigated isoform-specific functions of RSK. Surprisingly, contrary to conventional belief, we found that mTORC1 is not activated by RSK isoforms. Instead, eIF4B phosphorylation at S422 was RSK-dependent rather than mTORC1/S6K-dependent, with RSK1 exerting a more pronounced effect. Intriguingly, RSK1 and RSK2 displayed differential effects on translation, with RSK1 maintaining translation of specific mRNAs under conditions of reduced overall translation due to mTORC1 inhibition, unlike RSK2. Finally, we verified that while the translatome of RSK1KO cells show a downregulation of mRNAs affecting cell cycle, DNA replication and repair, RSK2 depletion impacted mitochondrial and respiratory genes. Notably, DKO cells exhibited compounded phenotypes, underscoring the existence of isoform-specific gene regulation programs orchestrated by RSK. Collectively, our findings offer mechanistic insights crucial for unraveling the role of RSK1 in GBMs.

overall_design: In order to define RSK-isoform specific functions, we applied the CRISPR/Cas9 technique to edit the genome of glioblastome-derived LN18 cells (LN18CRISPR) and thus generate knockout cells for RSK1 (RSK1KO) or RSK2 (RSK2KO), and also double-knockout cells for both RSK1 and RSK2 (DKO). Cells were pre-treated with Torin1 (or DMSO) before serum stimulation for 6 hours. Total and polysome-associated (poly) mRNA were analyzed by microarray.


title: Short chain fatty acids regulate the chromatin landscape and distinct gene expression changes in human colorectal cancer cells

status: Public on Jun 24 2025

city: Cleveland

first: Leah

last: Gates

state: OH

address: 10900 Euclid Avenue

country: USA

institute: Case Western Reserve University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Short chain fatty acids (SCFAs) are small metabolites that are produced through the activity of microbes and have important roles in human physiology. These metabolites have varied mechanisms in interacting with the host, of which one such mode is decorating the chromatin landscape. We previously detected specific histone modifications in the mouse gut that can be derived from SCFAs and are regulated by the microbiota. However, the roles of these SCFAs on chromatin and how they impact gene regulation in human cells is largely unknown. Now, our studies demonstrate these microbiota-dependent histone posttranslational modifications (PTMs) are associated with alterations in gene regulation in human cells. We show that histone butyrylation on H3K27 is detected in human colon samples. Furthermore, histone acetylation, butyrylation, and propionylation on H3K9 and H3K27 are responsive to levels of SCFAs in human colon cancer cell lines and are associated with active gene regulatory elements. In addition, treatment of human cancer cell lines with individual metabolites or combinations of SCFAs replicating the intestinal lumen environment result in distinct and overlapping gene program changes, with butyrate largely driving gene regulatory effects of SCFA combinations. Lastly, we define butyrate effects on gene expression that are independent of HDAC inhibition and are dependent on p300/CBP, suggesting potential gene programs regulated by histone butyrylation. Together, these results demonstrate that SCFAs are key regulators of the chromatin landscape and gene programs in human colorectal cancer cells.

overall_design: One experiment includes ChIP-seq of histone acyl modifications in HCT-116 cells treated with either butyrate or propionate. Other experiments are RNA-seq data from HCT-116 or Caco-2 cells treated with different short chain fatty acids or inhibitors targeting HDACs or p300/CBP. All RNA-seq samples are provided in biological triplicate.

first: Leah A.

first: Matthew R

last: Paul

first: Thomas S

last: Carroll


title: High Dimensional Analysis of Sputum Cell Transcriptomes Identifies novel pathways associated with Clinical Phenotypes of Asthma

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

summary:
Background: Asthma is a chronic inflammatory disease of the airways driven by interactions among structural cells of the airway, the immune system, and the environment. Characterization of cells isolated from the sputum has been used to study the pathogenesis of asthma and optimize treatment regimens, but the cellular transcriptomes and intercellular communication changes in the sputum of asthma are not well understood.
Methods: Single cell RNA sequencing was applied to cells isolated from the sputum from 16 patients with asthma and 8 non-asthmatic normal controls.  Cell identity was determined by analysis of curated cell marker genes combined with SingleR annotation. Cell specific gene expression and communication networks were compared between asthma and controls and were correlated with asthma phenotypes.
Findings: 15 different cell populations were identified, including several types of macrophages, monocytes, dendritic cells, and lymphocytes as well as several rare (<2%) cell types such as mast cells, innate lymphoid cells, and bronchial epithelial cells. Analysis of the intercellular communications demonstrated that signaling pathways are generally more active in asthma compared to control.  CD4+ cells and dendritic cells had the largest increase in outgoing signals to other cell types. One of the strongest signal was the ADAM12 and CCL22 ligand-receptor pathways showing the strongest shift between asthma and controls.
Interpretation: Analysis of cellular transcriptomes in the sputum demonstrates innate and adaptive mechanisms are increased in asthma. Increased expression of ADAM12 suggests a critical role in the pathogenesis of asthma.

overall_design: Cells from sputum samples of asthma patients and normal controls were isolated and analyzed using the 10x Genomics Chromium 3' single-cell RNA sequencing kit.

first: Geoffrey

last: Chupp

first: Qing

last: Liu


title: AP2X-1 is a negative regulator of Toxoplasma gondii sexual commitment

city: Lanzhou

first: JinLei

last: Wang

address: yanchangbao

country: China

institute: LVRI

summary: Toxoplasma gondii is a ubiquitous protozoan with a complex life cycle involving transitions between different hosts and developmental stages, each adapted to a unique niche within its host. However, the regulatory mechanisms controlling these life cycle transitions remain poorly understood. In this study, we characterized the AP2 factor AP2X-1, which is expressed during the tachyzoite and bradyzoite stages, but not in the mature merozoite stage. Knockout of ap2X-1 significantly impaired tachyzoite invasion and replication, while increasing the frequency of bradyzoite differentiation. As a component of the HDAC3/MORC complex, knockout of ap2X-1 led to the upregulation of bradyzoite and sexual stage-specific genes. Single-cell sequencing revealed that ap2X-1 knockout strains behaved as a mixed population of tachyzoites, bradyzoites, merozoites, and sporozoites. CUT&Tag analysis revealed substantial overlap between AP2X-1 and HDAC3/MORC complex binding at the promoters of bradyzoite and sexual stage-specific genes. Additionally, ATAC-seq analysis demonstrated that AP2X-1 modulates chromatin compaction and accessibility, suggesting that AP2X-1 recruits the HDAC3/MORC complex to repress bradyzoite differentiation and sexual commitment. The loss of ap2X-1 resulted in significant attenuation of T. gondii virulence and reduced the formation of brain cysts in vivo. These findings identify AP2X-1 as a critical negative regulator of T. gondii sexual development.

overall_design:
We report genome-wide AP2X-1 profiles in Toxoplasma gondii using CUT&TAG

We report  chromatin compaction and accessibility of AP2X-1 in Toxoplasma gondii using ATAC-Seq.

first: Li-Xiu

last: Sun

first: Meng

first: Tian-Yu

last: Zhang

first: Hany M

last: Elsheikha

first: Xiao-Nan

last: Zheng

first: Zhi-Wei

first: Bao-Quan

last: Fu

first: Xing-Quan

last: Zhu

first: Guo-Hua

first: Jin-Lei


title: 5-HT regulates resistance to aumolertinib by attenuating ferroptosis in lung adenocarcinoma

status: Public on Jun 20 2025

city: Tianjin

first: Feng

middle: Yuan

last: Ying

address: Tianjin

institute: Tianjin Medical University Cancer Institute and Hospital

summary: Resistance to epidermal growth factor receptor (EGFR) -tyrosine kinase inhibitor (TKI) remains a critical clinical challenge in EGFR mutant lung adenocarcinoma (LUAD). Therefore, it is urgent to explore personalized treatment strategies based on distinct resistance mechanisms to reverse EGFR-TKI resistance. Herein, we found that HER2 S310F mutation contributes to third-generation EGFR-TKI resistance, driven by the accumulation of neurotransmitter 5-hydroxytryptamine (5-HT). Mechanistically, 5-HT interacted with 5-HT3 receptor, triggering calcium ion (Ca²⁺) influx and subsequent activation of the Ca²⁺/CAMKK2/AMPK pathway. This pathway activation conferred ferroptosis resistance, thereby driving aumolertinib resistance. 5-HT3 receptor  (HTR3) antagonists were pinpointed as potential agents for reversing aumolertinib resistance through drug library screening and transcriptomics analysis. We demonstrated that pharmacologically targeting 5-HT/HTR3 signaling with the clinically approved HTR3 antagonist palonosetron effectively restores aumolertinib sensitivity. Importantly, we showed that elevated 5-HT levels in patient plasma play a potential role in predicting EGFR-TKI resistance. Ourdata highlight the critical role of 5-HT and ferroptosis in the development of aumolertinib resistance, and propose HTR3 antagonists as a novel combination therapy strategy for LUAD treatment with aumolertinib.

overall_design: RNA-seq profiling of H1975 EV (Empty vector) cells and H1975 HER2 S310F mutant stable cells

first: Yuanying

last: Feng

first: Hua

last: Guo


title: EDNRB2 regulates fate determination, migration and maturation of hair-cell precursors in regenerating avian auditory epithelia

status: Public on Jun 21 2025

city: Kyoto

first: Mami

last: Matsunaga

state: Kyoto

address: Kawahara cho 54, Shogoin, Sakyo-ku

department: Department of Otolaryngology, Head and Neck Surgery

country: Japan

institute: Kyoto university

summary: The mammalian cochlea loses the ability for hair cell (HC) regeneration after birth, while in the avian auditory epithelium, namely the basilar papilla (BP), supporting cells (SCs) retain the capability for HC regeneration throughout life. Our previous study using single-cell RNA sequencing indicated stepwise fate conversion of SCs to HCs via the precursor state, in which EDNRB2 exhibited specifically high expression, in the process of HC regeneration in chick BP. The present study aimed to reveal a distinct role of EDNRB2 in HC regeneration in chick BP. During HC regeneration in chick BP explant cultures, EDNRB2 expression emerged in a part of ATOH1-expressing SCs immediately after HC loss and decreased according to the progress of HC regeneration process. In embryonic chick BP, EDNRB2 expression was specifically identified in the precursor cell state, which confirmed that mature SCs were reprogrammed to the precursor state in response to HC loss. Pharmacological inhibition of endothelin receptor type B (EDNRB) signaling decreased regenerated HCs in chick BP explant cultures. RNA sequencing revealed that inhibition of EDNRB signaling downregulated genes for HC differentiation and maturation together with genes for cell migration. Histological assessments clarified the deterioration of migration of HC precursors and the delay of HC regeneration processes by inhibition of EDNRB signaling. These results indicate that the expression of EDNRB2 contributes to the fate determination of HCs and that EDNRB signaling regulates the migration and maturation of HC precursors during chick HC regeneration.

