title: Transcriptome analysis of Streptococcus mutans planktonic cells deficient in the DpnII restriction-modification system

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

country: Canada

institute: Faculty of Dentistry, University of Toronto

summary: Human pathogens use cell-cell communication systems, quorum sensing, to regulate virulence factors. Our recent work aiming at deciphering the quorum sensing regulon of Streptococcus mutans, a caries pathogen, revealed a locus encoding an atypical type II restriction-modification (R-M) system, DpnII, comprising two adenine methyltransferases. A recent survey of bacterial genomes demonstrated the widespread occurrence of methylated DNA, and the importance of DNA methylation was highlighted by the diverse processes in which they function. The present study aimed at deciphering the role of DNA methylation during S. mutans planktonic growth. A mutant strain, deficient in the DpnII R-M locus composed of the SMU.504 and SMU.505 genes encoding the two adenine methyltransferases and the SMU.506 gene encoding the DpnII restriction enzyme, was constructed in S. mutans wild-type (WT) strain. Transcriptome analysis was then performed to evaluate the differential planktonic gene expression between the WT cells and the DpnII R-M deficient cells.

overall_design: S. mutans cells deficient in the DpnII R-M locus were grown in THYE broth for 20 hours at 37°C in the presence of 5% CO2.  The gene expression profiling of the DpnII R-M mutant cells was compared to the one of the WT cells.

first: Haowei

last: Zhao

first: Celine

last: Levesque


title: FBXW7/GSK3β-mediated degradation of PRR11 inhibits RCC progression via oxidative DNA damage

status: Public on Mar 19 2025

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

country: China

institute: Zhongnan Hospital of Wuhan University

type: Expression profiling by high throughput sequencing

summary: In our previous study, we reported that proline-rich 11 (PRR11) expression is upregulated in renal cell carcinoma (RCC) and is involved in the regulation of cell cycle and apoptosis.  Here, we continued to investigate the pro-carcinogenic role of PRR11 and found that PRR11 regulates oxidative DNA damage via activation of the AKT pathway, which promotes the proliferation and migration of RCC.  Mechanistically, GSK3β recognizes and phosphorylates the CPD motif of PRR11, followed by FBXW7 binding to PRR11 and promoting its K48-linked ubiquitination and degradation via the CPD motif of PRR11.  In addition, PRR11 can inhibit GSK3β activity via activation of AKT signaling, which in turn prevents the formation of PRR11-phosphorylated CPDs, thereby preventing FBXW7-mediated ubiquitination and degradation of PRR11.  This PRR11-AKT interaction establishes a positive feedback loop that continually strengthens the expression of both and accelerates the progression of RCC.  Overall, we reveal the specific mechanism by which FBXW7-GSK3β targets PRR11 degradation in RCC and PRR11 affects RCC proliferation and migration by regulating oxidative DNA damage, providing a new target and interventions for RCC therapy.

overall_design: To investigate the downstream mechanism of PRR11 regulation of RCC, we performed RNA sequencing on two repeated siNC and siPRR11-treated ACHN cells.

first: Siming

last: Chen

first: Xinghuan

last: Wang


title: SOX4 facilitates brown fat development and maintenance through EBF2-mediated thermogenic gene program in mice [RNA-Seq]

city: Xia men

first: luo

last: ya

address: Xiang'an South Road

institute: School of Life Sciences, Xiamen University

summary: Brown adipose tissue (BAT) is critical for non-shivering thermogenesis making it a promising therapeutical strategy to combat obesity and metabolic disease. However, the regulatory mechanisms underlying brown fat formation remain incompletely understood. Here, we found SOX4 is required for BAT development and thermogenic program. Depletion of SOX4 in BAT progenitors (Sox4-MKO) or brown adipocytes (Sox4-BKO) resulted in whitened BAT and hypothermia upon acute cold exposure. The reduced thermogenic capacity observed in Sox4-MKO mice increases their susceptibility to diet-induced obesity. Overexpression of SOX4 enhances BAT thermogenesis counteracting diet-induced obesity. Mechanistically, SOX4 activates transcription of EBF2 which determines brown fat fate. Moreover, phosphorylation of SOX4 at S235 by PKA facilitates its nuclear translocation and EBF2 transcription. Further, SOX4 cooperates with EBF2 to activate transcriptional programs governing thermogenic gene expression. These results demonstrate that SOX4 serves as an upstream regulator of EBF2 providing valuable insights into BAT development and thermogenic function maintenance.

overall_design:
In brown adipose tissue (BAT), brown fat cells consume lipid and glucose to generate heat that is crucial for maintenance of body temperature and resistance to cold-induced hypothermia in mammals.  We next wondered how Sox4 regulates development and thermogenesis of BAT, therefore we performed RNA sequencing of BAT tissues from Sox4f/f and Sox4-MKO mice.
To further investigate the direct regulation of EBF2 transcription by SOX4, we performed ChIP-seq analysis in BAT SVFs.

first: Shuai

first: Ting

last: He

first: Ya

last: Luo

first: Kexin

last: Ren

first: Huanming

last: Shen

first: Lingfeng

last: Hou

first: Yixin

last: Wei

first: Tong

last: Fu

first: Wenlong

last: Xie

first: Peng

first: Jie

last: Hu

first: Qiyuan

last: Li

first: Weihua

first: Huiling

last: Guo

first: Boan


title: Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

city: Bethesda

first: Poonam

last: Poonia

state: MD

address: 6 Center Drive, Bldg 6, Room 240

department: NICHD

country: USA

institute: NIH

summary: Poly(A)-binding protein (Pab1 in yeast) is involved in mRNA decay and translation initiation, but its molecular functions are incompletely understood. In this study, we employed a comprehensive multiomics strategy encompassing Ribosome profiling, spike-in normalized RNA-seq, SMPAT-seq, and CAGE-seq to gain mechanistic insight into Pab1's role in Saccharomyces cerevisiae. We found that auxin-induced degradation of Pab1 reduced bulk mRNA and polysome abundance in a manner suppressed by deleting the catalytic subunit of decapping enzyme (dcp2Δ), demonstrating that enhanced decapping/degradation is the major driver of reduced mRNA abundance and protein synthesis at limiting Pab1 levels. An increased median poly(A) tail length conferred by Pab1 depletion was also nullified by dcp2Δ, suggesting that mRNA isoforms with shorter tails are preferentially decapped/degraded at limiting Pab1. In contrast to findings on mammalian cells, the translational efficiencies (TEs) of many mRNAs were altered by Pab1 depletion; however, these changes were broadly diminished by dcp2∆, suggesting that reduced mRNA abundance is a major driver of translational reprogramming at limiting Pab1. Thus, assembly of the closed-loop mRNP via PABP-eIF4G interaction appears to be dispensable for normal translation of most yeast mRNAs in vivo at normal mRNA levels. Interestingly, histone mRNAs and proteins are preferentially diminished on Pab1 depletion dependent on Dcp2, accompanied by activation of internal cryptic promoters in the manner expected for reduced nucleosome occupancies, revealing a new layer of post-transcriptional control of histone gene expression.

