title: Mechanical stretch induces senescence of alveolar epithelial cells and drives fibroblast activation by paracrine mechanisms III

city: Oviedo

first: Guillermo

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Severe lung injury requiring mechanical ventilation may lead to secondary fibrosis. Senescence, a cell response characterized by cell cycle arrest and a shift towards a proinflammatory/profibrotic phenotype, is one of the mechanisms involved in lung fibrosis. Here, we explore the contribution of mechanical stretch to senescence of the alveolar epithelium and its link with fibrosis. Human alveolar cells and fibroblasts were exposed in vitro to mechanical stretch, and senescence assessed. In addition, fibroblasts were exposed to culture media preconditioned by senescent epithelial cells and their activation was studied. Transcriptomic profiles from stretched, senescent epithelial cells and activated fibroblasts were combined to identify potential activated pathways. Finally, the senolytic effects of digoxin were tested in these models. Mechanical stretch induced senescence in alveolar epithelial cells, but not in fibroblasts. This stretch-induced senescence has specific features compared to senescence induced by doxorubicin. Fibroblasts were activated after exposure to supernatants conditioned by epithelial senescent cells. Transcriptomic analyses revealed notch signaling as a potential responsible for the epithelial-mesenchymal crosstalk, as fibroblast activation was inhibited by treatment with an inhibitor of g-secretase. Treatment with digoxin reduced the percentage of senescent cells after stretch and ameliorated the fibroblast response to preconditioned media. These results suggest that lung fibrosis in response to mechanical stretch may be caused by the paracrine effects of senescent alveolar cells. This pathogenetic mechanism can be pharmacologically manipulated to improve lung repair.

overall_design: MRC5 were exposed to culture media preconditioned by stretched and non-stretched A549. After 6 hours, cells were recovered, lysated and RNA was collected for RNAseq analysis.

first: Paula

last: Martín-Vicente


title: Mechanical stretch induces senescence of alveolar epithelial cells and drives fibroblast activation by paracrine mechanisms II

status: Public on Mar 25 2025

middle: M

type: Expression profiling by high throughput sequencing

overall_design: Two experimental groups were established. In the first condition  A549 were subjected to cyclic stretch (15% elongation, 15 cycles/min) for 24 hours, whereas in the other condition , A549 were treated with doxorubicin (100nM) for 24 hours.  Then, β-galactosidase (Bgal) staining was assessed after 6 days for stretched A549 and A549 treated with doxorubicin. Eventually,  positive cells for Bgal were sorted,  lysated and RNA was collected for RNAseq analysis.

last: Vicente


title: miR-183-5p-enriched extracellular vesicles promote the crosstalk between hepatocellular carcinoma cell and endothelial cell via SIK1/PI3K/AKT and CCL20/CCR6 signaling pathways

city: Harbin

first: Ye

last: Han

state: Heilongjiang

address: No. 157, baojian Road

country: China

institute: The second Affiliated Hospital of Harbin Medical University

summary: Background: The cancer-related mortality of primary liver cancer ranks third globally, and hepatocellular carcinoma (HCC) is predominant, posing a serious threat to patients' health. Understanding HCC's pathogenesis and target molecules is crucial for early diagnosis and prognosis. Extracellular vesicles (EVs) and their carried miRNAs impact tumor progression. This study aims to investigate miR-183-5p in HCC cell-derived EVs on angiogenesis, progression, and metastasis, and provide diagnostic and therapeutic evidence. Methods: q-PCR was used to evaluate the expression of miR-183-5p in HCC tissue and plasma EV samples. Contrast-enhanced ultrasound and The Cancer Genome Atlas evaluated its correlation with angiogenesis and prognosis. In vitro, cell counting kit-8 (CCK-8), colony formation, transwell, tube formation, and permeability assays examined the effect of HCC cell-derived EVs on human umbilical vein endothelial cells (HUVECs). Subcutaneous tumor and lung metastasis models in nude mice verified it in vivo effects. RNA sequencing and databases predicted downstream genes and pathways, and dual luciferase and western blotting assays verified binding and activation. Conditioned medium from treated HUVECs was used on HCC cells, and chemokine levels measured. The CCL20/CCR6 axis effect was studied in vitro and in vivo by knocking down CCR6. Results: This study revealed the abnormal upregulation of miR-183-5p in both tissues and plasma EVs from patients with HCC, and its association with unfavorable prognosis. In vivo experiments, the promoting effects of miR-183-5p in HCC cell-derived EVs on the progression, metastasis and angiogenesis were verified by employing subcutaneous tumor formation models and lung metastasis models in nude mice. We demonstrated that miR-183-5p in HCC cell-derived EVs induced HUVECs proliferation, migration, angiogenesis and permeability by downregulating SIK1 expression and activating the PI3K/AKT signaling pathway in vitro. Moreover, stimulated HUVECs could secrete the chemokine CCL20 and induce HCC progression and metastasis through the CCL20/CCR6 signal pathway in vitro and in vivo. Conclusion: The findings indicated that miR-183-5p delivered by EVs from HCC cells is crucial in mediating the communication between HUVECs and HCC cells by modulating the SIK1/PI3K/AKT and CCL20/CCR6 signaling pathways, and EVs-miR-183-5p might be a potential therapeutic target for HCC patients.

overall_design: RNA seq of  Human HUVEC Cells in control Hep3B-vector/Evs and experiment Hep3B-miR-183-5p mimics/EVs group


title: Mechanical stretch induces senescence of alveolar epithelial cells and drives fibroblast activation by paracrine mechanisms

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

overall_design: Refer to individual Series


title: c-Kit+ cells that intercalate with crypt Lgr5+ cells are distinctively multipotent in colonic epithelium renewal and repair

city: Chengdu

first: shi

middle: yu

last: jun

address: No. 37, Guoxue Lane

institute: West China hospital

summary: c-Kit+ cells  mark deep crypt secretory cells (DCSs) and supply Wnt3, EGF, and Notch signals to support their neighboring crypt bottom-intermingled Lgr5+ cells. We used single cells sequencing (scRNA-seq) to analyse the diversity and stemness of  c-Kit+ cells in the colonic epithelium.

overall_design: The whole colonic epithelium cells were isolated from c-Kit-creERT2 mice, and c-Kit+ cells derived cells (GFP+ cells) of c-Kit-creERT2;Rosa26-mTG mice isolated by Fluorescences-activated cells  cell sorting (FACS) according to prescense and absence of GFP signal and analysed using scRNA-seq.

first: Qing

last: Xu

first: Yuting

last: Zeng

first: Lan

last: Jiang

first: Yongjie

last: Zhou

first: Yuwei

last: Chen

last: Tao

first: Yuke

last: Shu

first: Xiaoyue

last: Cao

first: Mingyang

last: Shao

first: Yujun

last: Shi

first: Wei

last: Huang

first: Jiayin

last: Yang


title: Mature Megakaryocytes Acquire Immune Characteristics in a Mouse Model of Aplastic Anemia

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: National Institutes of Health

summary:
Results: Megakaryocytes gain immune characteristics over the course of murine bone marrow failure; Megakaryocytes with immune characteristics serve as antigen-presenting cells and suppress hematopoietic stem cell function.
Conclusion: Our results demonstrate the acquisition of immune functions by mature megakaryocytes in an alloimmune context.

overall_design: We compared transcriptomes of enriched megakaryocytes and other hematopoietic cells from bone marrow failure mice with those from normal control mice.

first: Xingmin

last: Feng


title: Single-cell multiome of human RPE and choroid

city: Stanford

first: Sean

middle: K

last: Wang

state: CA

address: 269 Campus Drive

department: Genetics

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We present a joint scRNA-seq and scATAC-seq atlas of adult human retinal pigment epithelium (RPE) and choroid. We integrate this atlas with a HiChIP enhancer connectome to predict noncoding variants with causal roles in age-related macular degeneration (AMD).

overall_design: Single-cell RNA-seq, single-cell ATAC-seq, and HiChIP

first: Howard

middle: Y

last: Chang


title: Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network [ChIP-Seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: We profiled the H3K27ac mark on chromatin, in HCEC-1CT parental cells and a CREBBP KO single cell clone, to determine whether or not there are differences in the levels and/or distribution of the mark between WT and CREBBP KO cells

overall_design: Chromatin was isolated from three independent populations of healthy growing cells of each cell type, at c70% confluence and 10-20 passages within our laboratory.

first: Eirini

last: Moysidou

first: Marta

last: Milan


title: Skin regional specification and higher-order HoxC regulation [Micro-C]

city: Los Angeles

first: Ya-Chen

last: Liang

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

summary: The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195–base pair (bp) duplication in HoxC10 intron. Micro-C analyses show that HoxC-containing topologically associating domain (TAD) is normally closed in the scalp but open in the dorsal and tail regions, allowing multiple long-distance contacts. In the PC scalp, the TAD is open, resulting in high HoxC expression. CRISPR-Cas9 deletion of the 195-bp duplication reduces crest feather formation, and HoxC misexpression alters feather shapes. The 195-bp sequence is found only in Archelosauria (crocodilians and birds) and not in mammals. These findings suggest that higher-order regulation of the HoxC cluster modulates gene expression, driving the evolution of adaptive integumentary appendages in birds.

overall_design: To understand how chromatin architecture relates to region-specific HoxC gene expression, we performed Micro-C experiments using embryonic day 9 (E9) WL scalp, dorsal, and tail dermis as well as  juvenile PC crest mesenchyme (Cm). To examine the Hox gene expression profile in different chicken skin regions, we performed RNA-seq analysis from E9 dermis and adult feather follicles in five regions along the anterior-posterior axis (scalp, neck, anterior back, posterior back and tail) in WL chickens. We then identified differentially expressed genes (DEGs) between the scalp vs back, back vs tail, and scalp vs tail, and showed specific marker genes for each region. To explore how different skin regions modulate their chromatin accessibility to control their HoxC cluster expression profiles, we conducted ATAC-seq on E9 scalp, anterior back, and tail dermis. To test HoxC8 gene function, replication-competent avian sarcoma virus (RCAS) was used to modulate HoxC8 expression. Virus was injected into WL E4 scalp skin, and the embryos were harvested at E13 to characterize skin phenotype changes. To identify downstream mediators and possible signaling pathways associated with the phenotypic change, we performed RNA-seq on HoxC8 over-expressing and empty vector control samples. To examine HoxC cluster regulation differences between PC long crest feathers and neighboring short cranial feathers at both transcriptomic and epigenetic levels, we performed RNA-seq and ATAC-seq comparisons of juvenile PC Cm and short cranial feather mesenchyme (Fm) .

first: Shu-Man

last: Hsieh Li

first: Ping

last: Wu

first: Ting-Xin

last: Jiang

first: Cheng-Ming

last: Chuong


title: Skin regional specification and higher-order HoxC regulation

first: Wen-Chien

last: Jea


title: Skin regional specification and higher-order HoxC regulation [ATAC-Seq]


title: Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network [RNA-Seq]

summary: We profiled gene expression in iCas9-expressing HCEC-1CT and HME1 cells that were either WT or knockout for ARID1A or CREBBP, to determine the cell type variability in expression levels of epigenetic regulators and the transcriptional consequences of epigenetic regulator loss.