overall_design: Bulk RNA-seq of chick basilar papaillae during hair cell regeneration using an explant culture

first: Takeuchi

last: Marie

first: Matsunaga

last: Mami

first: Nakagawa

last: Takayuki


title: Beneficial and detrimental consequences of AHR stimulation in intestinal infection

city: Solna

first: Oscar

last: Diaz Perez

address: Nobels väg 13

country: Sweden

institute: Karolinska Institutet

summary: The ligand dependent transcription factor aryl hydrocarbon receptor (AHR) is an environmental sensor whose activation can have physiologically beneficial or detrimental consequences for host immune responses depending on the ligand. Here we investigated the hypothesis that prolonged AHR activation either due to inefficient ligand metabolism or due to genetic manipulation may underlie the distinction between beneficial and detrimental effects. Our data indicate that prolonged AHR activation caused toxic endpoints for liver and thymus but was not per se interfering with the host response to infection with the intestinal pathogen C.rodentium. Genetically driven constitutive AHR activation improved resistance to infection, whereas prolonged AHR activation by the pollutant TCDD resulted in delayed clearance of C.rodentium. This was associated to a suppression in antibody production. Combined single cell RNAseq and ATAC-seq analysis provided evidence that TCDD, but not genetic AHR overactivation, affected dendritic cell functions such as activation, maturation and antigen presentation. Thus, the detrimental impact of environmental pollutants such as TCDD on immune responses cannot solely be attributed to aberrantly prolonged activation of AHR.

overall_design: Single nuclei were extracted on day 5 after infection with Citrobacter rodentium. Mice were treated with Vehicle or TCDD 6 days before infection. Joint snRNA-seq and scATAC-seq libraries were prepared using the 10x Genomics platform

middle: E

last: Diaz

first: Christopher

last: Barrington

first: Liang

last: Zhou

first: Dennis

last: Lindquist

first: Frederike

last: Graelmann

first: Emma

last: Wincent

first: Brigitta

last: Stockinger


title: Histone deacetylase 5 in prelimbic prefrontal cortex limits context-associated cocaine-seeking behavior

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary:
Background
Repeated cocaine use produces neuroadaptations that support drug craving and relapse in substance use disorders (SUDs). Powerful associations formed with drug-use environments can promote a return to active drug use in SUD patients, but the molecular mechanisms that control the formation of these prepotent drug-context associations remain unclear.
Methods
In the rat intravenous cocaine self-administration (SA) model, we examined the role and regulation of histone deacetylase 5 (HDAC5) in the prelimbic (PrL) and infralimbic (IL) cortices in context-associated drug seeking. To this end, we employed viral molecular tools, chemogenetics, RNA-sequencing, electrophysiology, and immunohistochemistry.
Results
In the PrL, reduction of endogenous HDAC5 enhanced context-associated, but not cue- or drug prime-reinstated cocaine seeking; whereas, overexpression of HDAC5 in PrL, but not IL, reduced context-associated cocaine seeking, but it had no effects on sucrose seeking. In contrast, PrL HDAC5 overexpression following acquisition of cocaine SA had no effects on future cocaine seeking. We found that HDAC5 and cocaine SA altered the expression of hundreds of PrL genes, including many synapse-associated genes. HDAC5 significantly increased inhibitory synaptic transmission onto PrL deep-layer pyramidal neurons, and it reduced the induction of FOS-positive neurons in the cocaine SA environment.
Conclusions
Our findings reveal an essential and selective role for PrL HDAC5 to limit associations formed in cocaine, but not sucrose, SA environments, and that it alters the PrL excitatory/inhibitory balance, possibly through epigenetic regulation of synaptic genes. These results further position HDAC5 as a key factor regulating reward-circuit neuroadaptations that underlie common relapse triggers in SUD.

overall_design: We investigated the role of HDAC5 in the Prelimbic Cortex, a subdivsion of the medial Prefrontal Cortex that is involved in prolonged drug seeking behaviors. We tested the role of the epigenetic enzyme HDAC5 in a variety of relapse tests following cocaine i.v. self-administration. We also examined changes in gene expression following re-exposure to the the self-administration context (in drug experienced and drug naive rats), and the changes in electrophysiological properties of PrL neurons as a result of HDAC5 expression.

first: Sarah

last: Barry

last: Cowan


title: Life long effects of radiation and high fat dieat on the mouse right ventricular tissue

city: New York

first: Davit

middle: A.

last: Goukassian

state: NY

address: One Gustave L. Levy Place, Box 1014

department: Cardiovascular Research Institute

institute: Icahn School of Medicine at Mount Sinai

summary: We studied the long-term effects of single whole-body gamma and simulated GCR irradiation (IR) and consumption of a Western Diet (WD) on the heart's right ventricle (RV). Three-month-old C57Bl/6J wild-type male and female mice were assigned to the following groups: 1) Gamma-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 2) simGCRsim-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 3) 270-days WD-fed animals with followup at 530 (males and females) and 750(males)/640(females). Control groups consisted of non-irradiated (non-IR) mice and normal diet-fed mice. Control groups were followed up similarly to the treatment groups. RV tissues were collected at follow-up and subjected to bulk RNA sequencing analysis. Total RNA was extracted from RV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use. A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit. The sequencing was performed on the Illumina NovaSeq-6000 platform to collect an average of 48 million 2x150bp paired-end reads per sample. FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) with STAR aligner (version 2.7.8a) with gene count quantification mode and obtained raw gene counts. Differential gene expression analysis and functional annotation were performed using DESeq2 and fgsea R packages. The results of the study provide insights into the long-term transcriptomic disturbances in response to irradiation and a Western diet and their association with structural and functional changes in the RV. Furthermore, the findings highlight pronounced sex-specific and irradiation type-dependent pathophysiological and transcriptomic alterations in the RV.

first: Siras

last: Hakobyan

first: Roksana

last: Zakharyan

first: Ani

last: Stepanyan

first: Arsen

last: Arakelyan

first: David

middle: A


title: Epigenetic profiles of response to transcranial magnetic stimulation in treatment resistant depression

status: Public on Jun 18 2025

city: Tampa

first: Jan

last: Dahrendorff

state: Florida

address: 3720 Spectrum Blvd

department: Department of Global, Environmental, and Genomic Health Science

institute: University of South Florida

type: Methylation profiling by genome tiling array

summary: Peripheral blood DNA methylation was profiled in 46 patients with treatment-resistant depression prior to treatment with transcranial magnetic stimulation (TMS). Genome-wide DNA methylation was measured using the Illumina Infinium MethylationEPIC BeadChip (850K array). Following quality control, data from 46 subjects were included in downstream analyses. Treatment outcomes were assessed using the PHQ-9 depression scale and included treatment response (≥50% reduction in PHQ-9), symptom trajectory (ΔPHQ-9), and remission (PHQ-9 score < 5). Methylation data were analyzed to identify differentially methylated regions (DMRs) associated with treatment outcomes. Both raw IDAT files and processed beta-value data are provided.

overall_design: Peripheral blood samples were collected and analyzed from 46 patients with treatment-resistant depression prior to a standardized 36-session course of transcranial magnetic stimulation (TMS) treatment. Genomic DNA was extracted and bisulfite converted for methylation profiling using the Illumina Infinium MethylationEPIC BeadChip (850K array). After sample-level quality control, 46 samples were retained for analysis. DNA methylation data were analyzed in relation to clinical outcomes based on PHQ-9 scores, including treatment response, symptom change, and remission status.

first: Monica

last: Uddin


title: Effect of depletion of Dnmt3a on gene expression during the appearance of endometriosis

status: Public on Jun 23 2025

city: Houston

first: Nuri

last: Sung

state: Texas

address: One Baylor plaza, Houston, Rm807

department: Molecular and Cellular biology

institute: Baylor college of Medicine

summary: Endometriosis is a benign yet invasive condition in which endometrial-like tissue grows outside the uterus. Recent evidence highlights the role of epigenetic mechanisms—particularly DNA methylation—in its development. DNA methyltransferases (DNMTs), including DNMT1, DNMT3B, and DNMT3A—regulate these modifications. DNMT3A is uniquely upregulated in the eutopic endometrium of women with endometriosis and may affect reproductive potential via altered gene expression.  To investigate DNMT3A's role, we compared the incidence of endometriosis and transcriptomic profiles in Dnmt3a knockout (KO) mice and wild-type controls. RNA sequencing of KO samples revealed upregulation of pathways such as E2F_TARGETS, MYC_TARGETS_V1, G2M_CHECKPOINT, and UNFOLDED_PROTEIN_RESPONSE, and downregulation of NOTCH_SIGNALING, COAGULATION, HEDGEHOG_SIGNALING, ANGIOGENESIS, and ADIPOGENESIS. Several immune-related genes were also differentially expressed, including IL-6, CXCL1, CXCL2, IL-1β, TNFα, CCL5, CXCL5, TGFβ1, IL-10, CXCL9, CXCL10, CX3CL1, CCL2, CCL22, CCL17, and CXCL12.  These findings suggest that elevated DNMT3A expression may contribute to immune suppression in endometriosis, and its loss leads to reactivation of immune response genes, highlighting DNMT3A as a potential therapeutic target.

overall_design: RNA-seq profiling was conducted on endometriosis samples using both wild-type DNMT3A and its knockout mice, four weeks post-disease onset.