overall_design: This study includes total 62 samples, 18 for ribosome profiling and 18 for total RNA-sequencing from triplicates cultures of WT, WT+NAA, pab1-AID, pab1-AID+NAA, dcp2∆+NAA and dcp2∆pab1-AID+NAA. Additionally, 12 samples for SMPAT-Seq using the same total RNA from WT+NAA, pab1-AID+NAA, dcp2∆+NAA and dcp2∆pab1-AID+NAA in triplicates. Additionally, the same total RNA in triplicates for WT+NAA, pab1-AID+NAA (6 samples) and total RNA in duplicates from spt6-1004, isogenic SPT6 WT, set1∆set1∆ and isogenic SET1SET2 WT (8 samples) were subjected to CAGE-sequencing. The strains WT, pab1-AID, dcp2∆ and dcp2∆pab1-AID were grown in YPD either with 1mM KOH or 1mM of 1-Napthaleneacetic acid (NAA) at 30ºC for 6h. The strains spt6-1004 mutant and isogenic WT, were cultured in SC medium at 30°C and shifted to 39°C for 90 min before harvesting. For set1∆set2∆ mutant and isogenic WT strain BY4741, cells were cultured in SC medium at 30°C

first: Vishalini

last: Valabhoju

first: Tianwei

first: James

last: Iben

first: Xiao

last: Niu

first: Zhenguo

last: Lin

first: Alan

middle: G

last: Hinnebusch


title: Effect of lentiviral silencing of Rcor2 in MC3T3-E1 cells during osteoblast differentiation

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Epigenetic regulation of bone formation is a complex network of active proteins and their cofactors. Recent developments in calcified tissue research have revealed several important pathways of epigenetic regulation leading to transcriptional changes in bone cells. Rest Corepressor 2 (Rcor2) is a coregulator of Lysine-specific histone demethylase 1 (Lsd1), a demethylase linked to osteoblast activity, hematopoietic stem cell differentiation and malignancy of different neoplasms. However, the role of Rcor2 in osteoblast differentiation has not yet been examined in detail. We have previously shown that Rcor2 is highly expressed in mesenchymal stromal cells (MSC) and particularly in the osteoblastic lineage. The role of Rcor2 in osteoblastic differentiation in vitro was further characterized and we demonstrate here that lentiviral silencing of Rcor2 in MC3T3-E1 cells led to a decrease in osteoblast differentiation, as shown by decreased alkaline phosphatase and von Kossa stainings as well as by decreased expression of several osteoblast-related marker genes. RNA-sequencing of the Rcor2-downregulated MC3T3-E1 cells revealed decreased repression of Rcor2 target genes, as well as significant upregulation of majority of the differentially expressed genes. While the heterozygous, global loss of Rcor2 in vivo did not lead to a detectable bone phenotype, conditional deletion of Rcor2 in limb-bud mesenchymal cells led to a moderate decrease in cortical bone volume, which was not accentuated by challenging bone formation by ovariectomy or tibial fracture. Furthermore, a global deletion of Rcor2 led to decreased amount of white adipose tissue in vivo and decreased the capacity of primary cells to differentiate into adipocytes in vitro, while the conditional deletion led to decreased adiposity in fracture calluses. Taken together, these results suggest that epigenetic regulation of mesenchymal stromal cell differentiation is mediated by Rcor2, which could thus play an important role in defining the MSC fate.

overall_design: To study the relevance of Rcor2 upregulation during osteoblast differentiation, we silenced Rcor2 expression in MC3T3-E1 cells by stable shRNA expression.

first: Kati

last: Tarkkonen

first: Lauri

last: Saastamoinen

first: Cristina

last: Valensisi


title: ZBTB20 triggerring PI3K/AKT-NF-kappaB signaling requires the suppression of Pten

city: Xi'an

first: Xue

last: Hao

address: Shanghua Road

institute: Xi'an Honghui Hospital

summary: Better understanding of the early molecular events and underlying mechanism will benefit the early-stage diagnose and clinical therapy of OA. In this study, we demonstrated the functions of ZBTB20 in OA pathogenesis via regulating ECM homeostasis. Chondrocytes-specific depletion of Zbtb20 in adult mice attenuated DMM-induced OA progress, restored the balance of ECM anabolism and catabolism. To investigate the underlying mechanism of ZBTB20 in OA progress, RNA-seq was carried out using cultured primary chondrocytes from control and Zbtb20-cKO mice, treated by IL-1β.

overall_design: To investigate the underlying mechanism of ZBTB20 in OA progress, we performed gene expression profiles analysisusing cultured primary chondrocytes from control and Zbtb20-cKO mice, treated by IL-1β.

first: Liu

last: Yang

first: Qiang

last: Jie


title: Cardiopulmonary bypass activates classical monocytes via shear-mediated activation of Store-Operated Calcium Entry

city: Seattle

first: Weiming

state: WA

address: 4032 8th ave ne

department: Center for developmental biology and regenerative medicine

institute: Seattle children's research institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Exposure to cardiopulmonary bypass (CPB) during cardiac surgery results in a significant inflammatory response that contributes to morbidity and mortality, which is especially prominent in neonatal patients. The molecular and cellular mechanisms that underpin this inflammatory process remain poorly understood. To gain deeper insight, we performed snRNA and snATAC sequencing on peripheral blood mononuclear cells (PBMCs) isolated from neonatal CPB patients prior to start of CPB, at the end of CPB, as well as 8 and 24 hours after CPB. The dramatic increase in the proportion of classic monocytes following bypass surgery indicates their essential role in inflammation associated with cardiopulmonary bypass (CPB). Immune dysregulation exhibited at activation of inflammatory genes in classical monocytes, as well as in other cell types, after CPB exposure. A series of in vitro experiments in non-adherent monocytic cells identified two novel genes SPTAN1 and RAF1 as effectors of hemodynamic stress. These two genes promoted STIM1 coupling to ORAI1 channel leading to calcium icon influx, thereby driving inflammation and cell death. snATAC-Seq revealed dynamically changing patterns of chromatin accessibility and transcription factors JUN and FOS binding motifs being highly enriched in classical monocytes after CPB exposure. Increased calcium in turn stimulates JUN binding to DNA, as suggested by CUT&RUN data derived from shear stressed non-adherent monocytic cells. Together, these data indicate that shear stress via a calcium dependent mechanism contributes to the CPB-associated activation of classic monocytes. These findings provide deeper insight not only in the pathogenesis of CPB-associated inflammation, but also have implications for the understanding of early stages of sterile inflammation and how non-adherent cells “sense” shear stress.