overall_design: A lentiviral dox-inducible Cas9 construct, adapted from Addgene 50661 for hygromycin resistance, was introduced to HME1 and HCEC-1CT cells. Knockout cell lines were generated by transfection of synthetic gRNA targeting ARID1A or CREBBP, and  clonal lines were raised, genotyped, and pooled for final populations containing 3-6 knockout clones per line. WT lines were also generated by clonal isolation and pooling.  RNA was isolated from three independent populations of healthy growing cells of each cell line, at c50% confluence and 10-20 passages within our laboratory.

first: Thomas

middle: S

last: Wilson

first: Harshil

last: Patel


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency (ChIP-seq Histone marks)

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: Inflammatory signals are key in development and cell differentiation but their orchestration with pluripotency and stemness signals is poorly understood. Our previous work identified a chromatin function of IκBα, the NF-κB inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of IκBα imposes a profound chromatin rewiring defect that impacts on DNA methylation, histone post-translational modifications and transcriptional regulation, stabilizing mouse embryonic stem cells (ESCs) in a ground state of pluripotency while preventing them from pluripotency exit and differentiation. By engineering separation-of-function mutants of IκBα with specific binding to either NF-κB or histones, we demonstrate that regulation of pluripotency state by IκBα is independent of NF-kB but requires the chromatin-related IκBα function.

overall_design: We performed ChIP-seq for H3K27me3, H3K9me3, H3K4me3, H3K27ac and H3K4me1 histone marks in mESCs. Per histone mark, three independent biological replicates were tested in two conditions: 3xWT and IκBα 3xKO samples.

first: Luis

middle: G

last: Palma

first: Daniel

last: Álvarez-Villanueva

first: María

last: Maqueda

first: Mercedes

last: Barrero

first: Arnau

last: Iglesias

first: Joan

last: Bertran

first: Damiana

last: Alvarez-Errico

first: Carlos

middle: A

last: García-Prieto

first: Cecilia

last: Ballaré

first: Virginia

last: Rodríguez-Cortez

first: Clara

last: Bueno

first: August

last: Vidal

first: Alberto

last: Villanueva

first: Pablo

last: Menéndez

first: Luciano

last: di Croce

first: Bernhard

last: Payer

first: Manel

last: Esteller

first: Lluis

last: Espinosa


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency

first: Anna

last: Bigas


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency (RNA-Seq)

overall_design: We performed bulk RNAseq analysis in mESCs and two early differentiation stages (EBs 48h and EBs 96h). Per timepoint, 3xWT and IκBα 3xKO independent biological replicates were tested resulting in a total of 18 samples.

first: Luis

last: Palma

first: Daniel

last: Álvarez-Villanueva

first: María

last: Maqueda


title: Chemokine Ligand 2 Expressing Fibroblast Recruitment of Macrophages Enhanced in Loeys-Dietz Syndrome Aortic Root Aneurysm Formation [24wk mouse]

city: Palo Alto

first: Alex

last: Dalal

state: California

address: CT Surgery, 870 Quarry Rd Ext

department: Cardiothoracic Surgery

summary: Loeys-Dietz Syndrome (LDS), caused by a spectrum of mutations in the TGF-β signaling cascade, leads to aggressive thoracic aneurysms. Given the ubiquitous nature of TGF-β signaling machinery, the exact cell type(s) responsible for initiation of LDS pathogenesis is poorly understood.

overall_design: Aortic root and ascending aortic tissue from 24-week-old Tgfbr2G357W/+ (Loeys-Dietz Syndrome) and WT littler mate control mice was subjected to tissue digestion and single-cell RNA sequencing. Male and female replicate were processed as individual libraries from each genotype, yielding 4 samples total.

first: A

middle: R

first: M

middle: P

last: Fischbein


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency (Methylation array)

summary: Inflammatory signals are key in development and cell differentiation but their orchestration with pluripotency and stemness signals is poorly understood. Our previous work identified a chromatin function of IκBα, the NF-κB inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of IκBα imposes a profound chromatin rewiring  defect that impacts on DNA methylation, histone post-translational modifications and transcriptional regulation, stabilizing mouse embryonic stem cells (ESCs) in a ground state of pluripotency while preventing them from pluripotency exit and differentiation. By engineering separation-of-function mutants of IκBα with specific binding to either NF-κB or histones, we demonstrate that regulation of pluripotency state by IκBα is independent of NF-kB but requires the chromatin-related IκBα function.

overall_design: Bisulphite converted DNA was hybridised to the Illumina Infinium  Mouse Methylation Beadchip (MM285) array in mESCs and one early differentiation stages (EBs 96h). Per timepoint, 3xWT and IκBα 3xKO independent biological replicates were tested resulting in a total of 12 samples.

first: Mercedes

last: Barrero

first: Arnau

last: Iglesias

first: Joan

last: Bertran

first: Damiana

last: Alvarez-Errico

first: Carlos

last: García-Prieto

first: Cecilia


title: An intersectional analysis of LncRNAs and mRNAs reveals the potential therapeutic targets of Bi Zhong Xiao Decoction in collagen-induced arthritis rats

city: Chang Sha

first: He

last: Cailin

state: Hu Nan

address: Kaifu district

institute: xiangya hospital

summary: Rheumatoid arthritis (RA) is a chronic progressive autoimmune disease of unknown etiology. Both clinical and experimental studies have revealed the effects of the traditional Chinese formula Bi Zhong Xiao Decoction (BZXD) in treating RA. However, the multifaceted mechanisms of BZXD in RA treatment are not comprehensively understood. In this study, we aimed to explore therapeutic targets of BZXD by using lncRNA and mRNA transcriptomics.

overall_design: Microarray expression profiling of mRNA and lncRNA was performed using RNA extracted from synovial tissue samples from four normal rats, four CIA rats, and Bi Zhong Xiao Decoction treated CIA rats.

first: Xingui

last: Xiong

first: Cailin

last: He

first: Yuqi

last: Wen

first: Siqing

last: Zeng


title: The transcriptome data of pig embryonic stem cells cultured without feeder cells

city: Seoul

first: Chang-Kyu

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: Here, we examined the effect of LDN-193189, an inhibitor of the BMP signaling pathway, on pig embryonic stem cells (ESCs) in the absence of feeder cells to develop a feeder-free culture system. Feeder cells play an important role in supporting the pluripotency of pig ESCs by blocking trophoblast and mesodermal differentiation through inhibition of the BMP pathway. Transcriptome analysis revealed that LDN-193189 treatment instead of coculturing with feeder cells could help maintain the pluripotency and homogenous cell population of pig ESCs by stimulating the secretion of chemokines and suppressing differentiation. We confirmed that LDN-193189-treated pig ESCs cultured without feeder cells maintained pluripotency for an extended period and were capable of differentiating in vivo and in vitro. The pig ESCs represented distinct characteristics of pig epiblasts as an in vivo counterpart at a transcriptomic level. In summary, we developed feeder-free culture systems for pig ESCs, and our findings will improve the understanding of pluripotency gene networks and comparative embryogenesis.

overall_design: The transcriptomic profiling of pig embryonic stem cells cultured with feeder cells, LDN-193189 treated pig embryonic stem cells cultured without feeder cells, and fetal fibroblasts.

first: Kwang-Hwan

last: Choi

first: Dong-Kyung


title: DNA supercoiling impacts alternative transcription start site selection in yeast

status: Public on Mar 24 2025

first: Folkert

last: van Werven

summary: Most genes are transcribed from multiple transcription start sites (TSSs), defined as alternative TSSs, which are highly regulated and can lead to various gene regulatory outcomes including changes in translation efficiency and protein isoforms. Transcription factors and chromatin regulators control alternative TSS selection. DNA supercoiling affects multiple aspects of transcription including transcription initiation. However, its regulatory effect on genes with multiple TSSs is not known. Here we investigated how DNA supercoiling impacts alternative TSS usage in Saccharomyces cerevisiae. We depleted topoisomerases during early meiosis, where alternative TSS usage is prevalent, and applied an improved TSS sequencing protocol. We show that supercoiling affects alternative TSS usage of almost 600 genes. Increased alternative and aberrant TSS usage were observed near and within open reading frames, likely resulting from transcription-induced supercoiling originating from upstream alternative TSSs. DNA supercoiling had the greatest impact on genes with a dominant alternative TSS, significant spacing between alternative TSSs, and greater overall length. Our results establish that DNA supercoiling release during transcription is critical for correct TSS selection.

overall_design: Top1/2 depletion at 0h and 6h in SPO. Controls Top1/2-AID, TIR, Top1/2 AID+TIR at 0h and 6h. Total 18 samples.

first: Eleanor

last: Elgood Hunt

first: Claudia

last: Vivori


title: Transcriptome Sequencing of Optic Nerve in a Rat Model of Neuromyelitis Optica Spectrum Disorder-Related Optic Neuritis (NMOSD-ON)

city: Guangzhou

first: Siqi

last: Chen

state: Guangdong

address: No.54 Xianlie South Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: This study established a rat model of NMOSD-ON by injecting patient-derived AQP4+ serum into the optic nerve sheath of rats. Optic nerve tissues were collected at 24 hours and 7 days post-modeling, along with a blank control group, for transcriptome sequencing. The aim was to explore gene expression changes during the early and peak phases of NMOSD-ON pathogenesis, thereby identifying potential disease mechanisms.

overall_design: Experimental design: The study included three groups: (1) healthy control group, (2) NMOSD-ON model group at 24 hours post-induction, and (3) NMOSD-ON model group at 7 days post-induction. Each group consisted of three biological replicates, totaling nine samples. The NMOSD-ON model was induced by injection of AQP4+ serum into the optic nerve sheath. Optic nerve tissues were collected for RNA-Seq analysis to compare gene expression profiles between the groups.

first: Hui

last: Yang


title: Formyl peptide receptor 2 contributes to intestinal epithelium homeostasis by regulating intestinal stem cell proliferation and differentiation

city: Shanghai

first: shuting

last: Yu

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

summary: In this study, we investigated the involvement of formyl peptide receptor 2 (FPR2) in intestinal epithelium homeostasis and the underlying mechanisms by comparing the transcriptome profiles of intestinal crypts from intestinal epithelial-specific knockout (Fpr2VKO) and control (Fpr2f/f) mice.

overall_design: Small intestinal crypts were isolated from Fpr2f/f and Fpr2VKO mice. Total RNA was isolated from the crypts and RNA sequencing was performed.

first: Shuting

first: Yingying

last: Le


title: CUT&RUN analyses of fetal Leydig cells and testicular interstitial cells

city: Bunkyo-ku

first: Shogo

last: Yanai

state: Tokyo

country: Japan

institute: TMDU

summary: Ad4BP/SF-1 is a transcription factor regulating gene expression related to steroidogenesis and energy metabolism. Previous studies have indicated that Ad4BP/SF-1 regulates fetal Leydig cell differentiation from progenitor cells. However, the underlying regulatory mechanisms remain unclear. Here, we reveal that Ad4BP/SF-1 directly regulates energy metabolisms in differentiated fetal Leydig cells through transcriptional upregulation.