first: Sang Jun

last: Han


title: Effect of MacroD1 knockout on gene expression of heart on mouse septic model

city: Shang hai

first: chen

middle: xiao

last: qiang

state: China

address: 650 New Songjiang Road

department: Department of Cardiology

institute: Shanghai General Hospital, Shanghai Jiaotong University School of Medicine

summary: Metabolic plasticity of tissues determines the degree and reversibility of organ damage under inflammatory challenges. While treating septic cardiomyopathy (SCM) with high mortality, metabolic management should be considered. Still, similar pan-organ metabolic anomalies usually yield contrasting results in each one, highlighting the necessity to identify cardiac-specific metabolic regulators. Nicotinamide adenine dinucleotide (NAD+) signaling is fundamental to cellular metabolic homeostasis and inflammatory response, and cardiomyocyte-enriched NAD+-consuming enzymes programming metabolism against sepsis and their roles in SCM remain undefined. In this study, we explored the expression patterns of NAD+-consuming enzymes of heart and found Mono-ADP-ribosyl hydrolase MacroD1 protein was distinctly enriched in rodent and AC16 human cardiomyocytes and upregulated during severe endotoxemia. Genetic and pharmacological inactivation of MacroD1 counteracted myocardial metabolic impairment, lipid accumulation, inflammatory infiltrate, cardiac dysfunction, and mortality risk induced by septic challenges in mice. Mechanistically, MacroD1 selectively modulated the activity of mitochondrial complex I (MCI), a proximal respiratory unit most vulnerable to early endotoxemia. Its inhibition enhanced MARylation of NDUFB9, an accessory assembly factor of MCI proton-pumping module ND5, and therefore binding to ND5 for preserving MCI activity in sepsis, restraining bioenergetic deficiency, oxidative stress-coupled NLRP3 inflammasome activation, and pyroptosis of cardiomyocytes. Our research reveals that MacroD1 dictates cardiac tolerance to sepsis by configuring MCI-coupled bioenergetic reserve and pyroptosis of cardiomyocytes. Blockade of MacroD1 promises specific prevention of SCM.

overall_design: A total of 8 samples were divided into 4 groups for analysis. After the 8-week-old cardiac-specific conditional MacroD1 knockout mice (Mac_ko) and control mice (WT) were treated with LPS (10mg/kg) or saline for 18 hours, the hearts were extracted for high-throughput sequencing analysis. The specific groups were as follows: WT, Mac_ko, WT+LPS, Mac_ko+LPS. (n=2 for each group).

first: Xiaoqiang

last: Chen

first: Tianyou

last: Yuan

first: Danchuan

last: Zheng

first: Fangfang

last: Li

first: Hao

last: Xu

first: Maoqing

last: Ye

first: Shaowen

last: Liu

first: Jun


title: Cardiomyocyte mitochondrial mono-ADP-ribosylation dictates cardiac tolerance to sepsis by configuring bioenergetic reserve

city: xiamen

first: XiaoQiang

address: 2999 Jinshan Road,Huli District,Xiamen,Fujian Province

institute: Xiamen Cardiovascular Hospital, Xiamen University School of Medicine

summary: The metabolic flexibility of tissues dictates the extent and reversibility of organ damage during inflammatory challenges. However, there are currently no countermeasures for myocardial metabolic breakdown in the treatment of septic cardiomyopathy (SCM). Nicotinamide adenine dinucleotide (NAD+) signaling is crucial for maintaining cellular metabolic homeostasis and modulating inflammatory responses. Through the use of single-cell sequencing technology, specifically the 10x Genomics scRNAseq approach, we have investigated the role of NAD+ signaling-related genes in SCM. Our findings reveal that both genetic and pharmacological inhibition of the mono-ADP-ribosyl hydrolase MacroD1, which is highly expressed in cardiomyocytes, can effectively counteract the myocardial metabolic impairment, inflammation, dysfunction, and mortality risk triggered by lipopolysaccharide exposure and cecal ligation and puncture in mice.

overall_design: We applied lipopolysaccharide via intraperitoneal injection in mice to establish a septic cardiomyopathy model, and harvested the hearts 18 hours post-administration. The cardiac tissues were enzymatically digested into a single-cell suspension and subjected to single-cell sequencing.


title: Effects on renal senescence, copper flux and respiration during stem cell-based therapy

city: Beijing

first: Kaiting

last: Zhuang

state: Beijing

address: 28 Fuxing Road, Haidian District

institute: 1st Medical Center of Chinese PLA General Hospital

summary: Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) can reverse senescence after acute kidney injury (AKI) via maintaining mitochondrial homeostasis. Copper accumulation could promote senescence, but its response to MSCs remains unclear. C57 mice with renal unilateral ischemia reperfusion injury (uIRI) were renal capsular transplanted with hUC-MSCs for two weeks then performed mRNA sequencing. Gene correlation analysis revealed that senescence regulation is associated with copper homeostasis and respiratory chain complex IV.

overall_design: RNA-seq profiling of sham, uIRI and MSCs transplantation at Day 14.

first: Kating

first: Wenjuan

last: Wang

first: Guangyan

last: Cai


title: RNA-seq analysis of intestinal organoids to investigate the roles of Rnaseh2b and Atg16l1 in gene regulation

status: Public on Jun 17 2025

city: Kiel

first: Konrad

last: Aden

address: Rosalind-Franklin-Straße 12

country: Germany

institute: Institute of Clinical Molecular Biology, CAU

summary: This dataset contains RNA-seq profiles of intestinal organoids derived from wild-type, Rnaseh2b knockout, Atg16l1 knockout, and Rnaseh2b/Atg16l1 double knockout mice. Rnaseh2b deficiency is associated with DNA damage and tumorigenesis, while Atg16l1 loss impairs autophagy and has been implicated in inflammatory bowel disease (IBD). Interestingly, the double knockout mice did not develop tumors, suggesting a complex interaction between DNA damage and autophagy pathways. This transcriptomic dataset offering insights into the molecular crosstalk underlying intestinal homeostasis, inflammation, and tumor suppression.

overall_design: RNA-seq profiling of intestinal organoids derived from wild-type, Rnaseh2b knockout, Atg16l1 knockout, and Rnaseh2b/Atg16l1 double knockout mice.

first: Joanna

middle: P

last: Bernardes

first: Nassim

last: Kakavand

first: Hang

last: Xiang


title: ERAP1 deficiency exacerbates DSS-induced colitis and alters sulfasalazine efficacy via immune dysregulation

city: Swon

first: Hye-Myung

last: Ryu

address: 206, World cup-ro

department: Microbiolgy

country: South Korea

institute: Ajou Hospital

summary:
UIntroduction: Ulcerative colitis (UC) is a life-threatening heterogeneous condition characterized by inflammation of the colon. Endoplasmic reticulum aminopeptidase 1 (ERAP1) is essential for antigen processing and immune regulation, however, its specific role in UC pathogenesis and therapeutic response remains unclear. This study aimed to investigate the role of ERAP1 in the response to sulfasalazine, a standard treatment for UC, using an ERAP1-heterozygous (ERAP1+/-) mouse model susceptible to colitis.

Methods: Wild-type (WT) and ERAP1+/- mice were treated with 2.5% dextran sulfate sodium to induce colitis, followed by sulfasalazine administration. Colitis severity was assessed through histopathology. Immune cell populations, including neutrophils, dendritic cells, T cells, and NK1.1+ cells, were analyzed using flow cytometry. RNA sequencing of colonic tissues was performed to assess gene expression changes associated with reduced ERAP1 expression.

Results: ERAP1+/- mice exhibited mildly increased susceptibility to DSS-induced colitis, with greater weight loss and distinct alterations in immune cell infiltration compared to WT mice. These differences were further pronounced after sulfasalazine treatment. RNA sequencing identified 428 differentially expressed genes between ERAP1⁺/⁻ and WT mice. Among these, 28 genes were previously associated with colitis or colorectal cancer, of which 11 were upregulated and 17 downregulated in ERAP1+/- mice. RT-qPCR confirmed significantly elevated expression of Anxa9, Atp2a1, and Hepacam2 in ERAP1+/- mice after sulfasalazine treatment, indicating a differential therapeutic response.

Conclusion: Collectively, our findings show that partial ERAP1 deficiency promotes immune dysregulation, alters the expression of inflammation-associated genes, and impairs sulfasalazine efficacy. Therefore, ERAP1 may serve as a key regulator in the pathogenesis of UC and a potential target for therapy.

overall_design: RNA-seq profiling of wild type and ERAP1 hetero type( ERAP1⁺/⁻ ) intestine.

first: HyeMyung

first: Bushra

last: Riaz

first: S. M. Shamsul

last: Islam

first: Rahar

last: Babita

first: Je Kyung

last: Seong

first: Ho

last: Lee

first: Eunjoo H

first: Seonghyang

last: Sohn


title: CRISPR Screen Reveals SOX2 as a Critical Regulator of CD133 and Cellular Stress Response in Glioblastoma II

city: Hamilton

first: Sheila

last: Singh

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

institute: McMaster University

summary: Glioblastoma (GBM) remains a formidable challenge in clinical settings due limited treatments available. The surface protein CD133 marks glioblastoma stem cells (GSCs), cells capable of overcoming therapeutic pressures and correlate with more aggressiveness tumor phenotypes. In this study, we employed a CRISPR-Cas9 functional screen to deconvolute CD133 dynamics in tumors. This led us to establish that SOX2 is a key player in controlling the PROM1 gene, which in turn influences how cells react to stress factors, including those induced by chemoradiation treatment. The discoveries in this study shed light on the complex web of mechanisms that control the survival and resistance of GSCs, offering promising new avenues for targeting and potentially overcoming therapy resistance.

overall_design: The CRISPR screen was established, where 1E8 cells were transduced with the TKOv3 lentivirus library at an MOI of 0.3, representing more than 400-fold coverage per sgRNA after selection with puromycin. Media was changed 24 hours after infection to puromycin-containing medium (1.2µg/mL). 72 hours after transduction, 3E7 puromycin-selected cells were collected for genomic DNA extraction at starting timepoint, and 9E7 cells were evenly divided into triplicates (3E7 cells each, 2.5E6 cells per 15cm dish). Passaging subsequently occurred every 7 days (approximately 3 cell doublings), where 3E7 cells in each replicate were reseeded until the 12th doubling (T12) when sorting was performed. A representative portion of the final population of cells (bulk/unsorted) was collected for sequencing prior to staining for flow cytometry followed by the top and bottom 5th-percentiles of CD133 surface expression being collected in cooled flow tubes. Collected cells were centrifuged and stored at -80 °C until genomic extraction as described below.