overall_design:
We performed either snRNA-Seq or 10X Genomics Multiome snRNA/ATAC-Seq on samples collected from neonatal patients  prior to start of CPB, end of CPB, 8 hours after the end of CPB, and 24 hours after the end of CPB (workflow outlined in Figure 1A) to answer questions about the cell types and gene expression in an unbiased and systematic manner. PBMCs were isolated since granulocytes such as neutrophils are technically challenging to study using the 10X Genomics Multiome snRNA/ATAC-Seq pipeline.
Bulk RNA seq for sheared vs. static THP-1 cells
Bulk ATAC seq for sheared vs. static THP-1 cells
CUT&RUN for sheared vs. .static THP-1 cells

first: Lan

middle: N

last: Tu

first: Lance

last: Hsieh

first: Julian

middle: R

last: Smith

first: Yi-Ting

last: Yeh

first: Anothony

last: Sinyagin

first: Majid

last: Ghassemian

first: Andrew

last: Timms

first: Lyubomyr

last: Bohuta

first: Christina

last: Greene

first: Juan

last: Carlos del Alamo

first: Ram

last: Savan

first: Vishal

last: Nigam


title: SIRT6-dependent functional switch via K494 modifications of RE-1 Silencing Transcription factor [REST_experiment_2]

city: Beer Sheva

first: Adam

last: Zaretsky

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gutrion University of the Negev

summary: RE-1 Silencing Transcription factor (REST) is a key repressor of neural genesREST functions as a key factor for cell differentiation, repressing neural genes in non-neural somatic tissues. REST is upregulated under stress signals, aging, and neurodegenerative diseases, but loses its function in Alzheimer's Disease. However, why it becomes inactive remains unclear. Here we show that the NAD-dependent deacetylase SIRT6 regulates REST expression, location, and activity. In SIRT6 absence, REST is overexpressed, but mis localized and inactive. SIRT6 deficiency abrogates REST and EZH2 interaction, perturbs its location to heterochromatin Lamin B ring, and leads to REST target gene overexpression. SIRT6 reintroduction or REST methyl-mimic K494M expression rescues this phenotype, while an acetyl-mimic mutant loses its function even in WT cells. Our studies define a novel regulatory switch, where the function of a critical repressor is regulated by post-translational modifications on K494 depending on SIRT6 existence, in turn modulating neuronal gene expression.

overall_design: ChIP-seq against endogenous human RE-1 Silencing transcription factor (REST) was performed on WT SHSY-5Y cells transfected with REST-WT, REST K494A mutant, REST K494M mutant, REST K494Q mutant, CMV-Flag (as empty vector). The experiment was conducted 3 times  (N1, N2, N3). For each replicate, ChIP was performed Avti-Flag beads. For each sample, an input sample was allocated before antibody introduction for background signal. Per replicate, 10 samples were sequenced (REST WT + Input, REST K494A + Input, REST K494M+ Input, REST K494Q+ Input, CMV-Flag+ Input)

first: Alfredo

last: Venzor

first: Dmitrii

last: Smirnov

first: Deboarh

last: Toiber


title: Targeting Vdac2 overcomes immunotherapy resistance by inducing tumor cell death and inflammation [scRNA-seq]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Uncovered IFNg signal and mitochondrial stress shaping tumor immune evasion

overall_design: We used scRNAseq to compare gene transcriptome profiles of CD45+ immune cells and tumor cells from B16-OVA-Cas9-sgNTC/sgVdac2 tumors at day 14 after tumor inoculation in C57BL/6 mice

first: Hao

last: Shi

first: Sujing

last: Yuan


title: SOX4 facilitates brown fat development and maintenance through EBF2-mediated thermogenic gene program in mice [ChIP-Seq]

first: luo

last: ya

overall_design: To further investigate the direct regulation of EBF2 transcription by SOX4, we performed ChIP-seq analysis in BAT SVFs.  We also performed ChIP-Seq to visualize the binding of SOX4 on EBF2 promoter in the presence or absence of induction medium.

first: Shuai

last: Wang

first: Ting

last: He

first: Ya

last: Luo

first: Kexin

last: Ren

first: Huanming

last: Shen

first: Lingfeng

last: Hou

first: Yixin

last: Wei

first: Tong

last: Fu

first: Wenlong

last: Xie

first: Peng

first: Jie

last: Hu

first: Qiyuan

last: Li

first: Weihua

first: Huiling

last: Guo

first: Boan


title: Chronic intermittent hypoxia inhibits the revascularization of the ischemic retina and aggravates neurodegeneration and neovascularization

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

summary: Neovascular retinopathies and edema are sign threatening complications of ischemic retinopathies, such as retinopathy of prematurity (ROP) and diabetic retinopathy (DR). Sleep apnea that leads to chronic intermittent hypoxia (CIH) is an independent risk factor for severe disease, but the underlying mechanisms are unknown. Here we show that experimental CIH during the ischemic phase of oxygen induced retinopathy in mice severely reduces beneficial revascularitzation of the ischemic retina, and increases neuronal loss and pathological neovascularization. Mechanistically we demonstrate that CIH reduces both colony stimulation factor 1 (CSF-1) expression and the ischemia-induced increase of retinal microglial cells that promotes the revascularization of the ischemic retina in the absence of CIH. Local CSF1R inhibition during ischemic retinopathy reduced the number of microglial cells, inhibited revascularization, and exacerbated pathological neovascularization, recapitulating several effects of CIH. Our findings provide a novel mechanism by which sleep apnea and CIH aggravate ischemic retinopathies, underscoring the importance of treating apnea in ROP and DR to help prevent sight threatening severe disease.

overall_design: C57BL/6J mice at postnatal (PN) day 8 (PN8) were exposed, with their mothers, for 5 days to hyperoxic conditions (75% O2), inducing vaso-obliteration and subsequent capillary loss of the central retinal vasculature known as oxygen-induced retinopathy (OIR). At PN13, mice were returned to room-air conditions which induces extensive neovascularization in all experimental mice with maximum effects on PN18 (group named OIR-Norm), or were placed in chronic intermittend hypoxia (CIH) conditions (group named OIR-CIH). Control animals (OIR-Norm) were exposed to the same flow (and noise) of gasses, without affecting O2 concentrations. Fresh eyes (3 eyes from the OIR-Norm group, 3 eyes from the OIR-CIH group, all at PN18) were dissected on ice to isolate retinas immediately after enucleation. Retinal RNA was extracted and bulk RNA sequencing was performed. OIR-Norm samples are controls and OIR-CIH samples are the experimental condition.

first: Tianxiang

last: Yang

first: Kaitryn

middle: E

last: Ronning

first: Sébastien

last: Augustin

first: Frédéric

first: Caroline

last: Nous

first: Foteini

last: Argyriou

first: Sara

last: Touhami

first: Cécile

last: Delarasse

first: Xavier

last: Guillonneau

first: Florian

last: Sennlaub


title: Targeting Vdac2 overcomes immunotherapy resistance by inducing tumor cell death and inflammation

first: Hongbo

last: Chi

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression profile of control and NGB knockdown human cerebral organoids at day 24 and 35

city: Nankang

first: Yuan-Hsuan

last: Liu

state: Taipei

address: 128, Section 2, Academia Road

department: Research Center for Applied Sciences

country: Taiwan

institute: Academia Sinica

summary: We use single cell RNA sequencing (scRNA-seq) to analyze the impact of NGB on early neural development based on cerebral organoids model.