overall_design: Ad4BP/SF-1 profiling of fetal Leydig cells (S-EGFP cells) and testicular interstitial cells (W-EGFP cells) was performed using CUT&RUN.

first: Miki

last: Inoue

first: Takashi

last: Baba

first: Ken-ichirou

last: Morohashi


title: ChEC-seq2 profiling of yeast Gcn4 and Crm1-T539C localization after treatment with Leptomycin B.

city: Evanston

first: Tiffany

last: Ge

state: IL

address: 2205 Tech Drive

institute: Northwestern University

summary: Nuclear pore proteins (Nups) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC. In vitro, Crm1 binds both Gcn4 and Nup2 directly. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-GTP nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates docking of transcription factor-bound enhancers at the NPC.

overall_design: ChEC-seq2 was used to determine yeast Gcn4 and Crm1-T539C binding patterns in LMB-sensitive strains after Leptomycin B (LMB) treatment to inhibit crm1-T539C. Control samples were treated with ethanol (solvent) instead of LMB.

first: Jason

middle: H

last: Brickner


title: ChEC-seq2 profiling of Crm1 and Nup2 during degradation of Nup2 or inhibition/degradation of Crm1, respectively

overall_design: ChEC-seq2 was used to determine Crm1 binding patterns after degradation of Nup2 using 3-IAA in AID strains as well as Nup2 binding patterns after inhibition of Crm1 by Leptomycin B (LMB) in LMB-sensitive strains or degradation of Crm1 using estradiol + 5-Ph-IAA treatment in grAID strains.

first: Donna


title: Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

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

relation:
SuperSeries of: GSE288515
SuperSeries of: GSE288549
SuperSeries of: GSE288550
SuperSeries of: GSE288633

overall_design: Refer to individual Series


title: Angiotensin Converting Enzyme (ACE) expression in microglia reduces amyloid β deposition and neurodegeneration by increasing SYK signaling and endolysosomal trafficking.

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Angiotensin Converting Enzyme (ACE) has been studied for its role in the regulation of myeloid cell bactericidal and antitumor activity. Here, we generated a mouse model with Tamoxifen-dependent ACE expression with Cx3CR1-Cre control. These mice were crossed to 5xFAD and 9 month forebrains were harvested for their nuclei to assess the ACE-dependent changes in amyloid-reactive microglia.

overall_design: Dissociated nuclei were stained with NeuN, Sox9 and Sox10 and microglia were enriched by negatively selecting for these markers.

first: Warren

last: Tourtellotte

first: Andrew

last: Gomez


title: Identification and characterization of a novel StAR-related lipid transfer protein in Entamoeba histolytica that shuttles phosphoinositides between the nucleus and the cytoplasm: role in growth, stress defense, membrane traffick, and pathogenesis.

city: Tokyo

first: Sota

middle: ミズカミソウタ

last: Mizukami

institute: The university of Tokyo

summary: Phospholipids, their biosynthesis, and functional implications in the nucleus have been recently unraveled from eukaryotes. However, how the phospholipid precursors are trafficked between the nucleus and the cytoplasm and how nuclear lipids are  synthesized sis and degradedation is regulated for homeostasis in the eukaryotic cell still largely unknown. In the present study, we have identified for the first time a lipid transfer protein (LTP) from a protozoan parasite E. histolytica (EhLTP15) that is involved in nuclear-cytoplasmic lipid transport and regulation of nuclear lipid metabolism and homeostasis. EhLTP15 translocated from the nucleus to the cytoplasm under nutrient deprived conditions, which mimics encystation conditions, thus can potentially functions as intracellular communicator during stage conversion. EhLTP15 was also involved in exocytosis of pinocytosed fluid phase maker and secretion of lysosomal enzymes, cysteine proteases, which are implicated for virulence and tissue invasion of this enteric pathogen. EhLTP15 was also involved in the defense against oxidative stress. Furthermore, EhLTP15 was necessary to maintain the levels of nuclear phosphoinositides. This study has provided a link between non-vesicular lipid transport and nuclear lipid metabolism for the first time in any unicellular eukaryotes.

overall_design: To investigate the effects of gene silencing we established cells lines in which target gene has been gene silenced by epigenetic silencing. We then performed gene expression analysis using the data obtained from the RNA-seq of pSAP (mock transfected),  LTP15 gene silenced strains (n=3)

first: Das

last: Koushik

first: Natsuki

last: Watanabe

first: Tomoyoshi

last: Nozaki


title: ChEC-seq2 profiling of Crm1, Nucleoporins (nups), and RNA Pol II from budding yeast grown in SDC

overall_design: ChEC-seq2 was used to assess Crm1, Nups, and Pol II localization in synthetic complete medium containing glucose (SDC) in budding yeast.

first: Jake

last: VanBelzen


title: Transcriptome analysis of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of wild-type medaka and phod1 knockout medaka kept under short-day or long-day conditions

city: Nagoya

last: Yoshimura

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary: Expression profile of the brain (ventral part of telenchephalon, hypothalamus and pituitary) of wild-type medaka and phod1 knockout medaka kept under short-day or long-day conditions

overall_design: To examine the effects of phod1 knockout, medaka kept under short-day conditions were transferred to long-day conditions, and wild-type and phod1 knockout brains were sampled at 12:00 before and 12 days after the transfer. Using these samples, we performed RNA-sequencing (RNA-seq) analysis.

first: Tomoya

last: Nakayama


title: Skin regional specification and higher-order HoxC regulation [RNA-Seq]

first: Ya-Chen

last: Liang

overall_design: To understand how chromatin architecture relates to region-specific HoxC gene expression, we performed Micro-C experiments using embryonic day 9 (E9) WL scalp, dorsal, and tail dermis as well as  juvenile PC crest mesenchyme (Cm). To examine the Hox gene expression profile in different chicken skin regions, we performed RNA-seq analysis from E9 dermis and adult feather follicles in five regions along the anterior-posterior axis (scalp, neck, anterior back, posterior back and tail) in WL chickens. We then identified differentially expressed genes (DEGs) between the scalp vs back, back vs tail, and scalp vs tail, and showed specific marker genes for each region. To explore how different skin regions modulate their chromatin accessibility to control their HoxC cluster expression profiles, we conducted ATAC-seq on E9 scalp, anterior back, and tail dermis. To test HoxC8 gene function, replication-competent avian sarcoma virus (RCAS) was used to modulate HoxC8 expression. Virus was injected into WL E4 scalp skin, and the embryos were harvested at E13 to characterize skin phenotype changes. To identify downstream mediators and possible signaling pathways associated with the phenotypic change, we performed RNA-seq on HoxC8 over-expressing and empty vector control samples. To examine HoxC cluster regulation differences between PC long crest feathers and neighboring short cranial feathers at both transcriptomic and epigenetic levels, we performed RNA-seq and ATAC-seq comparisons of juvenile PC Cm and short cranial feather mesenchyme (Fm) .

first: Shu-Man

last: Hsieh Li

first: Ping

last: Wu

first: Ting-Xin

last: Jiang

first: Cheng-Ming

last: Chuong


title: thiol(SH)-linked alkylation for the metabolic sequencing (SLAM-seq) of RNA after Crm1 inhibition and Nup1/Nup2 degradation

first: Tiffany

last: Ge

overall_design: thiol(SH)-linked alkylation for the metabolic sequencing (SLAM-seq) was used to investigate the impact of Crm1 inhibition and degradation of Nup1 or Nup2 on the nascent and total transcriptome in budding yeast.

first: Nikita

last: Marcou


title: Transcriptome analysis of the liver of wild-type medaka and phod1 knockout medaka kept under long-day conditions

first: Takashi

summary: Expression profile of the liver of wild-type medaka and phod1 knockout medaka kept under long-day conditions

overall_design: To examine the effects of phod1 knockout, liver of wild-type and phod1 knockout medaka kept under long-day conditions were sampled at 12:00. Using these samples, we performed RNA-sequencing (RNA-seq) analysis.


title: Oral Ketone β-Hydroxybutyrate Supplement Retards the Loss of GFR in Alport Mice on Dual Renin-Angiotensin System/ Sodium-Glucose Transporter 2 Blockade

city: Munich

first: Linus

middle: Paul

last: Schreier

address: Goethestraße 31

country: Germany

institute: Ludwig-Maximilians-Universität

summary: Background: Several studies suggest that dietary beta hydroxybutyrate supplementation delays the progression of chronic kidney disease (CKD) by suppressing inflammation and fibrosis. We hypothesized that the oral supplementation with the beta-hydroxybutyrate (BHB) precursor 1,3-butanediol in addition to inhibitors of the renin-angiotensin system (RAS) and sodium-glucose transporter (SGLT)2 would be superior to dual RAS/SGLT2 blockade alone in attenuating the loss of glomerular filtration rate in Col4a3-deficient mice with Alport nephropathy, a spontaneous model of progressive CKD. Methods: We performed a placebo-controlled study in Col4a3-deficient mice with Alport nephropathy. Treatment was initiated at a late stage of the disease at the age of six weeks. Mice were fed food admixes of 10 μg/g ramipril plus 30 μg/g empagliflozin with or without addition of 0,04g/g 1,3-butanediol (concentration per gram of bodyweight). The mice were monitored daily and sacrificed upon reaching renal failure. The glomerular filtration rate (GFR) was measured at the start of the treatment and after one and four weeks. Results: The addition of beta hydroxybutyrate significantly attenuated the loss of glomerular filtration rate beyond the effect of dual RAS/SGLT2 blockade. The mean glomerular filtration rate after four weeks of treatment was 1.4±5.0 μl/min (vehicle), 61.3±51.1 μl/min (RASi + SGLT2i), and 138.9±68.5 μl/min (RASi + SGLT2i + 1,3-butanediol). No additional effects on lifespan could be observed. Kidney RNA sequencing revealed significant protective effects on inflammation when adding the beta hydroxybutyrate precursor 1,3-butanediol to RAS/SGLT2 inhibition. In histopathology, antifibrotic effects were seen upon beta hydroxybutyrate addition. Conclusion: The results in mice suggest that beta hydroxybutyrate supplementation improves the GFR in Alport syndrome by suppressing inflammation and fibrosis. However, the effects did not lead to a significant increase in lifespan. Furthermore, the observed effects stay behind the effects of finerenone as a combination partner, which was tested earlier in the same mouse model.

relation:
Reanalysis of: GSM7073825
Reanalysis of: GSM7073826
Reanalysis of: GSM7073827

overall_design:
Comparison in kidneys of Col4a3-/- mice fed with Ramipril/Empagliflozin (Data available with GSM7073816) vs Ramipril/Empagliflozin/1,3-butanediol regarding RNA expression of significantly altered canonical pathways.
This study includes re-analysis of publicly available samples: GSM7073825, GSM7073826 and GSM7073827. Data for these samples are included in the files:
GSM7073825: counts_without_BHB_1.csv, Col4a3_KO_Ram_Empa_1.csv
GSM7073826: counts_without_BHB_2.csv, Col4a3_KO_Ram_Empa_2.csv
GSM7073827: counts_without_BHB_3.csv, Col4a3_KO_Ram_Empa_3.csv

first: L

first: HJ

last: Anders

first: Z

last: Zhu

first: Y

last: Kusunoki

first: C

last: Li

first: J

last: Ku

first: M

last: Klaus


title: Disrupting the interaction between androgen receptor and its coregulator WDR77 delays the growth of treatment-resistant prostate cancer