first: Neil

last: Savage

middle: K

first: Chirayu

middle: R

last: Chokshi

first: Chitra

last: Venugopal

first: Kevin

last: Brown

first: Jason

last: Moffat


title: Whole blood gene expression data of thrombotic and non-thrombotic critically ill COVID-19 patients

city: Amsterdam

first: Cosimo

last: Cristella

address: Meibergdreef 9

department: Medical microbiology and infection prevention

country: Netherlands

institute: Amsterdam University Medical Centers

summary:
Background: COVID-19 has revealed novel pathological mechanisms, particularly hypercoagulability leading to increased thrombotic risk in critically ill patients. This study investigates transcriptional signatures associated with thrombosis development in COVID-19 intensive care unit (ICU) patients and evaluates their predictive potential.
Methods: We performed whole blood transcriptional profiling of 57 mechanically ventilated COVID-19 patients, comparing those with thrombotic complications (TC, n=36) to those without (non-TC, n=21) using differential gene expression and machine learning approaches.
Results: TC patients showed greater transcriptome disruption and 283 differentially expressed genes compared to non-TC patients. Key features included enhanced neutrophil activation, inflammatory responses, and monocyte activation alongside suppressed lymphocyte function. An OPLS-DA model achieved excellent classification performance (AUC=0.961, 95% CI: 0.905-0.997). The maltase-glucoamylase gene (MGAM) was the top discriminatory biomarker outperforming traditional clinical markers like D-dimer and C-reactive protein (AUC=0.94).
Conclusions: Thrombotic complications in critically ill COVID-19 patients are characterized by distinct transcriptional signatures reflecting heightened neutrophil activation and inflammatory dysregulation. MGAM represents a novel potential biomarker that outperforms traditional clinical markers for identifying patients at high thrombotic risk, offering new opportunities for personalized risk stratification and management in severe COVID-19.

overall_design: This was a retrospective, observational study conducted at Erasmus medical center, The Netherlands, during the first wave of COVID-19 pandemic and precisely between 2nd March 2020 and 20th of April 2020. In brief, 77 patients with COVID-19 admitted to the ICU with ARDS were included in a biobank study (CIUM). If indicated by clinician, patients underwent computed tomographic pulmonary angiography, which was subsequently repeated 7 days after admission, or if the patient’s clinical condition abruptly deteriorated. Whole blood samples were available from 57 subjects at day 2 of ICU admission and were used in the presented research. Healthy controls were obtained from convalescent subjects enrolled as part of the MERMAIDS-ARI clinical observational study and were matched with cases based on age, gender, pulmonary, cardiovascular and metabolic disease infromation.

first: Matthijs

last: Raadsen

first: Karen

last: de Haan

first: Sarah

last: van Leeuwen

first: Mohammad

last: Toliat

first: Nina

last: Dalibor

first: Marion

last: Koopmans

first: Menno

middle: D

last: de Jong


title: Chromosome 8 gain drives cancer progression by hijacking the translation factor 4E-BP1 sensitizing for targeted CDK4/6 inhibition [II]

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary:
We report that chr8 gain-driven gene expression patterns correlate with poor overall survival of EwS patients. This effect is predominantly mediated by increased expression of the translation initiation factor binding protein 4E-BP1 encoded by EIF4EBP1 on chr8.
Integrated multi-omics profiling uncovered that 4E-BP1 orchestrates a pro-proliferative proteomic network. Consistently, silencing of 4E-BP1 in the EwS model reduced cell proliferation, clonogenicity, spheroidal growth in vitro, and tumorigenesis in vivo. Drug screens and functional assays revealed that high 4E-BP1 expression sensitizes for pharmacological CDK4/6-inhibition in preclinical models

overall_design: We transduced EwS cell lines with a lentivirus containing a vector-system (pLKO Tet-on) with doxycycline (Dox)-inducible shRNAs, specifically directed against EIF4EBP1 or a non-targeting control shRNA (shCtr)

first: Cornelius

middle: M

last: Funk

first: Anna

middle: C

last: Ehlers

first: Felina

last: Zahnow

first: Julian

last: Musa

middle: G

last: Grünewald


title: CircESR1 and HNRNPAB function in estrogen receptor positive (ER+) breast cancer [RNA-Seq]

city: Hefei

first: Xu

last: Junchao

state: Anhui

address: No. 443, Mount Huangshan Road, Daoxiangcun Street

institute: University of Science and Technology of China

summary: Breast cancer (BC) is the most prevailing type of cancer among women in the world. ERα protein, which is transcribed and translated by estrogen receptor gene ESR1, is one of the marker molecules for clinical classification of BC. However, whether circRNAs specifically expressed in hormone receptor-positive BC play a role which is independent of ERα (estrogen receptor alpha) protein activity and signaling pathways is unknown. Whether these circRNAs could impinge on the sensitivity of ER+ BC cells to the endocrine therapy and targeted drug therapy is also unexplored.By screening circRNAs involved in estrogen receptor (ER) signaling, circESR1 was identified as a circRNA exhibiting high specificity of expression in ER+ breast cancer. Our studies elucidate a novel signaling complex centering around circESR1 and HNRNPAB in ER+ breast cancer and suggest that circESR1 might represent a potential therapeutic target for this disease.

overall_design: Unbiased transcriptome sequencing (bulk RNA-seq) was performed to have identified differentially expressed genes (DEGs) due to circESR1 or HNRNPAB depletion in MCF-7 cells. In details, MCF-7 cells were infected circESR1 or HNRNPAB shRNAs with lentivirus. Then the RNA was isolated. Total RNA sample was extracted and quantified with OD 260/280 ratio > 1.8 and OD 230/260 ratio > 2 were sent to BGI Genomics (Shenzhen, China) for sequencing.

first: Junchao

last: Xu

first: Tao

last: Zhu


title: HNRNPAB interacted with mRNAs in estrogen receptor positive (ER+) breast cancer [RIP-Seq]

summary: Breast cancer (BC) is the most prevailing type of cancer among women in the world. HNRNPAB belongs to heterogeneous nuclear ribonucleoproteins (hnRNPs) subfamily.In recent years, studies have found that HNRNPAB can be involved in the progression of various human cancers. It not only combines with DNA and RNA, but also mediates mRNA nuclear transport, regulates gene transcription and translation, and regulates the proliferation, migration, invasion, aging, and other phenotypes of tumor cells. HNRNPAB is closely related to the poor prognosis of cancer patients. In addition, HNRNPAB is also involved in regulating the infection process of influenza virus. It has been simply reported that the relevance of HNRNPAB as a prognostic value in BC.

overall_design: RIP assay was performed by using anti-HNRNPAB antibody (ab199724, Abcam, Cambridge, UK) and according to the manufacturer’s protocol of the EZ-Magna RIP™ Kit (17-701, Millipore, Darmstadt, Germany). Finally, RNA was purified after proteinase K digestion and extracted using TRIzol reagent (GK20008, GlpBio, California, USA). Then we sent the RIP experiment's input group and the anti-HNRNPAB antibody enrichment group to Aksomics (KangChen Bio-tech, Shanghai, China) for RIP-seq.


title: Chromosome 8 gain drives cancer progression by hijacking the translation factor 4E-BP1 sensitizing for targeted CDK4/6 inhibition


title: Let-7b-5p loaded Mesenchymal Stromal Cell Extracellular Vesicles reduce Pseudomonas-biofilm formation and inflammation in CF Bronchial Epithelial Cells

status: Public on Jun 16 2025

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary: Chronic Pseudomas aeruginosa infection in the lung is a common in people with cystic fibrosis (CF). Current therapies for CF fail to eliminate persistent bacterial infections, chronic inflammation, or irreversible lung damage. Our group engineered mesenchymal stromal cell (MSC)-derived extracellular vesicles (EVs) to carry the microRNA let-7b-5p as a dual anti-infective and anti-inflammatory treatment. In a preclinical CF mice model, we found that let-7b-5p-loaded MSC EVs reduced P. aeruginosa burden, immune cells and proinflammatory cytokines in the lungs. This research hypothesized two mechanisms of the observed effects in the mouse model: anti-inflammatory properties of the let-7b-5p-loaded MSC EVs and inhibition of antibiotic-resistant P. aeruginosa biofilm formation in CF airways. Primary human broncial epithelial cells (pHBECs) were exposed to P. aeruginosa and treated with differet MSC EV conditions. The results demonstrated that MSC EVs engineered to contain let-7b-5p effectively blocked the formation of P. aeruginosa biofilms on pHBECs while also reducing P. aeruginosa-induced inflammation by CF-pHBECs.

overall_design: pHBECs from 3 different CF donors (22F, 32G, 29H) were cultured in a monolayer. P. aeruginosa was exposed to the apical side for 1 hour, after which the culture was given 1 of 4 different conditions for 5 hours: process control (PC), negative control (NC) MSC Evs, let-7b-5p-loaded MSC EVs, or  no EVs. Additionally, one sample from each donor was not exposed to P. aeruginosa or EVs (untreated, UT).

first: Lily

last: Taub

first: Bruce

last: Stanton

first: Barnaby

last: Roxanna


title: Quiescent fibroblast-like synovial cells alleviate inflammatory bowel disease by modulating the gut immune microenvironment [dataset2]

status: Public on Jul 01 2025

city: Shijiazhuang

first: Jiayu

last: Zhang

address: No. 361 Zhongshan East Road

institute: Hebei Medical University

summary: To explore the potential of stem cellsfromhuman exfoliated deciduous teeth (SHED) for the treatment of inflammatory bowel disease (IBD) by addressing their in vivo mechanisms.

overall_design: scRNA-seq of CD45+ immune cells extracted from mouse colon with different treatment.


title: Knockout of all nematode-specific NSPC genes expressed exclusively in excretory gland cell results in transcriptomic signatures indicating affected insulin signaling

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: The nematode Caenorhabditis elegans is one of the best-studied model organisms in molecular biology; however, many aspects of its physiology and the functions of many genes remain poorly understood. In this study, we investigated the role of nematode-specific NSPC proteins, recently identified as primary targets of poly(A) polymerase TENT-5. Surprisingly, we found that NSPCs are exclusively expressed in the excretory gland cell, a cell with still unclear functionality. Using an optogenetic approach, we precisely ablated the excretory gland cell and observed that nematodes exhibited no transcriptomic or physiological changes in its absence. Additionally, we generated and thoroughly studied a strain with deletion of all 18 NSPC genes, which revealed that, despite previous indications, NSPCs lack antimicrobial activity. Instead, the transcriptomic analysis showed that the absence of NSPCs strongly impacts DAF-2/DAF-16 insulin signaling, suggesting that NSPCs may function as neuropeptides influencing key C. elegans signaling pathways. Although further studies are required to elucidate the physiological effects of this regulation, our findings provide new insights into this unexplored part of nematode physiology.

overall_design: We implemented Illumina RNA sequencing to investigate differences in gene expression after ablation of the excreotry gland cell or deletion of nspc genes in C. elegans (either in CRISPR knockouts or RNAi silenced worms). Moreover, we checked the potential involvement of NSPCs in TENT-5 mediated polyadenylation by using Nanopore Direct RNA Sequencing .