overall_design: Three-dimensional cultured human cerebral organoids, derived from human induced pluripotent stem cells (hiPSCs), possess the remarkable capability to reconstitute in vivo three-dimensional cell arrangements. Moreover, they can faithfully recapitulate functional neural activity and gene expression profiles akin to those observed in the human brain. In this study, we employed lentiviral vectors to transduce short hairpin RNA (shRNA) targeting the NGB sequence, thereby generating an hiPSC line with NGB knockdown. Subsequently, this hiPSC line was utilized to generate cerebral organoids with NGB knockdown (shNGB) for future experimental analyses.

first: Yuan

middle: H

first: Meng

middle: T

last: Chung

first: Hsiao

middle: M

last: Wu

first: Yi

middle: C

last: Tung


title: RNA  sequencing reveal impact of radiation on cardiac tissues

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

institute: 301 hospital

summary: To study radiation-induced cardiac damage in mice, two groups of control and radiation mice were created, and cardiac tissues were obtained for bulk RNA sequencing.

overall_design: To explore the impact of radition on heart, mice were received 30 Gy 60Co γ-rays for irradiation. Subsequently, heart tissues were taken at 1 day and 6 weeks after irradiation for transcriptome sequencing. We performed bulk RNA sequencing to establish a comprehensive transcriptome profile of cardiac tissues under radiation.

first: Jingqi

last: Shi


title: RNA-seq for Healthy HSPC

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore RNA-seq results for Healthy HSPC.

overall_design: 6 Healthy HSPC samples

first: Jian

last: Pan

first: Shaoyan

last: Hu


title: Allogeneic red blood cell transfusion impairs antigen presentation and stimulates inflammatory response

city: Chengdu

first: Ping

last: Yang

state: 中国 +86

address: 37 Guo Xue Alley, Wuhou District

institute: West China Hospital

summary: Allogeneic red blood cell transfusion increases risk of infection and organ injury, which we here attempted to explain by analyzing gene expression in various types of immune cells. We prospectively compared adverse events and transcriptomic profiles in immune cells between patients who received transfusion of red blood cells (not plasma or platelets) during or after on-pump cardiac surgery and patients who did not. The composite rate of adverse events was significantly more frequent among patients who received transfusions (4 of 16, 25%) than among those who did not (3 of 60, 5%, p = 0.03). Transfusion downregulated in monocytes several genes involved in antigen presentation, such as HLA-DQA2 and HLA-DPB1, as well as several ligand-receptor pairs linking monocytes to natural killer cells (HLA-C-KIR2DL1, HLA-E-CD94:NKG2A) and T cells (CD28-CD86, CD2-CD58) for antigen presentation. Transfusion upregulated the early activation marker CD69 and pro-inflammatory and chemotactic factors (IL-6, TNFR1, TNFR2, CXCL9 and CCL3) in T, B and natural killer cells. Transfusion volume correlated positively with the percentage of CD69+ CD8+ T cells, which in turn correlated positively with composite risk of adverse events. Our findings may help explain how transfusion causes immunosuppression and systemic inflammation, thereby increasing risk of adverse events. Our work may provide clues to developing preventive or mitigating measures in order to optimize prognosis of patients who receive blood cell transfusions.

overall_design: We performed single-cell RNA sequencing of peripheral blood mononuclear cells from two patients in the exploration phase who received RBC transfusion(Trans-RBC) and three who did not (No-Trans) at Pre-surgery and at End CPB. The sequencing profiles were used to cluster the cells into the following four immune cell types based on expression of well-established markers: monocytes, T cells, B cells, and natural killer cells.


title: Histone trimethylations and HDAC5 regulate spheroid subpopulation and differentiation signaling of human adipose-derived stem cells

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

institute: National Cheng Kung University

summary: Human adipose-derived stem cells (ASCs) have shown immense potential for regenerative medicine. Our previous work demonstrated that chitosan nano-deposited surfaces induce spheroid formation and differentiation of ASCs for treating sciatic nerve injuries. However, the underlying cell fate and differentiation mechanisms of ASC-derived spheroids remain unknown. Here, we investigate the epigenetic regulation and signaling coordination of these therapeutic spheroids. During spheroid formation, we observed significant increases in histone 3 trimethylation at lysine 4 (H3K4me3), lysine 9 (H3K9me3), and lysine 27 (H3K27me3), accompanied by increased histone deacetylase (HDAC) activities and decreased histone acetyltransferase activities. Additionally, HDAC5 translocated from the cytoplasm to the nucleus, along with increased nuclear HDAC5 activities. Utilizing single-cell RNA sequencing (scRNA-seq), we analyzed the chitosan-induced ASC spheroids and discovered distinct cluster subpopulations, cell fate trajectories, differentiation traits, and signaling networks using the 10x Genomics platform, R studio/language, and Ingenuity Pathway Analysis (IPA). Specific subpopulations were identified within the spheroids that corresponded to a transient reprogramming state (Cluster 6) and the endpoint cell state (Cluster 3). H3K4me3 and H3K9me3 were discovered as key epigenetic regulators by IPA to initiate stem cell differentiation in Cluster 6 cells and confirmed by qPCR and their specific inhibitors of SNDX-5613 (a KMT2A inhibitor for H3K4me3) and SUVi (an SUV39H1 inhibitor for H3K9me3). Moreover, H3K9me3 and HDAC5 were involved in regulating downstream signaling and neuronal markers during differentiation in Cluster 3 cells. These findings emphasize the critical role of epigenetic regulation, particularly H3K4me3, H3K9me3, and HDAC5, in shaping stem cell fate and directing lineage-specific differentiation.

overall_design:
We conducted droplet-based scRNA-seq (10X Genomics, California, USA) on the samples of ADSC and ADSC sphere
-------------------------------------
Authors state, "We still can't find the raw data."

first: Ming-Min

last: Chang

first: Chia-Ching


title: Decoding Genome-wide Dysregulation of Translation in eIF2B-mutant Astrocytes: Implications for Vanishing White Matter Disease

city: Tel Aviv

first: Shir

last: Mandelboum

address: chaim levanon

department: Sagol School of Neuroscience

institute: Tel Aviv University

summary: eIF2B is a master regulator of translation initiation and mediator of the integrated stress response (ISR). Partial-loss-of function mutations are associated with eIF2B-leukodystrophy termed Vanishing White Matter Disease (VWMD), a recessive neurodegenerative disorder. Astrocytes, the brain homeostasis keepers, are central to VWMD owing to their hyper-sensitivity to eIF2B activity, as manifested by their phenotypic deficits due to the mutation. Here we used astrocytes isolated from the brains of WT and eIF2B5R132H/R132H mice to assess their transcriptome and translatome responses upon cytokine-mediated activation, an mTOR-driven process critical for brain homeostasis. We found that: (i) a mild eIF2B mutation has the power to disrupt translation regulation programs involving ~30% of the expressed genes; (ii) a common compensatory strategy to overcome the translation regulation failure is manipulation of mRNA abundance; and (iii) dysregulation of functionally related genes can be used to reliably predict deficits of corresponding cellular functions. Specifically, the study illuminates the molecular anomalies responsible for the impaired ribogenesis and mitochondrial respiration of eIF2B-mutant astrocytes. Moreover, it reliably predicts, for the first time, impaired cholesterol biosynthesis in eIF2B-mutant astrocytes. This work demonstrates the strength of combined transcriptome/translatome approach to decipher links between mild expression anomalies and downstream cellular defects associated with VWMD.