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Continued reliance on androgen receptor (AR) after androgen deprivation therapy (ADT) has failed causes 35,000 American prostate cancer (CaP) deaths annually. AR’s transcriptional activity is an attractive target to overcome this acquired resistance but has been challenging to pursue. We demonstrate the therapeutic potential of disrupting interactions between AR and its coregulator WDR77. WDR77 stimulated growth of CaP cells and xenografts and its overexpression associated with worse patient survival. AR and WDR77 cistromes overlapped considerably, AR- and WDR77-bound genes correlated with aggressive CaP features, and the AR cistrome was reduced after WDR77 loss. We delineated direct interaction between WDR77 and AR, which when disrupted prevented AR-WDR77 complex formation, reduced AR DNA-binding and AR-dependent gene expression. Such disruption decreased cell proliferation to the same extent as ADT, and inhibited cell growth when ADT-resistant AR action was modelled and after ADT-resistance without impacting AR-negative CaP cells or benign cells. Blocking AR-WDR77 cooperation also delayed growth of organoids generated from patient-derived xenografts and fresh CaP specimens. Disrupting coregulator control over AR action may thus improve survival from ADT-resistant CaP.

overall_design: In a first study, LNCaP cells were transfected with an expression construct encoding WDR77-peptide 3 or empty vector.  The next day, medium was changed to androgen-deprived medium. One day later, androgen-deprived medium was refreshed and cells were treated with 5nM of the synthetic androgen R1881 or vehicle (ethanol).  48h later, cells were harvested in Trizol, RNA was extracted and column-purified.  Biological triplicates were generated for each treament group.  300,000 cells were seeded per well of a 6 well plate. In a second study, LNCaP cells were transfected with siRNAs targeting WDR77 or non-targeting control siRNA.  The next day, medium was changed to androgen-deprived medium. One day later, androgen-deprived medium was refreshed and cells were treated with 5nM of the synthetic androgen R1881 or vehicle (ethanol).  48h later, cells were harvested in Trizol, RNA was extracted and column-purified. Biological triplicates were generated for each treatment group. 300,000 cells were seeded per well of a 6 well plate.

first: Ujjwal

last: Dahiya

first: Song

last: Liu

first: Tao

first: Hannelore

middle: V

last: Heemers


title: Epigenetic regulation of CD8+ effector T cell differentiation by PDCD5

city: Beijing

first: Yujia

last: Wang

state: Beijing

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

institute: Peking university school of basic medical sciences

summary: Epigenetic modification is critical in the establishment of the transcriptional program for CD8+ effector T cell differentiation. How this is regulated at an early stage before the expression of master transcription factors remains elusive. Here, we identify PDCD5 as an activation-induced molecule that is required for proper differentiation and expansion of antigen-specific CD8+ effector T cells in a chronic viral infection mouse model. Genetic deletion of Pdcd5 diminished effector T cell formation and function, leaving T cell activation, metabolic reprogramming, and memory/exhausted T cell differentiation largely unaffected. At the molecular level, reduced chromatin accessibility and transcription of Tbx21 and its regulated genes were found in Pdcd5-/- CD8+ T cells. We further identify PRDM9 that facilitates the H3K4me3 modification of effector signature genes in CD8+ T cells. The interaction of PDCD5 with PRDM9 promoted the translocation and lysine methyltransferase activity of PRDM9. These data indicate a pivotal role of PDCD5/PRDM9 axis in epigenetic reprogramming at the early stage of effector CD8+ T cell fate determination.

overall_design: CD8+ splenic T cells from LCMV Cl13-infected WT and cKO (Pdcd5fl/fl-Cd4-Cre) mice at 10 dpi.

first: Lixue

last: Jin

first: Xin

last: Zhang

first: Jingyi

first: Ke

first: Zhuolin

first: Pingzhang

first: Xiuyuan

last: Sun

first: Jie

last: Hao

first: Hounan

first: Xiaojun

last: Huang

first: Rong

first: Dan

last: Lv

first: Qing


title: PPDPF is not a key regulator of human pancreas development

city: Ulm

first: Alexander

last: Kleger

state: Baden-Württemberg

address: Albert-Einstein-Allee 23

department: Institute of Molecular Oncology and Stem Cell Biology (IMOS)

institute: University Hospital Ulm

summary: Given their capability to differentiate into each cell type of the human body, human pluripotent stem cells (hPSCs) provide a unique platform for developmental studies. In the current study, we employed this cell system to understand the role of pancreatic progenitor differentiation and proliferation factor (PPDPF), a protein that has been little explored so far. While the zebrafish orthologue exdpf is essential for exocrine pancreas specification, its importance for mammalian and human development has not been studied yet. We implemented a four times CRISPR/Cas9 nicking approach to knockout PPDPF in human embryonic stem cells (hESCs) and differentiated PPDPFKO/KO and PPDPFWT/WT cells towards the pancreatic lineage. In contrast to data obtained from zebrafish, a very modest effect of the knockout was observed in the development of pancreatic progenitors in vitro, not affecting lineage specification upon orthotopic transplantation in vivo. The modest effect is in line with the finding that genetic variants near PPDPF are associated with random glucose levels in humans, but not with type 2 diabetes risk, supporting that dysregulation of this gene may only result in minor alterations of glycaemic balance in humans. In addition, PPDPF is less organ- and cell type specifically expressed in higher vertebrates and its so far reported functions appear highly context-dependent.

overall_design: PPDPF KO/KO clones have been generated in the human pluripotent stem cells (hPSC) line HUES8. Two different PPDPF KO/KO and two different PPDPF WT/WT hPSC clones and their pancreatic differentiation derivates, namely definitive endoderm (DE), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage were sequenced. For DE, PE, and PP, RNA was isolated from four independent differentiations (differentiation started on different days). For hPSC control samples, 2 RNA samples were sequenced.

first: Markus

last: Breunig


title: Diesel exhaust particles Enhance Monocyte Recruitment, Accelerating Allergic Airway Inflammation

city: seoul

first: Youngmin

last: Song

address: 71, Ihwajang-gil, Jongno-gu, Seoul, Republic of Korea

institute: Seoul National Univeristy College of Medicine

summary: We performed single-cell RNA sequencing on CD45+ cells isolated from the lungs of C57BL/6 mice exposed to diesel exhaust particles via inhalation. The objective was to investigate which immune cells respond to particulate matter exposure.

overall_design: After DEP exposure, CD45+ immune cells were isolated from the lung tissues of C57BL/6J (wild-type) and Ccr2-/- (knockout) mice using fluorescence-activated cell sorting (FACS). The sorted cells were processed for single-cell RNA sequencing (scRNA-seq) to investigate transcriptional changes induced by DEP exposure. Control mice without DEP exposure were included for comparison. Libraries were prepared using the Chromium Next GEM Single Cell 3’ RNA kit v3.1 and sequenced on an Illumina NovaSeq 6000.

first: Yi Rang

first: Seung Hee

last: Han

first: Mi Reu

last: Jeong

first: Young Min

first: Yeon Ji

last: Park

first: Jihyun

last: Kim

first: Hye Yeong

first: Kwang Su

first: Moo Kyun

first: Seung Hyeok

last: Seok


title: Transcriptome analyses of fetal testicular interstitial cells (W-EGFP) treated with Smoothened Agonist (SAG)

first: Shogo

last: Yanai

summary: Fetal Leydig cells are essential for masculinization through androgen production during fetal development. Previous studies have indicated that Desert Hedgehog regulates differentiation from progenitor cells. Our previous research showed a significant upregulation of energy metabolism-related genes during fetal Leydig cell differentiation. However, the underlying regulatory mechanisms remain unresolved. Here, we reveal that Desert Hedgehog rapidly activates energy metabolisms in testicular interstitial cells (W-EGFP cells) containing fetal Leydig progenitor cells without activating gene expression.

overall_design: Transcriptomes of testicular interstitial cells (W-EGFP cells) from E16.5 FLE-EGFP mice were obtained with or without Smoothened Agonist treatment for 1 hour.

first: Miki

last: Inoue

first: Takashi

last: Baba

first: Ken-ichirou

last: Morohashi


title: Three-dimensional regulatory hubs support oncogenic programs in glioblastoma [Hi-C]

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: Enhancer-promoter communication in the context of the three-dimensional (3D) nucleus is critical for the regulation of transcriptional programs specific for cell identity. Here, we profile the 3D enhancer-promoter networks of primary patient-derived human glioma spheres (GSCs) in comparison with neuronal stem cells to identify candidate central nodes of GSC tumorigenic programs. We have identified highly interacting 3D enhancer-promoter “hubs” which strongly associate with robust and coordinated expression of tumor-associated genes, suggesting potentially central roles in the regulation of oncogenic programs. Integration of whole-genome sequencing (WGS) data from The Cancer Genome Atlas showed that 3D regulatory hubs are strongly enriched for recurrent point mutations in the larger cohort of glioblastoma patients. In a proof-of-concept experiment, epigenetic perturbation of a highly interacting and recurrent 3D enhancer hub in the GOLIM4 locus led to significant downregulation of multiple hub-connected genes and reduced clonogenicity along with a global shift in the transcriptional states. Finally, integration of published H3K27ac HiChIP from other cancer types enabled the identification of both “universal” and cancer type-specific 3D regulatory hubs which enrich for different oncogenic programs and potential regulators, and often associate with a worse prognosis. Overall, our study identifies complex 3D regulatory hubs in glioblastoma and provides computational and experimental support for their potential role in driving oncogenic programs and promoting tumorigenic properties.

overall_design:
Hic for 4 patient-derived glioma stem cell lines

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Effie

last: Apostolou


title: Mechanical stretch induces senescence of alveolar epithelial cells and drives fibroblast activation by paracrine mechanisms I

city: Oviedo

first: Guillermo

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Severe lung injury requiring mechanical ventilation may lead to secondary fibrosis. Senescence, a cell response characterized by cell cycle arrest and a shift towards a proinflammatory/profibrotic phenotype, is one of the mechanisms involved in lung fibrosis. Here, we explore the contribution of mechanical stretch to senescence of the alveolar epithelium and its link with fibrosis. Human alveolar cells and fibroblasts were exposed in vitro to mechanical stretch, and senescence assessed. In addition, fibroblasts were exposed to culture media preconditioned by senescent epithelial cells and their activation was studied. Transcriptomic profiles from stretched, senescent epithelial cells and activated fibroblasts were combined to identify potential activated pathways. Finally, the senolytic effects of digoxin were tested in these models. Mechanical stretch induced senescence in alveolar epithelial cells, but not in fibroblasts. This stretch-induced senescence has specific features compared to senescence induced by doxorubicin. Fibroblasts were activated after exposure to supernatants conditioned by epithelial senescent cells. Transcriptomic analyses revealed notch signaling as a potential responsible for the epithelial-mesenchymal crosstalk, as fibroblast activation was inhibited by treatment with an inhibitor of g-secretase. Treatment with digoxin reduced the percentage of senescent cells after stretch and ameliorated the fibroblast response to preconditioned media. These results suggest that lung fibrosis in response to mechanical stretch may be caused by the paracrine effects of senescent alveolar cells. This pathogenetic mechanism can be pharmacologically manipulated to improve lung repair.