first: Zuzanna

last: Mackiewicz

first: Vladyslava

last: Liudkovska


title: Hepatic Yap1 activates systemic catabolism and muscle loss during organ repair: evidence for a common mechanism with cancer cachexia

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 2730 S Moody Ave

department: CDCB

institute: OHSU

summary: Here, we report the gene expression changes that occur in the mouse liver and quadricep, 3 days following 70% partial hepatectomy (PHx) in mice.

overall_design: Using total RNA-sequencing, we analyzed livers and quadriceps from 5 adult C57BL6/J  male mice, 3days after 70% partial hepatectomy. Control animals received a sham surgery (laparotomy) with no partial hepatectomy. 3 sham control mice and 5 PHx mice were used for the RNA-Seq analysis.

first: Leonidas

last: Koniaris

first: Yanlin

last: Jiang

first: Tewfik

last: Hamidi


title: Endocardial primary cilia and blood flow regulate EndoMT during endocardial cushion development [Single Nuc-RNAseq_NCX]

city: New Haven

first: Kathryn

last: Berg

address: 333 Cedar St.

department: Genetics

institute: Yale University

summary: Blood flow is critical for heart valve formation, and cellular mechanosensors are essential to translate flow into transcriptional regulation of development.  Here, we identify a role for primary cilia in vivo in the spatial regulation of cushion formation, the first stage of valve development, by regionally controlling endothelial to mesenchymal transition (EndoMT) via modulation of Kruppel-like Factor 4 (Klf4). We find that high shear stress intracardiac regions decrease endocardial ciliation over cushion development, correlating with KLF4 downregulation and EndoMT progression. Mouse embryos constitutively lacking heart contractility do not upregulate KLF4 or undergo EndoMT. snRNA-seq revealed that Ncx1-/- embryos failed to transition to early-EndoMT and have reduced mesenchymal markers.

overall_design: Whole hearts of e9.5 mouse embryos (Ncx1+/+ (wildtype), Ncx1+/-, Ncx1-/-) were microdissected and flashfrozen. Five flashfrozen hearts of each genotype were pooled and prepared for single nuclei RNA-sequencing, 1 technical replicate per genotype.

first: Faith

last: Lundt

first: Joshua

last: Gorham

first: Jonathan

last: Seidman

first: Martina

last: Brueckner


title: Yap1 mediates a systemic catabolic resonse during liver growth and repair

summary: Here, we report the gene expression changes that occur in the mouse liver and quadriceps following the expression of the catalytically active form of Yap1 (Yap1S5A) in the liver. Yap1S5A was delivered to the liver by Adeno-Associated Virus (AAV).

overall_design: Using total RNA-sequencing, we analyzed livers and quadriceps from 4 adult C57BL6/J  male mice, 7 days after YAP1S5A hepatic expression


title: Genome reorganization and its functional impact during breast cancer progression [Micro-C]

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

summary: We used Micro-C to explore conformational changes in the cancer genome, using the MCF10 cell line as a model for breast cancer progression. We have generated 5kb-resolution maps in normal (MCF10A), pre-malignant (MCF10AT1), and metastatic (MCF10CA1a) breast cancer cell lines, and aim to identify differential enhancer-promoter interactions between the different stages of cancer progression that may contribute to oncogenesis.

overall_design: Micro-C in MCF10A, MCF10AT1, and MCF10CA1a cell lines (2 biological replicates per cell line, 4 technical replicates per biological rep). Micro-C was conducted by Cantata Bio.

middle: S

last: Metz Reed

first: Tom

last: Misteli

first: Andrew

last: Fritz

first: Haley

last: Greenyer

first: Seth

last: Frietze

first: Janet

last: Stein

first: Gary


title: Lactylation-driven NSUN2-mediated RNA m5C modification promotes perineural invasion in pancreatic cancer [mRNA-seq]

status: Public on Jun 15 2025

city: Guangzhou

first: Tianhao

last: Huang

state: Guangdong

address: No.106 Zhong Shan Er Road

institute: Southern Medical University

summary: Lactylation, a metabolic stress-induced modification, plays a pivotal role in regulating diverse biological processes. Its involvement in perineural invasion (PNI) of pancreatic ductal adenocarcinoma (PDAC), however, has not been clearly defined. Our study demonstrates that patients with severe PNI exhibit significantly elevated levels of global lactylation and lactate, correlating with poorer prognosis. We identified NSUN2, a methyltransferase, as a crucial mediator of lactylation-driven PNI. Inhibition of lactylation or NSUN2 markedly reduced the neural infiltration capabilities of tumor cells. Mechanistically, lactate accumulation leads to the lactylation of NSUN2 at lysine 692 (K692), subsequently inhibiting its ubiquitination and degradation. lactylation of NSUN2 mediated m5C modification on CDCP1 and STC11 mRNA, enhanced their mRNA stability. Consistently, analyses using a KPC mouse model demonstrated that the lactylation of NSUN2/CDCP1/STC11 axis enhanced PNI through m5C modification. Our findings reveal that lactylation-driven NSUN2-mediated RNA m5C modification plays a pivotal role in promoting PNI and suggest that targeting NSUN2 could offer a promising therapeutic strategy for PDAC.

overall_design: p1_nc, p1_lac, p1_sinc, p1_si

first: Shangyou

last: Zheng

first: Rufu

last: Chen

first: Xuebiao

last: Wei

first: Chonghui

last: Hu

first: Huimou

first: Honghui


title: Regulating white blood cell activity through the novel Universal Receptive System

city: New York

first: Maria

last: Vecherkovskaya

address: 101 Avenue of Americas 3rd floor

institute: Human Microbiology Institute

summary: Regulation of the leucocyte activity is critically important for a properly functioning immune response and the development of novel cell-based therapies. Our previous studies have demonstrated the existence of nucleic-acid-based receptors (Teazeled receptors, TezR), which govern the response of various cell types to a diverse array of environmental, factors.  Here, for the first time, we show that by modulating these TezR receptors, we can upregulate immune cell signaling, migration, endocytosis, and phagocytosis pathways in leukocytes.

overall_design: RNA-Seq profiling of human activated and non-activated human leucocytes

first: Victor

last: Tetz

first: Kristina

last: Kardava

first: Alireza

last: Khodadadi-Jamayran

first: Aristotelis

last: Tsirigos

first: George


title: Lactylation-driven NSUN2-mediated RNA m5C modification promotes perineural invasion in pancreatic cancer [RIP-seq]

overall_design: PANC1_lac_IP, PANC1_lac_Input, PANC1_nc_IP, PANC1_nc_Input.


title: Cellular and genetic mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas

city: La Jolla

first: Ceri

middle: J

last: Weber

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

summary: Limbs and vertebrae elongate by endochondral ossification, but local growth control is highly modular such that not all bones are the same length. Compared to limbs, which have a different evolutionary and developmental origin, far less is known about how individual vertebrae establish proportion. Using the jerboa and mouse tail skeleton, we find that cell number is a common driver of limb and vertebral proportion in both species. However, chondrocyte hypertrophy, which is a major driver proportion in all mammal limbs, is limited to the extreme disproportionate growth of jerboa mid-tail vertebrae. The genes associated with differential growth in the vertebral skeleton overlap significantly but not substantially with genes associated with limb proportion. Among shared candidates, loss of Natriuretic Peptide Receptor 3 in mice causes disproportionate elongation of the proximal and mid-tail vertebrae, in addition to the proximal limb. Our findings therefore reveal cellular and molecular processes tuning growth of individual vertebrae while also identifying natriuretic peptide signaling among genetic control mechanisms that shape the entire skeleton.

sample_organism:
Mus musculus
Jaculus jaculus

platform_organism:
Mus musculus
Jaculus jaculus

overall_design: RNA-seq comparison of pooled mouse and jerboa cranial growth cartilages from tail vertebrae 1 and 6 during rapid bone elongation at postnatal day 7 and postnatal day 16 respectively

first: Alexander

last: Weitzel

middle: Y

last: Liu

first: Erica

last: Gacasan

first: Susan

last: Chapman

first: Robert

middle: L

last: Sah

first: Kimberly

last: Cooper


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR

city: San Francisco

first: Raunak

last: Shrestha

department: Radiation Oncology

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [ATAC-seq]

summary: Comprehensively understanding the gene regulatory network that modulates the biology of the Androgen Receptor (AR) oncogene is a central goal of prostate cancer research. To study regulators of AR, we knock-in a split neon green fluorescent protein onto the AR in prostate cancer cells creating an endogenous AR reporter cell line. Using our endogenous AR reporter, we performed a genome-scale fluorescence-activated cell sorting based CRISPRi screen to comprehensively identify genes that modulate AR protein levels. We identify and validate known AR protein regulators including HOXB13, GATA2, GRHL2 as well as unexpected top hits including PTGES3, SAE1 and CSNK2A1. Loss of PTGES3 in multiple models of ARSI-resistant Pca resulted in loss of AR protein and thus AR’s oncogenic activity. Mechanistically, we demonstrate a novel nuclear co-factor function of PTGES3 facilitating AR-mediated transcription aside from its canonical co-chaperone function regulating AR protein levels. Lastly using a disulfide tethering chemical screen, we developed a PTGES3 inhibitor demonstrating PTGES3 is a therapeutically tractable target for the treatment of AR-addicted mCRPC.

overall_design: ATAC-seq was performed in PTGES3 knockdown in LNCaP prostate cancer cells

first: Haolong

last: Li

first: Meng

last: Zhang

first: David

last: Quigley

first: Luke

last: Gilbert

first: Felix

last: Feng


title: The Regulatory Logic of Planarian Stem Cell Differentiation [RNA-Seq]