overall_design: Three biological repetitions of Eif2b5-R132H-R132H mutant primary astrocytes were treated or not with 20ng/ml TNFα and 0.25ng/ml IL-1β  for 24 hr or 48 hr. A portion of each sample was treated with RNase-I to generate ribosome footprints used for Ribo-seq analysis, while an undigested portion was used for RNA-seq.

first: Liat

last: Lev-Ari

first: Andrea

last: Atzmon

first: Melisa

last: Herrero Boco

first: Naama

last: Brezner

first: Daniel

last: Ben-halevy

first: Orna

last: Elroy-Stein


title: NSUN2 regulates thyroid cancer-associated alternative splicing switches

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

summary: In this research, we find that both m5C deposition in splice site boundaries and in splicing, direct AS switches of specific thyroid cancer- associated transcripts. We also show that several of the AS events validated in vitro are associated with a poor overall survival rate for patients with thyroid cancer, suggesting the use of these AS events as a novel potential prognostic biomarker.

overall_design: We knockout NSUN2 in Cal-62 cells and performed the RNA-seq analysis in order to exam the transcriptome after NSUN2 KO.


title: Cellular RNA interacts with MAVS to promote antiviral signaling

first: Nandan

middle: S

last: Gokhale

address: 750 Republican St., E320

institute: University of Washington

summary: Immune signaling needs to be well-regulated to promote clearance of pathogens, while preventing aberrant inflammation. Interferons (IFNs) and antiviral genes are activated by the detection of viral RNA by RIG-I-like receptors (RLRs). Signal transduction downstream of RLRs proceeds through a multiprotein complex organized around the central adaptor protein MAVS. While protein-protein interactions and post-translational modifications are critical for the formation of the MAVS signalosome, whether RNA play a role in organizing these platforms is largely unknown. RNA can modulate protein complex function by allosteric regulation or by serving as a molecular guide or scaffold. We have found that MAVS directly interacts with the 3’ untranslated regions of cellular mRNAs through its central intrinsically disordered domain. Eliminating RNA by RNase treatment disrupts the MAVS signalosome and inhibits phosphorylation of the transcription factor IRF3. These findings support the hypothesis that RNA molecules scaffold the MAVS signaling platform to induce IFNs. Indeed, RNase treatment alters interactions between MAVS and newly identified regulators of RLR signaling. Together, this work uncovers a function for cellular RNA in promoting signaling through MAVS and highlights a generalizable principle of RNA regulatory control of cytoplasmic immune signaling complexes.

overall_design: We used targeted RNA editing mediated by APOBEC1 to identify MAVS-associated RNAs. Targeted APOBEC1-mediated editing can robustly identify the RNA interactomes of RBPs without relying on crosslinking or immunoprecipitation. Here, APOBEC1 fused to the protein of interest catalyzes C-to-U transitions in RNAs that interact with this protein, which can be detected as C-to-T mutations by RNA sequencing (Brannan et al. 2021; Flamand et al. 2022). To profile MAVS-associated RNAs, we fused FLAG-tagged APOBEC1 to the N-terminus of full-length MAVS (APOBEC1-MAVSFL). We used FLAG-APOBEC1 as a background control (CTRL), and FLAG-APOBEC1 fused to the C-terminal transmembrane helix of MAVS (MAVSC-term) as a mitochondrially-localized background control to account for off-target editing within the subcellular vicinity of MAVS. RNA-sequencing data from 293T cells transfected with these constructs were analyzed using the Bullseye pipeline to identify RNAs with increased C-to-T editing with APOBEC1-MAVSFL as compared to controls (https://github.com/mflamand/Bullseye; Flamand et al. 2022; Tegowski et al. 2022). C-to-T editing was detected at sites with at least 10 reads of coverage per sample, with an edit ratio between 2% and 95% (minEdit=5), and an edit ratio at least 1.5-fold higher than control samples (editFoldThreshold=1.5)

first: N

first: K

last: Somfleth

first: M

last: Thompson

first: R

middle: K

last: Sam

first: D

last: Marciniak

first: L

last: Chu

last: Park

first: S

last: Dvorkin

first: A

last: Oberst

last: Horner

first: S-E

last: Ong

last: Gale Jr

last: Savan


title: AMPK is necessary for Treg functional adaptation to microenvironmental stress during malignancy and viral pneumonia

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

type: Methylation profiling by high throughput sequencing

summary: CD4+FOXP3+ regulatory T (Treg) cells maintain self-tolerance, suppress the immune response to cancer, and protect against tissue injury in the lung and other organs. Treg cells require mitochondrial metabolism to exert their function, but how Treg cells adapt their metabolic programs to sustain and optimize their function during an immune response occurring in a metabolically stressed microenvironment remains unclear. Here, we tested whether Treg cells require the energy homeostasis-maintaining enzyme AMP-activated protein kinase (AMPK) to adapt to metabolically aberrant microenvironments caused by malignancy or lung injury, finding that AMPK is dispensable for Treg cell immune-homeostatic function but is necessary for full Treg cell function in B16 melanoma tumors and during acute lung injury caused by influenza virus pneumonia. AMPK-deficient Treg cells had lower mitochondrial mass and exhibited an impaired ability to maximize aerobic respiration. Mechanistically, we found that AMPK regulates DNA methyltransferase 1 to promote transcriptional programs associated with mitochondrial function in the tumor microenvironment. In the lung during viral pneumonia, we found that AMPK sustains metabolic homeostasis and mitochondrial activity. Induction of DNA hypomethylation was sufficient to rescue mitochondrial mass in AMPK-deficient Treg cells, linking DNA methylation with AMPK function and mitochondrial metabolism. These results define AMPK as a determinant of Treg cell adaptation to metabolic stress and offer potential therapeutic targets in cancer and tissue injury.

overall_design: AMPK-sufficient and -deficient Treg cells were flow cytometry sorted from mouse B16 melanoma tumors at day 15-post engraftment and from spleens of tumor-free mice. Reduced representation bisulfite sequencing (RRBS) was leveraged to profile the DNA methylation profile of AMPK-sufficient and -deficient Treg cells in the tumor microenvironment and the spleen at homeostasis.

middle: D


title: The global genomic profile of hippocampal endothelial cells in fefemale diabetic mice is associated with cognitive dysfunction via alterations in cell adhesion and vascular permeability.