overall_design: A549 were subjected to cyclic stretch (15% elongation, 15 cycles/min)  for 24 hours and  β-galactosidase (Bgal) staining was assessed after 6 days. Afterwards, B-gal positive and negative stretched cells  were sorted,  lysated and RNA was collected for RNAseq analysis.

first: Paula

last: Martín-Vicente


title: NR2F2 Regulation of Fetal Leydig Cell Differentiation: Insights into Differences of Sex Development [RNA-Seq]

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: Testicular fetal Leydig cells are specialized for androgen production during embryogenesis. Testosterone is essential for regulating sex differentiation, spermatogenesis, and fertility. Deficiencies in Leydig cell differentiation can lead to various disorders of sex development and male reproductive conditions, such as ambiguous genitalia, hypospadias, cryptorchidism, and infertility. Understanding the differentiation of fetal Leydig cells is essential for comprehending male sexual differentiation, reproductive health, and fertility.

overall_design: Three E14.5 testes (control or COUP-TFII KO) were pooled per sample. RNA was extracted using the Arcturus™ PicoPure™ RNA Isolation Kit (Applied Biosystems, KIT0204). Briefly samples were dissociated in 100 ml of in extraction buffer with a microtube homogenizer and incubated at 42°C for 30 minutes. Posteriorly samples were snap frozen for at least one hour. RNA was precipitated with 100 ml of 70% ethanol and loaded into a pre-conditioned column. Samples were centrifuged and the column was washed with Wash Buffer 1, followed by a step of DNA removal using the RNase-Free DNase Set (Qiagen, #79254). Samples were washed twice with Wash Buffer 2 and the columns were centrifuged to eliminate residual buffer. Samples were eluted in 12 ml of elution buffer.

first: Martin

last: Estermann


title: Effect of IFNT and PGF2A on gene expression of cultured luteal steroidogenic cells [Cultured cells]

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

summary: The effect of interferon tau (IFNT) on the uterus is critical for maternal recognition of pregnancy in ruminants, while its direct role in luteal function is less well understood. To address this, we performed two experiments. In experiment 1, cattle received intrauterine infusions of one of four treatments: bovine serum albumin (BSA; vehicle) from day 14 to 16 of the estrous cycle, vehicle with IFNT from day 14 to 16 (3-day IFNT), vehicle with IFNT from day 14 to 19 (6-day IFNT), and vehicle with IFNT from day 14 to 16 followed by vehicle with IFNT and pregnancy associated glycoprotein (PAG) from day 17 to 19 (IFNT+PAG). Corpora lutea (CL) were collected on day 17 or 20 and RNAseq was performed. In experiment 2, cultured luteal steroidogenic cells from cyclic (day 10-12) cattle were treated with IFNT and RNAseq was performed. In both experiments, IFNT resulted in luteal changes (in vivo: 130 transcripts; in vitro: 2981 transcripts), while additional treatment with PAG resulted in only 13 changed transcripts. Only 31% of the genes that changed in the CL during early pregnancy (Hughes et al., 2020) were regulated by IFNT. Gene ontology analysis revealed that these genes were regulators of antiviral and immune responses. In contrast, 50% of the genes that changed during early pregnancy were not regulated by IFNT in vivo or in vitro and were associated with cellular proliferation and extracellular matrix organization. It is suggested that the temporal changes in the CL during early pregnancy are only partially regulated directly by IFNT, drawing into question identities of other luteal regulators or the effect of age of CL.

overall_design: Luteal steroidogenic cells were treated with IFNT (1ng/mL), PGF2A (10 ng/mL) or combination of the two in vitro for 24hours.

first: Adelaide

middle: C

last: Hellmers

first: M

middle: I

last: da Silva

first: Troy

middle: L

last: Ott

first: Joy

last: Pate


title: Effect of intrauterine infusion of IFNT, PAG, or PAG and IFNT on luteal gene expression [in vivo]

overall_design: cattle received intrauterine infusions of one of four treatments: bovine serum albumin (BSA; vehicle) from day 14 to 16 of the estrous cycle, vehicle with IFNT from day 14 to 16 (3-day IFNT), vehicle with IFNT from day 14 to 19 (6-day IFNT), and vehicle with IFNT from day 14 to 16 followed by vehicle with IFNT and pregnancy associated glycoprotein (PAG) from day 17 to 19 (IFNT+PAG). Corpora lutea (CL) were collected on day 17 or 20 and RNAseq was performed.


title: NR2F2 Regulation of Fetal Leydig Cell Differentiation: Insights into Differences of Sex Development [multiome]

summary: Testicular fetal Leydig cells are specialized for androgen production during embryogenesis. Testosterone is essential for regulating sex differentiation, spermatogenesis, and fertility. Deficiencies in Leydig cell differentiation can lead to various disorders of sex development and male reproductive conditions, such as ambiguous genitalia, hypospadias, cryptorchidism, and infertility. Understanding the differentiation of fetal Leydig cells is essential for comprehending male sexual differentiation, reproductive health, and fertility.  Fetal Leydig cells originate from proliferating progenitor cells in the gonadal interstitium, marked by genes like Arx, Pdgfra, Tcf21, Wnt5a, and Nr2f2. However, the precise mechanisms governing the transition from interstitial cells to Leydig cells remain elusive. Through integrated approaches involving animal models and multiomics, we have demonstrated that fetal Leydig cells originate from a Nr2f2 positive non-steroidogenic interstitial cell population. NR2F2 promotes progenitor cell fate while suppressing Leydig cell differentiation. Moreover, embryonic deletion of Nr2f2 in mouse testes resulted in disorders of sex development, including reduced testicular size, Leydig cell hypoplasia, cryptorchidism, and hypospadias. Collectively, our findings highlight the critical role of Nr2f2 in orchestrating the transition from interstitial cells to Leydig cells during testicular development.

overall_design: Homozygous Nr5a1-cre mice were crossed with homozygous Rosa-tdTomato female. Whole testes were collected from E14.5 embryos in PBS and immediately frozen in liquid nitrogen for storage.


title: The Capicua-Ataxin 1L DNA Binding Transcriptional Repressor Complex Serves as a Gatekeepers of Cell Autonomous Antiviral Responses[Mouse RNA-Seq ]

city: Iowa City

first: Priya

middle: D

last: Issuree

state: IA

address: 431 Newton Road

department: Internal Medicine

institute: University of Iowa

summary: Early detection of viral infection and rapid activation of host antiviral defenses are critical for limiting viral replication and spread. At a cellular level, this is achieved through host pattern recognition receptors that sense viral nucleic acid as foreign and initiate antiviral defenses through transcriptional upregulation of antiviral cytokines interferons (IFNs) and interferon stimulated genes (ISGs). However, aberrant production of IFN in the absence of viral infection leads to auto-inflammation and can be detrimental to the host. Here, we show that the DNA binding transcriptional repressor complex composed of Capicua (CIC) and Ataxin-1 like (ATXN1L) bind to 8-nucleotide motif near IFN and ISG promoters and block aberrant expression under homeostasis. However, during respiratory viral infections, this active repression is relieved by rapid degradation of the CIC-ATXN1L complex via the activation Mitogen‑activated protein kinase (MAPK) pathway, thereby priming the host cells ready to mount robust antiviral responses through canonical interferon regulatory factors (IRF), and signal transducer and activator of transcription (STAT) transcription factors. Importantly, murine Cic-Atxn1L also repress expression from IFN and ISGs promoters, demonstrating the conservation of this regulatory mechanism in murine species. Together, our studies define a new paradigm for regulation of IFN and ISGs through the evolutionarily conserved CIC-ATXN1L DNA binding transcription repressor complex under homeostasis and viral infection conditions.

overall_design: To assess changes in mRNA expression following IAV infection, tamoxifen treated (R26-CreERT2 Cicf/f mice) and control mice (Cic f/f) were either mock infected or infected with IAV H1N1 PR8 strain at dose=10PFU. On day 5 post infection, lungs from mock and IAV infected mice were homogenized in 1ml of TRIzol and total RNA was extracted as per the manufacturer's recommendations. RNASeq was performed on the PolyA RNA.


title: In situ delivery of mRNA-encoded Gasdermin E promotes antitumor immunity via creatine-elicited type Ⅰ interferon signaling in monocytes

first: Hanjun

last: Li

address: No. 160, Pujian Road, Pudong New Area

department: Renji Hospital

institute: Shanghai Jiao Tong University

summary: Tumor microenvironment is highly immunosuppressive. Tumor immunotherapy aims to reverse the immunosuppressive tumor microenvironment, activating antitumor immune response, which becomes a hotspot in tumor therapy. mRNA lipid nanoparticle based gene therapy represents a promising strategy for tumor immunotherapy. Identifying novel mRNA target is critical for improving the effect of in vivo gene immunotherapy for cancer. Pyroptosis obtains the key characteristics of immunologic cell death, and GSDME is an essential effector molecule triggering pyroptosis. Here, we synthetized mRNA encoding GSDME encapsulated by LNP (LNP-Gsdme). In situ delivery of LNP-Gsdme through intratumoral injection suppressed tumor growth, boosting monocytes infiltration and CD8+ T cell activation. Mechanistically, LNP-Gsdme-induced pyroptosis and immunogenic cell death in tumor cells, releasing creatine as a novel metabolic damage associated molecular pattern as well as a metabolite biomarker of ICD, eliciting cGAMP-STING-TBK1-IRF3-IFN-I signaling pathway in monocytes, then activating CD8+ T cells in the tumor microenvironment. Furthermore, creatine synergized the antitumor efficacy of LNP-Gsdme. Our observations in this study elucidate the effect and mechanisms of LNP-Gsdme in reshaping tumor immune microenvironment, providing novel insights and therapeutic approach into cancer therapy.

overall_design: To explore the underlying mechanisms of the tumor immune microenvironment reshaping after LNP-Gsdme treatment, CD11b+ Ly6Chi Ly6G- monocytes were sorted from B16F10-mCherry tumor models. RNA sequencing was performed to unveil the global changes of gene expression and functional status of tumor-infiltrating monocytes after LNP-Gsdme treatment.


title: The Capicua-Ataxin 1L DNA Binding Transcriptional Repressor Complex Serves as a Gatekeepers of Cell Autonomous Antiviral Responses[Human ATAC-Seq]

overall_design: To assess changes in chormatin accessibility following IAV infection, WT and CICKO epithelial cells were infected with IAV or mock for 24 hours and cells for harvested and processed for ATAC-Seq.