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

country: United Kingdom

institute: University of Exeter

summary: Stem cell differentiation underlies development and regeneration in multicellular organisms. Cell type identity is determined by the expression of specific transcription factors (TFs) regulating target genes (TGs) via binding to open chromatin regions (OCRs). The regulatory logic of differentiation includes factors specific to one or multiple cell types, functioning in a combinatorial fashion. Single cell transcriptomics has emerged as a revolutionary approach to study gene expression with cell type resolution, but integrating it with single cell analysis techniques to study chromatin remains challenging. Planarians, with their pluripotent neoblast stem cells continuously giving rise to all cell types, offer an ideal model to attempt this integration. Despite extensive single cell transcriptomic studies, the transcriptional and chromatin regulation at the cell type level remains unexplored. Here, we investigate the regulatory logic of planarian stem cell differentiation by obtaining an organism-level integration of single cell transcriptomics and single cell ATAC-seq. We identify specific open chromatin profiles for major differentiated cell types and analyse their transcriptomic landscape, revealing distinct gene modules expressed in individual types and combinations of them. Integrated analysis unveils gene networks reflecting known TF interactions in each type and identifies TFs potentially driving differentiation across multiple cell types. To validate our predictions, we combined TF knockdown RNAi experiments with single cell transcriptomics. We focus on hnf4, a TF known to be expressed in gut phagocytes, and confirm its influence on other types, including parenchymal cells. Our results demonstrate high overlap between predicted targets and experimentally-validated differentially-regulated genes. Overall, our study integrates TFs, TGs and OCRs to reveal the regulatory logic of planarian stem cell differentiation, showcasing the potential of single cell methods for characterising differentiation trajectories and their regulation.

overall_design: Knockdown treatment consisted in injecting worms with 0.1 μg of either of the following combinations: (i) gfp ; (ii) hnf4 + gfp ;  (iii) hnf4 ; (iv) hnf4+nkx2-2 ; (v) hnf4+foxF-1. dsRNA was injected for 3 consecutive days.

first: Alberto

last: Perez-Posada

first: Helen

middle: H

last: Garcia-Castro

first: Elena

middle: E

last: Emili

first: Virginia

middle: V

last: Vanni

first: Cirenia

last: Arias-Baldrich

first: Siebren

last: Frolich

first: Simon

last: Van Heeringen

first: Nathan

middle: N

last: Kenny


title: The Regulatory Logic of Planarian Stem Cell Differentiation [scRNAseq]

overall_design: Four SPLiT-Seq RNA-Seq libraries of ACME-dissociated whole Schmidtea mediterranea animals in unperturbed conditions and two SPLiT-Seq RNA-Seq libraries of ACME-dissociated whole S. mediterranea animals in gfpi and hnf4i knock-down conditions.

middle: A


title: Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [mRNA-seq]

overall_design: mRNA-seq was performed in PTGES3 knockdown, with GAL4 knockdown as control in LnCaP prostate cancer cells


title: The Regulatory Logic of Planarian Stem Cell Differentiation [scATAC-Seq]

overall_design: One 10X scATAC-Seq library of trypsin-dissociated, whole S. mediterranea animals in unperturbed conditions.


title: The Regulatory Logic of Planarian Stem Cell Differentiation


title: Metastatic site influences driver gene function in pancreatic cancer [[InVitro ATAC-Seq]]

status: Public on Jun 12 2025

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells’ epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4’s tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To determine whether organ-biased differences in chromatin accessibility were maintained in vitro, we performed ATAC-seq on the Smad4-OFF primary tumor-derived cell lines used to generate liver and lung metastases, as well as on matched cell lines derived from the respective metastatic sites.

first: Kaloyan

last: Tsanov

first: Scott

middle: W

last: Lowe


title: To identify differentially expressed genes in ventricular tissue between wildtype control and the 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish at six months.

city: Baltimore

first: Yuji

address: 660 W. Redwood Street

institute: University of Maryland

summary: To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types, we performed whole transcriptome RNA-sequencing experiments using ventricular tissue isolated from 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish,and corresponding WT siblings.

overall_design: Total RNA was extracted from dissected ventricular tissue of 6-month-oldmtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic and corresponding  WT siblings.

first: Yonghe

last: Ding

first: Xiaolei

last: Xu


title: Endocardial primary cilia and blood flow regulate EndoMT during endocardial cushion development [Single Nuc-RNAseq_IFT]

first: Kathryn

last: Berg

summary: Blood flow is critical for heart valve formation, and cellular mechanosensors are essential to translate flow into transcriptional regulation of development.  Here, we identify a role for primary cilia in vivo in the spatial regulation of cushion formation, the first stage of valve development, by regionally controlling endothelial to mesenchymal transition (EndoMT) via modulation of Kruppel-like Factor 4 (Klf4). We find that high shear stress intracardiac regions decrease endocardial ciliation over cushion development, correlating with KLF4 downregulation and EndoMT progression. Mouse embryos constitutively lacking cilia exhibit a blood-flow dependent accumulation of KLF4 in these regions, independent of upstream left-right abnormalities, resulting in impaired cushion cellularization. snRNA-seq revealed that cilia KO endocardium fails to progress to late-EndoMT, retains endothelial markers and has reduced EndoMT/mesenchymal genes that KLF4 antagonizes. Together, these data identify a mechanosensory role for endocardial primary cilia in cushion development through regional regulation of KLF4.

overall_design: Whole hearts of e9.5 mouse embryos (Ift20+/+ (wildtype), Ift20+/-, Ift20-/-) were microdissected and flashfrozen. Five flashfrozen hearts of each genotype were pooled and prepared for single nuclei RNA-sequencing. Ift20+/+ had 3 replicates of this process; Ift20+/- and Ift20-/- had 2.

first: Faith

last: Lundt

first: Joshua

last: Gorham

first: Jonathan

last: Seidman

first: Martina

last: Brueckner


title: Metastatic site influences driver gene function in pancreatic cancer [InVitro RNA-Seq]

overall_design: SMAD4 acts as a transcription factor (TF) by forming a complex with the SMAD2/3 TFs to activate gene expression programs downstream of TGFβ receptors. Hence, we performed RNA-seq of the input cells in vitro after Smad4 restoration and TGFb treatment (see Methods), and compared the resulting pathway enrichment to our in vivo data from the pancreas, liver and lungs.


title: A noncanonical Pol III-dependent, Microprocessor-independent biogenesis pathway generates a germline enriched miRNA family

first: Katherine

last: McJunkin

state: Maryland

address: 50 South Dr

institute: NIDDK/ NIH

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression. In canonical miRNA biogenesis, primary miRNAs are transcribed from intergenic loci or intronic regions by RNA polymerase II, sequentially cleaved by the Microprocessor complex and Dicer, and resulting mature miRNAs are loaded into Argonaute to repress target mRNAs. A minority of miRNAs are generated via noncanonical biogenesis pathways that bypass the Microprocessor and/or Dicer. Here, we describe a new Pol III-dependent, Microprocessor -independent, and Dicer-dependent biogenesis pathway exemplified by the mir-1829 family in C. elegans. Although the mir-1829 family loci reside in intronic regions of protein-coding genes, we show that the miRNAs are derived from independent Pol III transcripts. Unlike other Pol III-dependent miRNAs, the mir-1829 family small RNAs are the dominant species derived from their loci, rather than fragments of a larger functional noncoding RNA. These germline-enriched miRNAs are loaded in multiple miRNA Argonautes, including the recently-characterized germline Argonaute ALG-5, which we demonstrate is repressive when tethered to a reporter transcript. We extend these findings, identifying additional Pol III-transcribed and noncanonical small RNAs in C. elegans and human datasets, including human miR-4521. These young, noncanonical miRNAs may represent an early snapshot in the evolution of de novo miRNA genes.

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: To determine the requirement of Dicer and RPC-1 in mir-1829 biogenesis as well as other miRNAs that may follow this novel biogenesis pathway (i.e. Pol III-transcribed, Microprocessor-independent, Dicer-dependent) in C. elegans and human. To determine which miRNAs are enriched in the germline by depleting Dicer solely in the germline in C. elegans.

first: Rima

last: Sakhawala

first: Reyhaneh

last: Tirgar

first: Karl-Frédéric

last: Vieux

first: Guoyun

last: Yu

first: Dustin

last: Haskell

first: Anna

last: Zinovyeva


title: The Regulatory Logic of Planarian Stem Cell Differentiation [ATAC-Seq]

first: Jordi

last: Solana

overall_design: One ATAC-Seq library of whole S. mediterranea animals in unperturbed conditions.

first: Alberto

last: Perez-Posada

first: Helen

last: Garcia-Castro

first: Elena

last: Emili

first: Virginia

last: Vanni

first: Cirenia

last: Arias-Baldrich

first: Siebren

last: Frolich

first: Simon

last: Van Heeringen

first: Nathan

last: Kenny


title: The ferret bleomycin-induced model of lung fibrosis shares features of human idiopathic pulmonary fibrosis

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

summary: In the present study, we report a bleomycin-induced ferret PF model characterized by an irreversible decrease in pulmonary compliance and increase of opacification, accompanied by “honeycomb cyst-like” structures, “proximalization” of distal lung epithelium. Cellular and molecular analysis by single-nucleus RNA sequencing analysis revealed a significant shift in distal lung epithelium towards proximal epithelial phenotype. Importantly, a histopathological pattern of bronchiolization encompassing divergent atypical epithelial cells, and KRT17+/TP63+/KRT5low “basaloid-like” cells, were present in the distal fibrotic lung lesions. Trajectory analysis revealed AT2 cells transition through multiple cell-states in bleomycin injured ferret lungs, particularly AT2 to KRT8high/KRT7low/SOX4+ to eventual KRT8high/KRT7high/SFN+/TP63+/KRT5low “basaloid-like” cells. Further, immunofluorescence analyses demonstrated KRT7 and KRT8 populations reside in close proximity to the ACTA2 positive myofibroblasts in fibrotic foci thereby driving fibrogenic phenotype in bleomycin injured ferret lungs. Collectively, our results provide evidence that the bleomycin ferrets can reproduce pathophysiological, cellular, and molecular features of human IPF disease, suggesting that they may be a reliable model for understanding mechanisms of IPF pathogenesis and for testing therapeutic strategies for treatment of IPF.

overall_design: Multiple (3x) low doses (2.5U/kg) of bleomycin were delivered to the lung of ferrets to induce a more rapidly progressive and irreversible pulmonary fibrosis. Lung structure/function studies (Pulmonary function tests and CT), cellular phenotyping by single nucleus RNA sequencing (snRNA-seq), and histopathologic cellular phenotyping were utilized to demonstrate the progressive and irreversible features of IPF that lead to honeycomb cysts and bronchiolization of the distal airspaces.

first: Engelhardt

last: John

first: Liu

last: Xiaoming

first: Shuang

last: Wu

first: Miyazaki

last: Hikaru

first: Shambhu

last: Smitha

first: Driver

last: Ian

first: Sontake

last: Vishwaraj


title: Single nuclei transcriptomic and bulk RNA-seq of Populus tremula x alba stem under well-watering and severe drought conditions

status: Public on Jun 10 2025

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

country: Spain

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

summary: We have employed snRNA-seq using Singleron technology to dissect the molecular mechanisms controlling secondary xylem plasticity, which allows poplar trees to cope with severe drought. We generated four snRNA-seq libraries using mature stem sections, two per treatment. In this study, we present new molecular drivers of wood plasticity under drought, which allow trees to generate secondary xylem with more and narrower vessels. This trait confers a better adaptation under this abiotic stress. We also performed bulk RNA-seq under the same conditions to evaluate the accuracy of snRNA-seq in our analyses.