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary: Type II diabetes mellitus (T2D) is a chronic metabolic disease, and a risk factor for cardiovascular disease and cerebrovascular dysfunction including vascular dementia. Sex differences in the prevalence of T2D, dementia, and global genomic changes in the brain have been observed; however, most studies have been performed in males exposing large knowledge gaps in females. Therefore, the aim of this study was to evaluate the consequence of T2D on cognitive function, and decipher underlying molecular transcriptomic mechanisms of endothelial cells in an important memory center, the hippocampus, in female diabetic mice. Adult female db/db and control wild type mice (n=10/group) were studied at age 18 weeks after which cognitive performance was assessed, metabolic parameters measured, and the hippocampus isolated for single nuclei RNA sequencing. db/db female mice exhibit characteristic T2D metabolism with hyperglycemia, hyperinsulinemia, and hyperlipidemia when compared to female WT mice. Female db/db mice presented cognitive decline compared to wild type mice. snRNAseq showed that T2D induced significant change in the global transcriptome profile of hippocampal endothelial cells by modulating expression of not only protein coding genes but also lncRNAs.  These genes regulate cell-cell junctions, cell chemotaxis, actin cytoskeleton organization and cell adhesion, suggesting that diabetes increases endothelial cell permeability and therefore blood-brain permeability (BBB). Observed genomic changes also correlated with clinical Alzheimer’s and vascular dementia. In conclusion, T2D, by multiomic transcriptional and post transcriptional regulation, modulates the expression of genes in brain endothelial cells, resulting in endothelial cell dysfunction predictive of increased BBB permeability, and negatively impacts cognitive function.

overall_design: Wild type (C57BL/6J) and db/db female mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and single nuclei RNA sequencing was performed. Brain hippocampal endothelial cells gene expression was analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors. Functional outcomes such as cognitive behavior and blood brain barrier permeability were also assessed.

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: Amparo

last: Villablanca


title: A single-nucleus transcriptomic atlas reveals cellular and genetic characteristics in the hippocampus of natural aging-inducing Alzheimer’s disease tree shrews

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

summary: Natural aging-inducing Alzheimer’s disease (AD) model is lacking in the current preclinical research. Here, we surprisingly screened 10 tree shrews (TS) with obvious AD phenotypes from 324 naturally aging TS. Using single-nucleus RNA sequencing, we generated the transcriptome atlas of cellular and genetic diversity underlying natural aging-inducing AD development in TS. Further analyses and immunostaining verified the larger proportion of citatory neuronal progenitors exhibiting two different trajectories to an excitatory neuron subtype and granule cells with higher AD relevance. The intensified cellular communication was also found between progenitors and oligodendrocytes. Intriguingly, cross-species analysis among human, TS, monkeys, and mice delineated the cellular heterogeneity and further confirmed higher similarities of TS to monkeys than mice. Overall, our study established the first single-nucleus transcriptomic atlas of hippocampus in a novel AD model, extending our understanding of progenitors in the natural aging processes, and providing striking reference for diagnosis and treatment of AD.

overall_design: Nuclei isolated from tissues are re-suspended, filtered and used for 10x channel loading, Using Chromium Next GEM Single Cell 3 ʹ Reagent Kits v3.1 in Chromium Controller (10 x Genomics) was prepared on mononuclear RNA - seq library.

first: Liu-Lin

last: Xiong

first: Rong

last: He

first: Ruo-Lan

last: Du

first: Lu-Lu

last: Xue

first: Li-Ren

last: Huangfu

first: Yong-Ping

last: Li

first: Si-Min

last: Zhang

first: Chang-Yin

last: Yu

first: Ting-Hua

last: Wang


title: Genomewide temporal landscape of DNA methylation in pregnant women delivering at term in GARBH-InI cohort

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

country: India

institute: National institute of Biomedical Genomics

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of peripheral blood DNA collected from pregnant individuals throughout three time points (11-14 weeks, 18-20 weeks, 26-28 weeks) across the period of gestation and at term delivery (>37 weeks of gestation). Illumina Infinium EPIC Human DNA methylation Beadchip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs. Maternal peripheral blood samples were collected in EDTA vacutainers. The goal was to identify temporal DNA methylation changes in maternal peripheral blood during the period of gestation and associate their impact on biological pathways critical for term delivery.

overall_design:
Genome wide DNA methylation profiling of peripheral blood DNA collected from pregnant individuals throughout the period of gestation and at delivery. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs. Maternal peripheral blood samples were collected in EDTA vacutainers.
(contributor) GARBH-Ini Team

first: Jagyashila

last: Das

first: Indranil

last: Bagchi

first: Shekhar

last: Ghosh

first: Nitya

last: Wadhwa

first: Uma

last: Chadramouli Natchu

first: Ramachandran

last: Thiruvengadam

first: Pallavi

last: Kshetrapal

first: Shinjini

last: Bhatnagar

first: Partha

middle: P

last: Majumder


first: Benjamin

last: Singer


title: Transcriptome analysis of EPCs in HNSCC

city: Wuhan

first: Zhi-Zhong

last: Wu

address: No.237 Luoyu Road

institute: School & Hospital of Stomatology, Wuhan University

summary: EPCs were accumulated in HNSCC host. To understand the mechanism of endothelial progenitor cells (EPCs), we collected CD45+ EPCs and CD45- EPCs for further analysis.

overall_design: Female C3H/HeN mice were injected with SCC7 tumor cells. When the tumors grew up, EPCs in spleen and tumor were sorted by FACS and were analyzed with RNA-seq.

first: Wei-Wei

last: Deng

first: Su-Wen

last: Zhu

first: Wen-Da

first: Hao

first: Zhi-Jun

last: Sun


overall_design: AMPK-sufficient and -deficient Treg cells were flow cytometry sorted from mouse B16 melanoma tumors at day 12- and day 15-post engraftment and from spleens of tumor-free mice. RNAseq was leveraged to profile the gene expression of AMPK-sufficient and -deficient Treg cells in the tumor microenvironment and the spleen at homeostasis.

first: Singer

last: Benjamin D.

first: Liu

last: Qianli


title: Anti-tumor effect of targeting EPC in Head and neck cancer

summary: Tumor-induced EPCs were contributed to weaken anti-tumor response through the interaction between spleen and tumor. Hence, it seemed a good strategy to targeting EPCs in vivo. To gain a mechanistic understanding of the alteration upon treatment, tumors treated with anti-CD71 were collected to perform RNA-seq.

overall_design: SCC7 tumor-bearing mice were treated with anti-CD71 on day 6 and day 9 and tumors of control group and anti-CD71 treatment group were harvested on day 10 to perform RNA-seq.

last: Wang

last: Li


title: Estrogen Effects on Abdominal Skeletal Muscle Fibroblasts in Inguinal Hernia Mouse Model [ChIP-seq]

first: Serdar

last: Bulun

state: IL

address: 250 East Superior Street, Suite 03-2303

department: Department of Obstetrics and Gynecology

institute: Feinberg School of Medicine at Northwestern University

summary: Humanized aromatase mice spontaneously develop hernias caused by fibrosis of lower abdominal skeletal muscle. To understand the estrogen action leading to herniation, fibroblasts were isolated and cultured under estrogen-replete and deplete conditions.

overall_design: ChIP-seq on primary mouse skeletal muscle fibroblasts with and without estrogen.

first: Tanvi

last: Potluri


title: NASH LiverModel transcriptome

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Mitochondrial reactive oxygen species (mROS) is central to normal physiology, but their excessive production correlates with the etiology of many human metabolic pathologies. We assessed in human liver biopsies from patients with non-alcoholic liver disease with different grades of liver steatosis and fibrosis the gene expression of ubiquinone genes and we uncover a positive relationship between QH2/Q ratio and the steatosis grade.  progresssion.