title: The HDL-Mimetic Peptide 4F Mitigates Vascular and Cortical Amyloid Pathology and Associated Neuroinflammation in a Transgenic Mouse Model of Cerebral Amyloid  Angiopathy and Alzheimer’s Disease

city: Minneapolis

first: Ling

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

summary: Alzheimer's disease (AD) is the most common cause of age-related dementia worldwide with limited effective treatments. Cerebral amyloid angiopathy (CAA) is one of the key pathological hallmarks of AD characterized by amyloid-β (Aβ) deposition in the cerebral vasculature and is associated with intracerebral hemorrhage, cerebrovascular dysfunction, and cognitive impairment. CAA is also considered to underlie the main adverse effect of anti-Aβ immunotherapies, the amyloid-related imaging abnormalities (ARIA). Substantial evidence from clinical and animal studies has shown that elevated levels of high-density lipoprotein (HDL), and its main protein component, apolipoprotein (APO) A-I, are associated with reduced CAA and superior cognitive function. 4F is an APOA-I/HDL-mimetic peptide that has advanced into clinical trials for cardiovascular diseases. The present study aimed to investigate whether treatment with the HDL mimetic peptide 4F modulates CAA and associated cognitive deficits and neuropathologies in the well-established transgenic Tg-SwDI mouse model of CAA/AD. Age- and sex-matched Tg-SwDI mice received daily treatments of 4F or vehicle (PBS), respectively, by intraperitoneal injections for 12 weeks. The results showed that the 4F treatment reduced CAA as well as overall Aβ plaque deposition, and attenuated microgliosis associated with CAA. Unbiased brain transcriptomic analysis revealed a heightened inflammatory state in the brain of SwDI mice, and that 4F treatment reversed the overactivation of vascular cells, in particular vascular smooth muscle cells, relieving cerebrovascular inflammation in CAA/AD mice. Our study provides experimental evidence for the therapeutic potential of 4F to mitigate CAA and its associated pathogenic processes in AD, including ARIA.

overall_design: We conducted bulk mRNA-seq to investigate the transcriptomic changes associated with cerebral amyloid angiopathy (CAA) in Tg-SwDI mice compared to wild-type mice and to evaluate the effect of 4F treatment in Tg-SwDI mice. RNA-Seq data were collected from the brains of 15 mice (8 males and 7 females) following 12 weeks of daily 4F or vehicle treatment. Sequencing was performed using the Illumina NovaSeq 6000 platform, generating 20 million reads per sample on a 150-bp paired-end run.

first: Rui

last: Zhong

first: Dustin

last: Chernick

first: David

last: Hottman

first: Yejun

last: Tan


title: The Capicua-Ataxin 1L DNA Binding Transcriptional Repressor Complex Serves as a Gatekeepers of Cell Autonomous Antiviral Responses[Human RNA-Seq]

overall_design: To assess changes in mRNA expression following IAV infection, WT and CIC KO A549 cells were infected with mock or H1N1 PR8 strain (MOI=5) for 16hrs. Total RNA was isolated using TRIzol reagent as per the manufacturer's recommendations and RNA-Seq analysis was performed.


title: Loss of an extensive ciliary connectome induces proteostasis and cell fate switching in a severe motile ciliopathy

city: St Louis

first: Amjad

last: Horani

address: 660S Euclid Ave

institute: Washington University

summary: CCDC39 is a motile cilia protein associated with primary ciliary dyskinesia. We used single cell RNA sequencing (scRNA-seq) to analyze the changes in cells types and gene expression profile of subjects with variants in CCDC39  compared to healthy individuals

overall_design: Airway cells were isolated and diffrentiated using Air-liquid phase conditions, and analyzed using scRNAseq.

first: Steven

last: Brody

first: Jiehong

last: Pan

first: Tao

last: Huang

first: Jian

last: Xu

first: Huihui

first: Jeffrey

last: Koenitizer

middle: K

last: Brennan

first: Rashmi

last: Nanjundappa

first: Thomas

last: Saba

first: Nisreem

last: Rumman

first: Andrew

last: Berical

first: Finn

middle: J

last: Hawkins

first: Xiangli

last: Wang

last: Zhang

first: Moe

last: Mahjoub

first: Susan

last: Dutcher


title: CRP-seq: a reliable and fast method for sequencing RNA G-quadruplexes transcriptome-wide

city: Nanjing

last: Shentong

address: Wei Gang Number1

institute: Nanjing Agricultural Unversity

summary: We report here on CRP-seq, followed by chemical-affinity capture with the G4-specific small-molecule, COL and target identification using sequencing. Our method can enrich G4 targets by centrifugation without magnetic bead, which allows for assessing the prevalence of RNA G4s in the transcriptome of human cells in a straightforward manner. Compared with BG4-RIP-seq, CORP-seq shines by its simplicity and practical convenience, which thus advances G4 sequencing further and addresses unmet needs in the field of G4omics.

overall_design: Two COL-enriched samples and two input control for three different conditions (Untreated, Li-treated, and K-treated) with 1 μg RNA input. We take CMS as control group for CRP-seq with 1 μg RNA input. To verify CRP-seq feasibility, we take two BG4-enrcihed samples,two flag and two input control. For the dosage of input RNA for sequencing, CRP-seq IP groups uses 1 μg and 500 ng RNA and BG4-seq IP groups empolys 10 μg and 1 μg RNA.

first: Shijiong

last: Wei

first: Xiaobo

first: Yilong

last: Feng

first: Shentong

last: Tao

first: Dehui

last: Qiu

first: Xinrong

last: Yan

first: Guangming

last: Li

first: Lionel

last: Guittat

first: Wenli

first: David

last: Monchaud

first: Jean-Louis

last: Mergny

first: Huangxian

last: Ju

first: Jun

last: Zhou


title: MiR-7a-Klf4 axis as a regulator and therapeutic target of neuroinflammation and ferroptosis in Alzheimer's disease

city: Bengaluru

first: Thimmaiah

last: Govindaraju

state: India

address: Jakkur

department: New Chemistry Unit

country: India

institute: JNCASR

summary: The miRNA expression profiling of annotated miRNA in wild type and APP/PSEN1 Tg mouse brain tissue

overall_design: The total RNA was extracted from cortex and hippocampus of WT and APP/PSEN1 Tg mouse model and subjcetd to miRNA expression profiling of annotated miRNA by Nanostring platform using nCounter Mouse v1 miRNA Panel (NS_M_miR_v1.5) having 599 unique miRNA barcodes for endogenous miRNA.

first: Madhu

last: Ramesh


title: Effects of prenatal maternal immune activation and exposure to circadian disruption during adolescence: exploring the two-hit model of neurodevelopmental disorders

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

summary:
Background: Around 80% of individuals with neurodevelopmental disorders (NDDs) such as schizophrenia and autism spectrum disorders experience disruptions in sleep/circadian rhythms. We explored whether prenatal infection, an established risk factor for NDDs, and environmental circadian disruption synergistically induced sex-specific deficits in mice.
Methods: A maternal immune activation (MIA) protocol was used by injecting pregnant mice with a viral mimic poly IC (9.5) or saline. Then, juvenile/adolescent offspring (3-7 weeks old) were subjected to either standard lighting (12:12LD) or constant light (LL).
Results: We found interactions of the two factors on behaviors related to cognition, anxiety, and sociability. Notably, poly IC exposure led to a more activated profile of hippocampal microglia in males only, while LL diminished these effects. Using RNA sequencing in the dorsal hippocampus, we found that poly IC exposure led to several differentially expressed genes in males (but not females), and fewer differential expressed genes were observed after LL exposure in both sexes. Using the WGCNA analysis, we found that modules of co-expressed genes associated with LL were enriched for pathways involved in synaptic transmission and vesicle mediated transport. Not only were many of these genes related to sleep/circadian rhythms and NDDs in humans, but they were also related to neurotransmission, suggesting that LL exerts its effects by disrupting the expression of proteins required for efficient neurotransmitter release.
Conclusions: Understanding the link between circadian disruption and MIA is crucial for NDD due to the widespread exposure to environmental circadian disruption in society and the high transmission of viral infections among pregnant individuals.

overall_design: Mice exposed to the viral mimetic poly I:C (polyinosinic:polycytidylic acid) on day GD9. Then, juvenile/adolescent offspring (3 weeks old) were subjected to either standard lighting (12:12LD) or constant light (LL) for 4 weeks. RNA-Seq was performed on 4 males and 4 females per treatment (MIA-exposed and saline-exposed) per lighting condition (12:12LD, LL).

first: Tara

last: Delorme

first: Danusa

middle: M

last: Arcego

first: Danae

last: Penichet

first: Nikki

last: Huebener

first: Patrícia

last: Silveira

first: Lalit

last: Srivastava

first: Nicolas

last: Cermakian


title: Gene expression profile at single cell level of the whole aorta from human.

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

summary: To comprehensively study molecular alterations in human aorta tissues,we characterized the cellular heterogeneity of the human aortic wall by performing scRNAseq.

overall_design:
We obtained nondiseased ascending aortic wall tissue from 1 heart transplant recipients and 2 heart donor and aortic wall tissue from 3 abdominal aortic aneurysm patients(AAA),3 aortic dissection patients (AD),1 Marfan syndrome patients (MFS)
NOTE FROM SUBMITTER: We cannot provide the raw data files due to patient privacy issue

first: Xiao

last: Xiaoyong

first: Liu

last: Xincheng


title: Improve cellular fitness of human stem cell-derived islets under hypoxia

city: Cambridge

first: Shlomi

middle: B

last: Brielle

state: MA

address: 7 Divinity Ave, Sherman Fairchild 361, Harvard University, HSCRB

department: Harvard Department of Stem Cell and Regenerative Biology

institute: Harvard University

summary: Stem cell-derived islet (SC-islet) cell therapy holds immense potential for the treatment of Type 1 Diabetes. However, low oxygen supply leads to cell dysfunction post-transplantation, especially in subcutaneous spaces and encapsulation devices. The response of SC-islets to hypoxia and effective strategies to alleviate its detrimental effects remain poorly understood. This study investigates the impact of hypoxia on SC-islets and elucidate the dynamics of hypoxia-induced stress. We performed transcriptional profiling of human SC-islets exposed to hypoxic conditions, and drew the transcriptomic and epigenetic profiles of single cells. Our findings demonstrate that β cells within SC-islets gradually undergo a decline in cell identity and metabolic function in response to hypoxia. The loss of expression from immediate early genes, specifically EGR1, FOS, and JUN, results in the downregulation of key transcription factors (TFs) that are essential for maintaining SC-islet cell identity under hypoxic conditions. By comparing SC-islets under low and high oxygen conditions, we identified genes that play a role in maintaining the fitness of SC-islets in a low-oxygen environment. Notably, the expression of EDN3, a potent vasoconstrictor gene that is enriched in native pancreatic β cells, significantly aids in preserving β cell identity under hypoxic conditions. Elevated expression of EDN3 in SC-islets effectively mitigated the deleterious effects of hypoxia by modulating genes involved in SC-islet maturation including genes associated with glucose sensing and regulation in β cells. These insights improve the understanding of SC-islets under hypoxic conditions, offering a potential point of intervention for future clinical applications in the treatment of Type 1 Diabetes

overall_design: Human embryonic stem cell maintenance and differentiation was carried out with Human Embryonic Stem Cells 8 (HUES8) as previously described 33. SC-islet cell differentiations were initiated 72 h after initial passage by aspirating mTeSR1 (STEMCELL Technologies, 85850) and replenished with stage- and day-specific media supplemented with the appropriate small molecules or growth factors as previously described. SC-islets after enrichment and reaggregation were maintained in 30 mL dispensable bioreactor to ensure gas equilibration and cultured in incubators (Eppendorf, C170i) with three different oxygen tensions-21%, 5% and 2% O2. All cell culture was maintained in a humidified incubator at 5% CO2 and 37 °C. Tissue culture incubators were adapted to maintain different oxygen tensions. A nitrogen compressor was used to pulse N2 into incubators with a feedback loop to maintain the specified oxygen tension. All tissue culture handling was done outside of hypoxia incubators (at environmental oxygen tensions of 21% O2). Enriched SC-islets were fed with fresh S6 medium before hypoxia challenge and every other day during hypoxic incubation.

first: Xi

last: Wang

first: Doug

last: Melton


title: In vitro patrolling monocytes in DLL cultures have similar gene expression profiles to their blood and bone marrow counterparts.