overall_design: For the severe drought treatments, in vitro-cultivated hybrid poplars of WT, were transferred to pots containing peat, and grown under LD and 22°C conditions for 6 weeks. Six weeks after potting, the plants were divided into two groups: control and severe drought treatment. Irrigation was carefully controlled during the two weeks of treatment. Control plants were well-watered, keeping the solid moisture around Field Capacity (FC) (0.46 m3/m3) during the treatment. The weight of each pot was calculated at the FC before treatments. Severe drought treatment was achieved by stopping irrigation until the soil reached 15 % of its FC. The wilting threshold was reached when soil moisture decreased to 0.10 m3/m3. Then, a small amount of water was added per pot daily to keep the 15 % of FC by weighing the pots daily during 14 days. Nuclei isolation was performed from the internodes 14 and 15 from one plant, for each library, and snRNA-seq libraries were generated following the Singleron protocol. Bulk RNA-seq was extracted from trees under control and severe drought conditions from the stem. 3 biological replicates were generated per treatment.

first: Daniela

last: Gómez-Soto

first: Wendell

last: Pereira

first: Alejandro

last: Piedrabuena-Díaz

first: Christopher

last: Dervinis

first: Matias

last: Kirst

first: Isabel

last: Allona

first: Mariano

last: Perales


title: Role of DDX3X in translation regulation in acute ER stress [mouse]

status: Public on Jun 09 2025

city: Baton Rouge

first: Anastasios

middle: A.

last: Vourekas

state: LA

address: 202 life sciences building

institute: Louisiana State University

summary: In eukaryotes, regulation of mRNA translation initiation greatly impacts gene expression, and is critical for cellular stress responses. DDX3X is a ubiquitous DEAD-box RNA helicase whose precise role in 5´ UTR scanning and start codon decoding in non-stressed and stressed cells is still elusive. Here we show that DDX3X engages with thousands of mRNAs as part of the 48S scanning complex, simultaneously acting to promote or suppress translation of select mRNAs in non-stressed conditions, and switches this regulation in opposite directions to establish a stress response translational program upon acute ER stress. We find distinct DDX3X binding patterns of differentially regulated mRNAs, which lead us to identify N4-acetylation of cytidines surrounding the start codon as a crucial feature for DDX3X-mediated selective regulation. Our findings highlight a novel co-dependence between an RNA helicase and a post-transcriptional modification in regulating mRNA translation

overall_design: Mouse Embryonic Fibroblasts were grown to ~80% confluency and treated with control (DMSO) or Thapsigargin (400 nM) containing full medium for 1 h to induce acute ER stress. The cells where then collected by trypsinization and kept in ice-cold HBSS during UV crosslinking (254 nm, 3x400 mJ/cm2). To ensure that the procedure is not inducing stress in the control cells, we checked levels of eIF2α-P and ATF4 by western blot, and performed DDX3X immunofluorescence to observe possible induction of stress granules. For the IP step our own custom rabbit polyclonal DDX3X antibody was used. The rest of the CLIP-Seq procedure was performed as previously described (Vourekas and Mourelatos, 2014).

first: Abd-El-Monsif

last: Shawky

first: Allison

last: Scarboro

first: Kenneth

last: Avanzino

first: Constantine

last: Simintiras

first: Maria

last: Hatzoglou


title: Role of DDX3X in translation regulation in acute ER stress

overall_design:
We prepared 10%-50% sucrose gradients in polyallomer tubes for SW-41 rotor using the Gradient Master 108, and collected the polysome profiles using the Piston Fractionator with a TRIAX Flowcell (260 nm) (BioComp). 293FT cells were seeded in 100-mm culture dishes (3 dishes per polysome profile sample) and grown to 80% confluency. 1.5 h prior to collection, cell culture media was replaced with full media containing DMSO (non-stressed condition) or 400 nM Thapsigargin (acute ER stress). Cells were incubated for the last 5 min of the treatment with cycloheximide (CHX) at a final concentration of 100 μg/mL. Cells were then washed twice with ice cold phosphate-buffered saline supplemented with CHX and centrifuged at 4,500 X g for 5 min at 4° C. Cell pellets were lysed in 800 μL of Hypotonic buffer (5 mM Tris HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 0.5% Triton X, 0.5% sodium deoxycholate, 100 μg/mL CHX, 2 mM DTT, 200 units/mL RNase inhibitor, 1X protease inhibitor cocktail). Cells were resuspended in the hypotonic buffer either by pipetting or vortexing for 5 sec followed by centrifugation at 17,000 xg for 7 min at 4° C. The supernatant (post-nuclear lysate) OD was measured at 260 nm to determine the amount of lysate needed to be added to sucrose gradient. Samples of the post-nuclear lysates were also kept for western blots and input RNA extraction 500 mL from the top of the sucrose gradient was removed and the lysate volume per condition was adjusted so they contain the same OD between 10 to 20 at 260 nm and added to the top of the sucrose gradient. Each gradient was weighed and balanced before ultracentrifugation at 222,222 xg for 2 hours at 4° C while using low brake option. 14 fractions of 800 μL were collected.
Immediately after polysome fractions were collected, 400 μL of each fraction was mixed with equal volume TRIZOL LS (Thermo) and kept at -80C. RNA extraction was carried out by manufacturer’s instructions. RNA was treated with RQ1 DNase (Promega), followed by phenol extraction and ethanol precipitation. The concentration and the purity of RNA was measured using nanodrop and pure RNA with a 260/280 ratio within 1.8 - 2.0 was acquired. To prepare polyA mRNA RNA-Seq libraries, approximately 800 ng of high-quality total RNA was used per sample. The quality was determined with a Nanodrop spectrophotometer, and only RNA that had a OD260/280 of 1.8-2.0 was used. We followed the Illumina Stranded mRNA Prep, Ligation Reference Guide, Document # 1000000124518 V03 protocol without changes.


title: Fetal liver macrophage development and function require Xpr1

city: Zurich

first: Sebastian

last: Stifter

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

summary: Erythroblastic island macrophages (EBI-Macs) support the development of red blood cells by recycling iron, producing growth factors,and clearing nuclei expelled from erythroblasts. In the developing embryo, the liver is the primary site of hematopoiesis,andfetal liver macrophagesperform the function ofEBI-Macs.Here, weshowthatthephosphate exporterXpr1is critical for the development offetal macrophagesin the liver and the spleen.Single-cellRNA-seqand flow cytometryanalysesin conditional mice lackingXpr1in hematopoietic and/orCD206+cellsrevealedloss of the Kupffercelltranscriptional program anda shift in the development offetal livermonocytes towards an interferon-activated monocyte/macrophage state.Functionally, thisled tothefailure to clear pyrenocytes.In adulthood,splenic red pulp and bone marrow macrophages were alsoabsent upon lossof intrinsicXpr1.Collectively,these findings reveal thatXpr1is required for the development, identity, and function ofEBI-Macs.

overall_design: E15.5 embryonic livers were dissociated and cells isolated. Three Xpr1fl/fl and three Vav1iCre Xpr1fl/fl were pooled and CD45+CD19-CD3-B220-Ter119-CD49b-CD90.2- cells sorted from each pooled sample and subjected to scRNA-seq.

first: Melanie

last: Greter


title: Role of DDX3X in translation regulation in acute ER stress [human]

overall_design: HEK293FT were grown to ~80% confluency and treated with control (DMSO) or Thapsigargin (400 nM) containing full medium to induce acute ER stress. The cells where then collected by trypsinization and kept in ice-cold HBSS during UV crosslinking (254 nm, 3x400 mJ/cm2). To ensure that the procedure is not inducing stress in the control cells, we checked levels of eIF2α-P and ATF4 by western blot, and performed DDX3X immunofluorescence to observe possible induction of stress granules (Figure S1). For the IP step our own custom rabbit polyclonal DDX3X antibody was used. The rest of the CLIP-Seq procedure was performed as previously described (Vourekas and Mourelatos, 2014).


title: Fetal liver macrophage development and function require Xpr1 [RNA-Seq]

summary: Erythroblastic island macrophages (EBI-Macs) support the development of red blood cellsby recycling iron, producing growth factors,and clearing nuclei expelled from erythroblasts. In the developing embryo, the liver is the primary site of hematopoiesis,andfetal liver macrophagesperform the function ofEBI-Macs.Here, weshowthatthephosphate exporterXpr1is critical for the development offetal macrophagesin the liver and the spleen.Single-cellRNA-seqand flow cytometryanalysesin conditional mice lackingXpr1in hematopoietic and/orCD206+cellsrevealedloss of the Kupffercelltranscriptional program anda shift in the development offetal livermonocytes towards an interferon-activated monocyte/macrophage state.Functionally, thisled tothefailure to clear pyrenocytes.In adulthood,splenic red pulp and bone marrow macrophages were alsoabsent upon lossof intrinsicXpr1.Collectively,these findings reveal thatXpr1is required for the development, identity, and function ofEBI-Macs.

overall_design: CD45+ F4/80hi CD11blow fetal liver macrophages were sorted from E15.5 Xpr1fl/fl and Mrc1Cre Xpr1fl/fl embryonic livers. Gene expression analysis was performed on four Xpr1fl/fl and five Mrc1Cre Xpr1fl/fl samples


title: We want to check chromotin conformation changes and chromotin accesiblility. We also want to compare gene profile with and without indusilam resistant tumors in mouse genetic model

status: Public on Jun 05 2025

city: Memphis

first: Xiang

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St.Jude Children's Research Hospital

summary: the transcriptomic and epigenetic map of ADRN and MES types of neuroblastomas using murine models treated with indisulam, a selective RBM39 degrade.

overall_design: The TH-MYCN/ALKF1178L mice were treated with vehicle or 25mg/kg of indisulam for 3  weeks in our study. The tumor samples were harvested and processed through 10X Single Cell MultiOME ATAC+Gene expression kit.