overall_design: Transcriptome analysis on liver biopsies from patients at different steatosis stages

first: I

last: Graupera

first: M

last: Coll


title: Estrogen Effects on Abdominal Skeletal Muscle Fibroblasts in Inguinal Hernia Mouse Model [ATAC-Seq]

overall_design: ATAC-seq on primary mouse skeletal muscle fibroblasts with and without estrogen.


title: The synergistic effect of c-Myb hyperactivation and Pu.1 deficiency in inducing Pelger-Huët anomaly and promoting sAML transformation

city: Guangzhou

first: Wei

last: Liu

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

summary: Patients with acute myeloid leukemia developed from myelodysplastic syndrome (MDS/AML) have poor prognosis with more complex genetic mutations. Genomic analyses have shown complex association among mutant genes, including co-occurring and mutually exclusive. It has been reported that hyperactivation of MYB or deficiency of PU.1 could induce myeloid preleukemia. The simultaneous abnormal expression of these two proteins has been documented in some AML patients. However, the association of MYB and PU.1 in the pathogenesis of malignant hematopoiesis remains unclear. In this study, we used the c-Myb-hyperactivation and Pu.1-deficient double-strain (c-mybhyper;pu.1G242D/G242D) zebrafish to clarify the synergistic role of c-Myb and Pu.1 in promoting MDS/AML development. We found that the c-mybhyper;pu.1G242D/G242D mutant displayed excessive expansion and differentiation arrest of neutrophils, and progressed to MDS/AML with a high ratio. Interestingly, a group of poorly differentiated Pelger-Huët-like neutrophils was identified in c-mybhyper;pu.1G242D/G242D adulthood and might be associated with MDS/AML progression. Moreover, treated the c-mybhyper;pu.1G242D/G242D zebrafish with a combination of the cell cycle inhibitor cytarabine (Ara-C) and the differential inducer all-trans retinoic acid (ATRA) could effectively relieve the leukemic symptoms. Our findings revealed that c-Myb hyperactivation and Pu.1 deficiency synergistically induced MDS/AML. Furthermore, c-mybhyper;pu.1G242D/G242D zebrafish might serve as a suitable MDS/AML model for drug screening.

overall_design: Kidney marrow of the wildtype, c-mybhyper, pu.1G242D/G242D, c-mybhyper;pu.1G242D/G242D zebrafish were isolated separetely. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.

first: Song'en

last: Xu

first: Jiaxin

last: Hong

first: Jiehao

last: Lin

first: Meimei

last: Dongye


title: Estrogen Effects on Abdominal Skeletal Muscle Fibroblasts in Inguinal Hernia Mouse Model [RNA-Seq]

overall_design: RNA-seq on primary mouse skeletal muscle fibroblasts with and without estrogen.


title: Longitudinal DNA methylation profile of peripheral blood in women delivering preterm informs predictive biomarkers

first: Arindam

last: Maitra

summary: Genome wide DNA methylation profiling of peripheral blood DNA collected from pregnant individuals throughout the period of gestation and at delivery. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs. Maternal peripheral blood samples were collected in EDTA vacutainers.

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

first: Jagyashila

last: Das

first: Soumi

last: Sarkar

first: Indranil

last: Bagchi

first: Shekhar

last: Ghosh

first: Nitya

last: Wadhwa

first: Uma

last: Chadramouli Nachu

first: Ramachandran

last: Thiruvengadam

first: Pallavi

last: Kshetrapal

first: Shinjini

last: Bhatnagar

first: Partha

last: Majumder

first: GARBH-Ini

last: Team


title: Estrogen Effects on Abdominal Skeletal Muscle Fibroblasts in Inguinal Hernia Mouse Model

first: Serdar

last: Bulun

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

overall_design: Refer to individual Series


title: Pattern of variation in DNA methylation during pregnancy among mothers who delivered preterm in the GARBH-Ini cohort

last: Nachu


title: SMART-Seq analysis to understand the differences between WT and SRC-3-/- Tregs transcriptome

city: Houston

first: Prashi

last: Jain

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor college of Medicine

summary:
SMART-seq analysis is used for single cells or for a small amount of purified total RNA from low number of cells. The goal of this study to compare the quantitative differences between the SRC-3+ and SRC-3-/- Tregs cell transcriptomes.
Method: Tregs were isolated from FOXP3cre SRC-3f/f (SRC-3KO) and FOXP3 cre monogenic (WT) mice and sorted for GFP expression and the expression of cre

overall_design: Transcriptome differences between WT and SRC-3KO Tregs explored to explain the anti-tumor effects of SRC-3KO Tregs

first: Sang

middle: J

last: Han

first: David

last: Lonard

first: Bert

middle: W

last: O'Malley


title: DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell [RNA-seq]

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary:
Purpose: Explore how DEK genome widely bind RNA and affect the alternative splicing in cancer
Methods: DEK was overexpressed by transfecting HeLa cells with a DEK-overexpressing plasmid and RNA_seq was used to analyze gene expression profile and splicing pattern of DEK overexpression and control cells. Then, an improved RIP-seq was conducted to explore genome-widely binding characteristic of DEK in HeLa cell. Bioinformatics analysis and qPCR/RIP-PCR were performed to identify and validate the bound and regulated targets of DEK, respectively
Results:The results showed DEK overexpression did not affect transcript level expression of those high expressed genes (with FPKM > 1), but splicing pattern of 411 genes (RASGs) was regulated by DEK in HeLa cells, which were enriched in Hippo signaling pathway. Moreover, DEK broadly bind the RNA of a total of 11, 112 genes, with a biased binding the GGUAA motifs at the CDS and intronic regions
Conclusions: our results indicated DEK could broadly bind and regulate the pre-mRNA splicing process, which provide new insights of mechanisms that DEK functions in various biological processes including cancer

overall_design: Transcrptional profile of  Hela cells with/without DEK overexpression were generated

first: Dong-bo

last: Liu

first: Ping

last: Peng


title: DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell [RIP-seq]

overall_design: RIP-seq was conducted to explore genome-widely binding characteristics of DEK in HeLa cell

first: Dong-Bo


title: Gene expression data from skin biopsy of involved or uninvolved in Atopic Dermatitis (AD)

city: Kobe

first: Hayao

last: Ebise

address: 1-5-2 Minatojima Minamimachi, Chuo-ku

country: Japan

institute: Racthera Co., Ltd.

summary:
Analysis of differences and similarities of gene expression among AD-involved, AD-uninvolved and normal skins.
Microarray analysis is performed to find out genes characteristic of AD and classified those genes according to expression patterns.

overall_design: Total RNA samples were extracted from frozen skin biopsy specimens and hybridized with Affymetrix GeneChip HG-U133A microarrays.