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

summary: Patrolling monocytes (pMos) scavenge debris from vessel walls, mediate antibody dependent cellular-cytotoxicity (ADCC) and -phagocytosis (ADCP), and recruit natural killer cells to tumors. Pmos are therefore attractive cell therapy candidates to treat Alzheimer’s disease, atherosclerosis and cancers. However, protocols to generate large numbers of pMos currently do not exist. To address this, we developed a two-step procedure to produce large numbers of pMos in vitro. We optimized cytokine combinations to facilitate (1) myeloid progenitor expansion from murine bone marrow (BM) over day 1-4, and (2) pMos development on a monolayer expressing DLL1 from day 5-12. In vitro pMos development depended on BM progenitors and Notch signaling, and the pMos expressed Nur77 and canonical pMos surface markers. Bulk RNA sequencing revealed that in vitro pMos expressed pMos genes, including Nr4a1 (Nur77), Cx3cr1, Itgax (CD11c), Fcgr4, and Cd274 (PD-L1), and their gene signatures clustered closely with blood and BM pMos. Further, in vitro pMos, but not cMos, performed ADCP on breast cancer cells, indicating that they reflect circulating cMos and pMos. Importantly, when cultured pMos were adoptively transferred into mice, they maintained a pMos phenotype and homed to blood and vascular organs such as the lungs and liver. The ability to propagate large numbers of functionally competent pMos, that can be transferred into mice will facilitate in vitro and in vivo studies of pMos biology and therapies.

overall_design: RNA-seq study of mouse in vitro monocyte subsets (cMos, intMos, cMos) with 3 replicates per subset.

first: Jessica

middle: A

last: Silva

first: Kenneth

middle: W

last: Harder


title: Siglec-1−/FSClow alveolar macrophages exhibit pro-inflammatory phenotypes in chronic obstructive pulmonary disease

city: Sendai

first: Takuya

last: Saito

state: Miyagi

address: 1-1 Seiryomachi, Aobaku

department: Department of Respiratory Medicine

institute: Tohoku University Graduate School of Medicine

summary: Alveolar macrophages (AMs) in patients with chronic obstructive pulmonary disease (COPD) orchestrate persistent inflammation in the airway, however, sub-populations of alveolar macrophages predominantly participating in chronic inflammation have been poorly characterised. We recently reported that Siglec-1 was involved in recognition and engulfment of non-typeable Haemophilus influenzae and that the expression of Siglec-1 on AMs was decreased in COPD lung tissues. Here, based on the expression of Siglec-1 and the intensity of forward scattergram (FSC) using flow cytometry, we identified three subsets present in alveolar macrophages: Siglec-1+/FSChi, Siglec-1−/FSChi, Siglec-1−/FSClow subsets. The Siglec-1−/FSClow subset increased in number in the lungs of COPD subjects. RNA-sequencing revealed that the Siglec-1−/FSClow subset exhibited pro-inflammatory and protease-producing phenotypes compared to other two subsets. Clinically, a decrease in the intensity of Siglec-1 expression in macrophages of induced sputum from COPD subjects was correlated with exacerbation rates in prospective four years. Collectively Siglec-1− AMs showed the pro-inflammatory properties and that their emergence in COPD airways was a risk factor in exacerbation. The Siglec-1−/FSClow subset might serve as “pathogenic macrophages” which could lead to poor clinical outcomes for patients with COPD

overall_design: Examination of monocytes and AMs in control never smoker (CNS), control ex-smoker (CES) and COPD patient

first: Naoya

last: Fujino

first: Yoshinao

last: Ono

first: Mitsuhiro

last: Yamada

first: Hisatoshi

last: Sugiura


title: Aberrant super-enhancer landscape in enzalutamide-resistant prostate cancer cells

first: Qinwei

last: Liu

address: kangda road 1

institute: First Affiliated Hospital Of Guangzhou Medical University

summary: Background: Castration-resistant prostate cancer (CRPC), which has developed resistance to next-generation antiandrogens such as enzalutamide (Enz), is a lethal disease. Furthermore, transcriptional regulation by super enhancers (SEs) are crucial for the growth and spread of prostate cancer, as well as drug resistance. The functions of SEs, a significant class of noncoding DNA cis-regulatory elements, have been the subject of numerous recent studies in the field of cancer research.  Methods: The goal of this research was to identify SEs associated with Enz resistance in C4-2B cells using chromatin immunoprecipitation-sequencing and cleavage under targets and tagmentation (CUT&Tag). Using HOMER analysis to predict protein-gene binding motifs, we identified master transcription factors (TFs) that may bind to SE sites. Using small interfering RNA, WST-1 assays, and qRT-PCR, we then confirmed the associations between TFs of SEs and Enz resistance.  Results: 999 SEs were screened from C4-2B EnzR cells in total. Incorporating analysis with RNA-seq data revealed 46 SEs to be strongly associated with the promotion of Enz resistance. Additionally, we finally predicted that master TFs bind to SEs binding regions. Subsequently, we selected zinc finger protein 467 (ZFP467) and SMAD family member 3 (SMAD3) to confirm the functional connections of master TFs with Enz resistance via SEs (ZNF467).   Conclusions: In this study, SMAD3 and ZNF467 found to be closely related to Enz-resistant in CRPC. Our research uncovered a sizable group of SEs linked to Enz resistance in prostate cancer, dissected the mechanisms underlying SE Enz resistance, and shed light on potential clinical uses for SEs.

overall_design: The super enhancers of C42B enzalutamide-resistant prostate cancer cell lines were analyzed by CUT & Tag sequencing.

first: Jianming

last: Lu


title: Myeloid FtH deficiency accelerates kidney disease by inducing Snca and ferroptosis [Baseline WT-KO]

status: Public on Mar 23 2025

city: Birmingham

first: Abolfazl

last: Zarjou

state: AL

address: 618 Zeigler Research Building, 703 South 19th Street

department: Medicine

institute: University of Alabama at Birmingham

summary: To investigate impact of myeloid ferritin heavy chain (FtH) deletion in kidney iron metabolism under baseline conditions, we performed bulk RNA sequencing on kidney tissues from FtHfl/fl (wild-type) and FtHΔ/Δ (myeloid-specific FtH-deficient) mice.

overall_design: Total RNA was isolated from kidney using Trizol from wild-type (FtHfl/fl) n=4 and myeloid specific FtH deficient (FtHΔ/Δ) n=4 mice under quiescent conditions. We then perfomed gene expression profilling analysis using RNA -Seq

first: Tanima

last: Chatterjee

first: Sarah

middle: E

last: Machado

first: Kellen

last: Cowen

first: Mary

last: Miller


title: Gene expression analysis of N1E-115 cells using RNA-seq

city: Hachioji

first: Hideji

last: Yako

address: 1432-1, Horinouchi

institute: Tokyo University of Farmacy and Life Science

summary: To evaluate the characterisation of N1E-115 neuroblast cells, we conducted the comprehensive gene expression in the N1E-115 cells using RNA-seq.

overall_design: RNA-seq profiling of N1E-115 cells of growth cultured condition.

first: Junji

last: Yamauchi


title: Chondroitin sulfate N-acetylgalactosaminyltransferase 1 promotes the progression of renal fibrosis mediated by versican 1 in mouse remnant kidney

city: Niigata

first: Yuya

last: Suzuki

address: 1-757 Asahimachi, Chuo-ku, Niigata

institute: Niigata university

summary: Aim: Renal fibrosis is a final common pathway for progressive chronic kidney diseases. Immune cell infiltration and production of tumor growth factor-β (TGF-β) are essential factors for fibrosis development. We examined the role of chondroitin sulfate (CS) proteoglycan, which is one of the main extracellular matrix components induced by TGF-β signaling. We also examined CS N-acetylgalactosaminyltransferase 1 (T1), an enzyme that catalyzes the first step of CS-specific synthesis. Methods: T1-/- mice, genetically lacking T1, and T1+/+ mice underwent 5/6 nephrectomy (Nx) or sham operation. Kidney function, urine marker, mRNA expression, and TGF-β signaling were evaluated 1 month after Nx or sham operation. Renal fibrotic area was quantified 3 months later. Results: Both T1+/+ and T1-/- mice with Nx showed equivalent loss of kidney function, however, a tubular damage marker, upregulation of TGF-β and collagen expression, and renal fibrosis were suppressed in T1-/- mice with Nx. Versican, one of the core proteins of CS proteoglycan, was exclusively upregulated in T1+/+ mice with Nx. Among the versican splicing variants, versican 1 (V1) was expressed in the medullary interstitium of the remnant kidney in T1+/+ mice. V1 was produced in the interstitial macrophages, fibroblasts/myofibroblasts, and endothelial cells, whereas TGF-β was expressed in endothelial cells. Phosphorylation of the TGF-β signaling molecules Smad2/3 was not induced in T1-/- mice with Nx. In vivo administration of TGF-β inhibitor into Nx mice reduced V1 and Tgfb expression. Conclusion: T1 was essential for the initial induction of V1 upregulation,  effective TGF-β signaling, and subsequent renal fibrosis.

overall_design: Eleven-week-old male T1+/+ mice underwent five-sixth nephrectomy. Briefly, the right kidney was exposed through a flank incision and removed. After a week, the left kidney was exposed and the upper and lower poles were ligated with a 3-0 non-absorbable suture until the coil diameter was half of the kidney. For control animals (sham), each flank of the kidney underwent sham surgery by incising flanks, exposing the kidney, and suturing each flank. Four weeks after surgery, the mice were sacrificed under anesthesia to collect kidney samples.  Each single nucleus was captured using the Chromium System (10x Genomics) from frozen kidney samples for single-nucleus RNA sequencing.