first: Shivendra

last: Singh

first: Jie

last: Fang

first: Hongjian

last: Jin

first: Lee

last: Velde

first: Andrew

last: Cortes

first: Jiani

first: Sivaraman

last: Natarajan

first: Jun

last: Yang


title: Full transcriptome analysis of the mechanism of tuberculosis ESAT6-Fc2a in alleviating allergic asthma in mice

city: 银川市

first: 天松

last: 王

state: 宁夏回族自治区

address: 兴庆区大新镇胜利街1160号

institute: 宁夏医科大学

summary: In the early stage, an OVA-induced mouse allergic asthma model was constructed and treated with ESAT6-Fc2a fusion protein, which proved that ESAT6-Fc2a fusion protein could reduce the infiltration of inflammatory cells in the lungs and had a therapeutic effect on asthma. In order to further explore the mechanism of action, we carried out transcriptomics sequencing, screened out related genes, enriched them, and focused on pathways with significant differences. In the later stage, q-PCR experiments will be performed for verification.

overall_design: There were three groups in this experiment, namely the normal group, the model group, and the treatment group (ESAT6-Fc2a). In order to make the study statistically significant, three samples in each group were labeled with N, M and E in the transcriptome.

first: Jing

last: Wang

first: Qiaofeng

last: Wan


title: Overexpression of Mir-197 und Mir-769 in human iPSCs

status: Public on Jun 04 2025

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in many essential biological processes. Recently, targeted searches for human miRNA orthologs revealed that 15 miRNA families are lost in the Eumuroidea lineage, including the model organisms mouse and rat, but not in other mammals. We here characterize this loss in more detail and investigate potential consequences for the Eumuroidean regulatory network. We confirm that the miRNA loss was not compensated by other miRNAs in rat or mouse, and we identify a significant overlap in the function of their target genes. We heterologously express two human miRNAs, Mir-197 and Mir-769, in mouse inducible pluripotent stem cells (iPSCs) and compare effects on the transcriptome to those of induced miRNA levels in human iPSCs. This reveals overlapping sets of down-regulated mRNAs in the two species, likely representing remnants of an ancient miRNA-dependent regulatory network that predates the diversification of the human and mouse lineages.  The consequent elimination of established miRNA regulatory connections on the Eumuroidean lineage is accompanied by the lineage-specific loss of 37 transcription factors. Our results indicate that mouse and rat have modified their regulatory network of gene expression on transcriptional and post-transcriptional level compared to other vertebrate model organisms. This regulatory shift likely adds noise to studies of gene expression that, for example, use murine cells to study human diseases.

overall_design: Differential gene expression analysis upon overexpression for 48h of either miRNA Precursor hsa-miR-197-3p or miRNA Precursor hsa-miR-769-5p in human iPSCs compared to miRNA Precursor Negative Control

first: Felix

last: Langschied

first: Matthias

last: Leisegang

first: Fabian

last: Hahner

first: Ralf

middle: P

last: Brandes

first: Ingo

last: Ebersberger


title: Inactivation of the SRF cofactors Mrtfa and Mrtfb in MEFs results in proliferation defects and reduced expression of cytoskeletal and cell cycle progression genes

city: London

first: Richard

last: Treisman

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The MRTFs (Myocardin-related transcription factors) are cofactors of the SRF transcription factor, and together they control dozens of growth factor-responsive, cytoskeletal and muscle specific genes. We used a conditional knockout strategy to demonstrate that in fibroblasts, inactivation of both Mrtfa and Mrtfb, or Srf, induces a severe defect in proliferation. This state exhibits features of both quiescence and senescence, with MRTF-null cells upregulating similar cell cycle regulators to serum-deprived wildtype cells, but is fully reversible by MRTF re-expression. We analysed gene expression in three MEF pools derived from Wildtype (Rosa26Tam-Cre) animals, and three MEF pools derived from Mrtfa-/-;Mrtfbfl/fl;Rosa26Tam-Cre mice. RNA was collected 0, 2, 4 or 12 days after 4-hydroxytamoxifen treatment, which inactivate Mrtfb in Mrtfa-/-;Mrtfbfl/fl;Rosa26Tam-Cre and generate MRTF-null cells. The data indicate that substantial numbers of genes exhibit altered expression in Mrtfa-/-;Mrtfb-/- cells, the difference being most pronouced 12 days following 4-OHT treatment. Genes downregulated at this point include many genes identified as serum-inducible MRTF-SRF target cells in NIH3T3 cells (Esnault et al, 2014, DOI: 10.1101/gad.239327.114) or as derepressed in MEFs following inactivation of all members of the TCF family of SRF cofactors (Gualdrini et al, 2016, DOI: 10.1016/j.molcel.2016.10.016). They are most enriched in GO categories related to actin cytoskeletal dynamics and cell signalling, and GSEA hallmarks connected with cell growth, division, and cell cycle.

overall_design: mRNA library was prepared using polyA_KAPA_mRNA_Hyper_Prep of 24 samples consisting of three biological replicates of WT MEFs (Rosa26Tam-Cre) and three biological replicates of MRTF-floxed MEFs (Mrtfa-/-;Mrtfbfl/fl;Rosa26Tam-Cre) each treated with 1µM 4-hydroxytamoxifen for 2 days before switching back to regular medium. RNA was collected 0, 2, 4, and 12 days after tamoxifen treatment.

first: Julie

last: Nielsen


title: Microbial Product Cocktails for Personalized Cancer Immunotherapy

status: Public on Jun 03 2025

city: University Park

first: Pak kin

last: Wong

state: State College

address: 513 Chemical and Biomedical Engineering Building

institute: the Pennsylvania State university

summary: Microbial product cocktails induce a cytokine secretion profile in bladder cancer.

overall_design: The cytokine secretion profiles of three human bladder tumor samples (PPS 1–3), treated with or without microbial product cocktails, were compared using the RayBiotech Q1200 Array for Human Microbial Product-Induced Cytokine Detection.

first: Yue

last: Yan

first: Hawhan

last: Yen

first: Mike

last: Mao


title: GATA Transcription Factors Coordinate Developmental Progression in the Arabidopsis Root

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

summary: For proper organ development, cell proliferation and cellular differentiation must balance in a tightly regulated spatiotemporal manner. Here, we show that a phased gene expression profile from meristematic cells at the Arabidopsis root niche, to differentiating cortex- and endodermis cells, is defined by the action of distinct transcription factor (TF) families. We show that while chromatin accessibility serves as a strong predictor of the activation of developmental genes, a key expression ‘switch’ from dividing- to elongating/differentiating cells is underpinned by a considerable level of chromatin rearrangement. Within this structure, a GATA TF subfamily is proposed to sit at the heart of a mutually antagonistic regulatory module, acting to promote differentiation and feedback on cell proliferation through the regulation of both lineage specific differentiation processes and general maturation programs. Key to this is integration of the auxin- and cytokinin responsive PLT- and ARR-B TF families. This model provides a level of coordination in the regulation of meristem size and the timing of differentiation, at both the tissue- and organ levels.

overall_design:
Roots of six day old seedlings or A. thaliana Col-0 were cut 0.5 - 0.7 cm from their tip and a total of 180 mg of root tissue was collected. Single cell ATAC-seq libraries were produced from freshly isolated nuclei in accordance with the 10X Genomics Chromium Single Cell ATAC-seq kit protocol (v 1.1 protocol, Rev D).
Bulk RNA-seq samples are added.
Two previously published (Denyer et al., 2019) datasets (Series GSE123818; samples GSM3511858 and GSM3511859) were reanalyzed to improve atlas quality. Reads from two replicates were processed with Cell Ranger (v7.1.0; 10X Genomics) using the TAIR10 reference genome and TAIR10.55 genome annotation. Downstream processing was done with the Seurat R package (v5.1.0; Hao et al., 2024). Cells with fewer than 500-, or more than 100,000 UMIs, were removed from subsequent analysis, as were genes detected in fewer than five cells. Further, cells containing more than 5 % reads mapped to mitochondrial genes were removed. Count matrices were normalized with the ?SCTransform? function, and replicates integrated following Seurat?s integration pipeline using the canonical correlation analysis (CCA) method and 50 principal components. Genes previously identified as induced by the protoplasting procedure (Denyer et al., 2019) were excluded from the integration procedure. UMAP visualizations were generated using integrated dimensionality reduction and cell clusters identified with the resolution of 0.5. Clusters were annotated using tissue specific marker genes as previously described (Denyer et al., 2019).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Tom

last: Denyer

first: Pavel

last: Solansky

first: Francesco

last: de Martino

first: Efthymia

last: Symeonidi

first: Arvid

last: Herrmann

first: Valentin

last: Brösamle


title: Inhibition of de novo fatty acid synthesis in Mycobacterium tuberculosis

status: Public on Jun 02 2025

city: Ithaca

first: Emma

last: Roszkowski

state: NY

address: 930 Campus Rd

institute: Cornell University

summary: De novo fatty acid synthesis produces the acyl units needed to generate phospholipids, lipoproteins, enzyme prosthetic factors, polyketides, and mycolic acids in Mycobacterium tuberculosis (Mtb). Here, we identifed sALT629, a novel butoxyphenyl-tetrazole-acetamide compound that inhibits de novo lipid synthesis in Mtb. This compound disrupts the Mtb lipidome and prevents incorporation of metabolic tracers into acyl chains of Mtb lipids. Unexpectedly, we also found that sALT629 treatment significantly depleted triacylglycerol (TAG) pools as a metabolic compensation mechanism when de novo fatty acid synthesis was inhibited. Resistance to sALT629 was mediated by loss of function mutations in HadC, the non-essential hydroxyacyl-ACP-dehydratase subunit involved in the synthesis of long-chain oxygenated mycolic acids. Inactivating HadC rescued sALT629-mediated inhibition by sustaining TAG pools to fulfill Mtb’s biosynthetic demand for acyl chains. Lastly, loss of function HadC resistance mutations resulted in cell wall perturbations that confer fitness defects in vitro and in vivo suggesting that this specific resistance mechanism is unlikely to arise in Mtb in a clinical setting.

overall_design: RNA-seq of WT Mtb treated with different antitubercular compounds (sALT629, INH, and ISO) for 4 hours in standard rich medium.

middle: K

first: Sarita

last: Charap

first: Christine

middle: R

last: Montague

first: Paridhi

last: Sukheja

first: Case

last: McNamara

first: Paul

last: Soma

first: M

last: Islam

first: Barbara

last: Graham

first: Anna

last: Grzegorzewicz

first: Mary

last: Jackson

first: Peter

last: Schultz

first: Anthony

last: Hay

first: David

last: Russell

first: John

middle: T

last: Belisle

first: Brian

last: VanderVen