first: Yoshikatsu

last: Kaneko

first: Kaho

last: Sato

first: Kosei

last: Takeuchi

first: Michihiro

last: Igarashi

first: Ichiei

last: Narita


title: Fabp4 is Essential for the Maintenance of Leukemia Stem Cells while Sparing Hematopoietic Stem Cells

city: changsha

first: Cheng

last: Xing

state: Hunan Province

address: Department of Hematology, the Second Xiangya Hospital, Central South University,

department: Department of Hematology

summary: Fatty acid-binding protein 4 (FABP4) plays a crucial role in the uptake, transport, and metabolic regulation of fatty acids. Previous research has found that the abnormal expression of FABP4 is associated with certain cancers, and it may become a new target for tumor therapy. We discovered that a haploinsufficient or absent dosage of Fabp4 does not affect the function of hematopoietic stem cells in mice, but significantly impacts the maintenance of leukemia stem cells (LSC). Our findings indicate that while Fabp4 does not influence the  initiation of acute myeloid leukemia (AML) transformed by MLL-AF9 (MA9) in mice, it markedly promotes the progression of AML. A haploinsufficient or absent dosage of Fabp4 significantly extends the survival time of MA9 mice. Our research reveals the key role and mechanism of Fabp4 in MA9-LSC, suggesting that Fabp4 is a potential target for selectively eliminating MLL-rearranged leukemia.

overall_design: Three murine bone marrow samples, each a mixture of bone marrow cells from two wild-type, two heterozygous knockout, and two homozygous knockout mice for Fabp4.


title: Mitochondrial HSP90 is involved in cellular physiology

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: We generated TRAP1 KO in HeLa and observed extensive transcriptional reprogramming. The KO does not activate the canonical heat-shock response but an alternate transcriptional response.

overall_design: Examination of transcriptional changes upon TRAP1 knock-down

first: Erik

last: Hansen

first: Ritwick

last: Sawarkar

first: Len

last: Neckers


title: Genome-scale DNA methylome and transcriptome profiles of early prostate cancer recurrence after prostatectomy [RNA-seq]

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: Prostate cancer (PCa) is a major health burden world-wide and despite early treatment, a very large proportion of patients present with biochemical recurrence (BCR) post-treatment, reflected by a rise in PSA over a clinical threshold. Novel transcriptomic and epigenomic biomarkers can provide a powerful tool for clinical management of PCa. Here we provide matched RNA-Sequencing and array-based genome-wide DNA methylome data of PCa patients (n = 17) with, or without, evidence of BCR following early radical prostatectomy. We have utilized Formalin-Fixed Paraffin-Embedded tissues to generate this data and included technical replicates to provide further validity of the data. We describe the sample features, experimental design, methods and bioinformatic pipeline for processing these multi-omic data. Importantly, we provide comprehensive clinical, histopathological, and follow-up data for each patient to enable correlating transcriptome and methylome features with clinical features. Our data will contribute towards the efforts of developing epigenomic and transcriptomic markers for BCR and also facilitate a deeper understanding of the molecular basis of PCa recurrence.

overall_design: Herein we aimed to generate the methylomic and transcriptomic profiles of PCa patients with, or without, evidence of BCR following early radical prostatectomy. DNA and RNA was extracted from FFPE tissues from a cohort of 17 radical prostatectomy patients.  We have generated matched, high-depth, genome-scale profiles of the DNA methylome (MethylationEPIC v2.0 array) and RNA transcriptome (RNA-Seq). Six samples showed a mean detection p-value >0.05 and hence were not considered for MethylationEPIC v2.0 array analysis. Additionally, we have also added technical replicates for methylome and RNA-Seq samples for assessing reproducibility.

first: Jim

last: Smith

first: Euan

last: Rodger


title: Highly cross-reactive and competent effectors dominate the CD8+ T cell response in Trypanosoma cruzi infection

city: Philadelphia

first: Molly

last: Bunkofske

state: Pennsylvania

address: 380 S University Ave

institute: University of Pennsylvania

summary: CD8+ T cells are key effectors in immune control of Trypanosoma cruzi infection. Within C57BL/6 mice, the T. cruzi-specific CD8+ T cell response is higly focused on several immunodominant epitopes including TSKb20. These immunodominant epitopes all elicit non-protective T cell responses that are entirely dispensable for immune control, suggesting that other, subdominant CD8+ T cells of unknown specificities might play an important role in mediating parasite control. We assessed the relative effector capacity of TSKb20 T cells compared to other responding T cells at the site of reinfection using paired scRNA and TCR sequencing to evaluate the gene expression profiles of particular T cell clonotypes.

overall_design: Chronic T. cruzi-infected (336 dpi) Nur77-GFP reporter mice were reinfected in the muscle and then T cells were isolated from the site (13 days post reinfection) for assessment of their gene expression via paired scRNA-seq and TCR-seq. TSKb20 tetramer bound and TCR-activated (based on Nur77-GFP reporter expression) CD8+ T cell populations from 5 individual mice were each isolated, sorted, and then combined for library preparation.

first: Rick

last: Tarleton


title: Forced expression of MSR repeat transcripts breaks heterochromatin organization

city: Freiburg im Breisgau

first: Galina

last: Erikson

summary: Mouse heterochromatin is characterized by transcriptionally competent major satellite repeat (MSR) sequences and it has been proposed that MSR repeat RNA contributes to the integrity of heterochromatin. We established an inducible dCas9-effector system in mouse embryonic fibroblasts, where we can target dCas9-VPR (transcriptional activator) and dCas9-KM (transcriptional repressor) to MSR repeat sequences. We show that induction of dCas9-VPR forces significant MSR RNA output, while induction of dCas9-KM silences MSR transcription. Both approaches perturb heterochromatin organization, where the dCas9-VPR leads to an immediate dispersion of heterochromatin and dCas9-KM induction results in a delayed aggregation of heterochromatin. MEF cells with the forced expression of MSR RNA are not viable and the defects in heterochromatin organization cannot be reverted. This study highlights the importance of restricting MSR RNA output to maintain heterochromatin integrity and also reveals that the structural organization of heterochromatin is governed by the transcriptional state of the underlying MSR repeats.

overall_design: To investigate the effect of modulating MSR repeat transcription on repeat dysregulation genomewide. MEF cell lines were created where chromatin effectors can be inducibly expressed. These chromatin effectors are targeted to MSR repeats utilizing the CRISPR/dCas9 system: dCas9-control, dCas9-KM (transcriptional repressor), dCas9-VPR (transcriptional activator).

first: Reagan

last: Ching

first: Thomas

last: Jenuwein


title: Genome-scale DNA methylome and transcriptome profiles of early prostate cancer recurrence after prostatectomy

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: RNA-seq data from naturally-occurring early canine urothelial carcinoma detected through screening of dogs in a high-risk breed (Scottish Terriers)

city: West Lafayette

first: Deborah

last: Knapp

address: 625 Harrison Street

institute: Purdue University

summary: Screening for urinary bladder cancer was performed in dogs in a breed (Scottish Terriers) with a very high inherited risk for bladder cancer. Naturally-occurring urothelial carcinoma in dogs serves as a relevant model for muscle invasive bladder cancer in humans. Urothelial carcinoma was detected in dogs with no outward evidence of the cancer. RNAseq data analyses were performed on these "early" tumors, and the sequencing files are included here. RNA-seq data from additional dogs has been deposited in the NCI Integrated Canine Data Commons (ICDC UBC02).

overall_design: Dogs were screened for bladder cancer with urinalysis and ultrasonography. Cystoscopic biopsies were collected from dogs wtih positive screening tests.

first: Deepika

last: Dhawan

first: Sagar

last: Utturkar

first: Jose

last: Ramos-Vara


title: Low initial cell density promotes the differentiation and maturation of human pluripotent stem cells into erythrocytes

city: beijing

first: qian

last: dong

address: No. 27 Taiping Road ，Haidian Distric

institute: Beijing Institute of Radiation Medicine

summary: Human pluripotent stem cell (hPSC)-derived red blood cells (RBCs) possess great potential for compensating for shortages in transfusion medicine. For better RBC generation from hPSCs, we compared the cell seeding density in the embryoid body formation-based hPSC induction protocol. In the selection of low- and high-density inoculation conditions, we found that low-density culture performed better in the final RBC product with more cell output and increased average cellular hemoglobin content. An elaborate study using flow cytometry demonstrated that low inoculation density promoted endothelial-to-hematopoietic transition, followed by improved hematopoietic progenitor formation and erythrocyte generation. The improved transformation from glycolysis to mitochondrial oxidation and reduced apoptosis might be responsible for this effect. Hints from RNA sequencing suggested that molecules involved in microenvironment interaction and metabolic regulation might respond for the different developmental potential. One of the possible mediators between outer message and intracellular response could be the nutrition sensors FOXO, PRKAA1 (AMPK) and MTOR genes. It is possible that low inoculation density triggered metabolic regulation signals, promoted mitochondrial oxidation, and resulted in enhanced cell amplification and hematopoietic differentiation. The low cell culture density will improve RBC generation from human PSCs.

overall_design:
To investigate the impact of human pluripotent stem cell seeding density on erythroid differentiation and metabolism of these cells, we seeded human embryonic stem cell H1 by 6×105/well and 2×105/well for each well of a 6-well-plate, induced these cells towards erythroid cells by step-wise induction.
Comparative gene expression profiling analysis of RNA-seq data for 2×105 seeding group and its control 6×105 seeding group.
Cells derived from different seeding density (6×105/well and 2×105/well) hESCs were harvested by erythroid induction day 6 and day 15. We then performed gene expression profiling alalysis using data obtained from RNA-seq of 2 different seeding desnity at two time points.

first: Xiaoyan

last: Xie

first: Liqing

last: Liang

first: Lei

last: Xu

first: Qian

last: Dong


title: FBXO44 Regulates Rac1 Spatiotemporal Dynamics: An Exploitable Therapeutic Vulnerability for Actin Cytoskeleton-Targeted Treatment in Gastric Cancer

status: Public on Mar 22 2025

city: Hangzhou

first: Guangzhao

last: Pan

address: Dongfang street

department: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences

summary: The dynamic homeostasis of the cytoskeleton represents a critical vulnerability in tumor cells, yet the molecular mechanisms governing this equilibrium remain elusive. In the present study, we identify FBXO44 as a crucial regulator of Rac1 nucleocytoplasmic shuttling through its interaction with MTSS1. In gastric cancer (GC), FBXO44 orchestrates dual ubiquitination programs on MTSS1: K63-linked polyubiquitination promotes Rac1 nuclear translocation to drive cytoskeletal remodeling, whereas K11-linked modification triggers MTSS1 proteasomal degradation to restrict Rac1 nuclear trafficking. Structural analysis reveals that FBXO44 engages MTSS1 through distinct domains, dynamically balancing these opposing ubiquitination events through precise control MTSS1 protein levels, thereby calibrating actin cytoskeletal dynamics. Clinically, this regulatory axis maintains an oncogenic equilibrium-FBXO44 overexpression correlates with Rac1 signaling activation in progressive GC patients. Therapeutically, pharmacological disruption of this balance using the novel inhibitor DQ2405 achieves dual anti-tumor effects: suppressing tumor growth and metastatic capacity. Our findings establish FBXO44-mediated Rac1 spatiotemporal control as a druggable strategy for actin-cytoskeleton targeted therapy, providing both mechanistic insights into cytoskeletal homeostasis and a translational framework for GC treatment.

overall_design: RNA-sequencing (RNA-seq) of MKN74 cells expressing MTSS1 to reveal its molecular effects on host cells.

first: Qianqian