first: Hisashi

last: Sugiura


title: DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell


title: Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation

status: Public on Mar 18 2025

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: The memory CD8+ T cell pool contains phenotypically and transcriptionally heterogeneous subsets with specialized functions and recirculation patterns. Here, we examined the epigenetic landscape of CD8+ T cells isolated from seven non-lymphoid organs across four distinct infection models, alongside their circulating T cell counterparts. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we found that tissue-resident memory T (TRM) cells and circulating memory T (TCIRC) cells develop along distinct epigenetic trajectories. We identified organ-specific transcriptional regulators of TRM cell development, including FOSB, FOS, FOSL1, and BACH2, and defined an epigenetic signature common to TRM cells across organs. Finally, we found that although terminal TEX cells share accessible regulatory elements with TRM cells, they are defined by TEX-specific epigenetic features absent from TRM cells. Together, this comprehensive data resource shows that TRM cell development is accompanied by dynamic transcriptome alterations and chromatin accessibility changes that direct tissue-adapted and functionally distinct T cell states.

overall_design: Tissue resident memory (TRM) T cells were isolated following 35-36 infection of LCMV from four organs and profiled via 10x scATAC-seq

first: Frank

last: Buquicchio

first: Raissa

last: Fonseca

first: Ansuman

last: Satpathy

first: Laura

last: Mackay


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [bulk ATAC-seq]

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

summary: We explore how the tightly regulated molecular response triggered by acute restraint stress becomes altered after repeated restraint exposure. Transcriptomic sampling of the mouse hippocampus at multiple time points revealed that repeated stress leads to widespread habituation, damping stress-induced gene expression of all stress-responsive genes. However, we find no evidence for the emergence of new response profiles or alterations in baseline gene expression. Using single-cell multi-omics, we show that these findings hold true across cell types, and we reveal cell type specific patterns of habituation. Transcriptomic and chromatin accessibility profiles identify two distinct mechanisms that contribute to the observed habituation patterns: an early cAMP-associated mechanism that is related to blunted transcription after chronic stress, and a late corticosterone-dependent mechanism that is linked to a shortened transcriptional response.

overall_design: Restraint stress involves placing the mice in a 50 ml Falcon tube with a large air hole for 1h30. Chronically stressed animals were subjected to daily restraint for 10 consecutive days at varying time of day before the final (acute) stress exposure, while handling animals were handled gently (lifting the animals by the tail, simulating the handling method used before restraint stress). Following this treatment, animals were single-housed 24 hours before being subjected once again to the same restraint stress, and the samples were collected 45min following stress initiation (time point 0min indicates an absence of acute stress, i.e. homecage animals). All stress exposures were carried out between 10:00 and 17:00 in the animals’ active phase (i.e. reverse light cycle).

first: Rebecca

last: Waag

first: Johannes

last: Bohacek


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [snATAC-seq]

overall_design: Restraint stress involves placing the mice in a 50 ml Falcon tube with a large air hole for 1h30. Chronically stressed animals were subjected to daily restraint for 10 consecutive days at varying time of day before the final (acute) stress exposure, while handling animals were handled gently (lifting the animals by the tail, simulating the handling method used before restraint stress). Following this treatment, animals were single-housed 24 hours before being subjected once again to the same restraint stress, and the samples were collected at various timepoints (see ‘ARS timepoint’ column) following stress initiation. All stress exposures were carried out between 10:00 and 17:00 in the animals’ active phase (i.e. reverse light cycle).

first: Emanuel

last: Sonder


title: Direct cell-to-cell transmission of retrotransposons [RNA-seq]

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: Transposable elements are abundant in host genomes but are generally considered to be confined to the cell in which they are expressed, with the notable exception of endogenous retroviruses. Here, we identify a group of LTR retrotransposons that infect the germline from somatic cells within the Drosophila ovary, despite lacking the fusogenic Envelope protein typically required for retroviral entry. Instead, these elements encode a short transmembrane protein, sORF2, with structural features reminiscent of viral cell-cell fusogens. Through genetics, imaging, and electron microscopy, we show that sORF2 localizes to invasive somatic protrusions, enabling the direct transfer of retrotransposon capsids into the oocyte. Remarkably, sORF2-like proteins are widespread among insect retrotransposons and also occur in piscine nackednaviruses and avian picornaviruses. These findings reveal a noncanonical, Envelope-independent transmission mechanism shared by retrotransposons and non-enveloped viruses, offering important insights into host-pathogen evolution and soma-germline interactions.

overall_design:
Comparative poly(A)-enriched RNA-seq of ovaries from somatic piRNA pathway knockdown Drosophila flies vs. control (Tj>vretenoGD vs. Tj>arrestinGD)
Comparative poly(A)-enriched RNA-seq of ovaries from Drosophila flies expressing the retrotransposons 412 and Stalker2 vs. control (Flam-del-412St2;iso-1 vs. FRT;iso-1)

first: Maya

last: Voichek

first: Andreas

last: Bernhard

first: Maria

last: Novatchkova

first: Paul

last: Möseneder

first: Baptiste

last: Rafanel

first: Peter

last: Duchek

first: Kirsten-André

last: Senti

first: Julius

last: Brennecke


title: Synergistic Potential of CDK4/6 Inhibitors and ATRA in non-APL AML.

city: Jena

first: Tino

last: Schenk

state: Thüringen

address: Am Klinikum 1

department: KIM II

country: Germany

institute: University Hospital Jena

summary: Background: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by diverse genetic abnormalities. The standard of care remains to be chemotherapy and stem cell transplantation. In acute promyelocytic leukemia (APL), differentiation therapy with all-trans retinoic acid (ATRA) has significantly improved outcomes. Despite this, the success of ATRA has yet to be transferred to non-APL AML. Exploring combinations to enhance the efficacy of ATRA in non-APL AML remains a key focus. Objective: To investigate the therapeutic effect of ATRA in combination with cyclin-dependent kinase 4/6 (CDK4/6) inhibitors in non-APL AML. Methods: Non-APL AML cells and primary patient samples were treated with ATRA and CDK4/6 inhibitors. Key outcomes included differentiation, proliferation, cell viability, and colony-forming capacity. Combination synergy was evaluated, and gene expression analysis identified pathways associated with therapeutic effects. Results: The combination demonstrated dose-dependent effects, enhancing differentiation and reducing proliferation, cell viability, and colony-forming capacity. A synergistic effect was observed across AML cell lines. Gene expression profiling revealed the co-regulation of differentiation-associated genes, unveiling the mechanisms driving therapeutic synergy. Conclusion: Combination of CDK4/6 inhibitors with ATRA shows potential for differentiation-based AML treatment. This approach offers a promising avenue for improved outcomes in non-APL AML.

overall_design: RNA-seq profiling of HL-60 cells 3h following treatment with 500 nM palbociclib, 100 nM ATRA or the combination.

first: Rafał

last: Skopek

first: Setenay

last: Özcan

first: Paulina

last: Chmiel

first: Stephanie

last: Morgner

first: Jacqueline

last: Schuett

first: Faezeh

last: Ghazvini Zadegan

first: Clara

last: Stanko

first: Małgorzata

last: Palusińska

first: Karolina

last: Maślińska-Gromadka

first: Yordan

last: Sbirkov

first: Sven

last: Stengel

first: Martin

last: Fischer

first: Annamaria

last: Brioli

first: Arthur

last: Zelent

first: Lukasz

last: Szymanski


title: Ruxolitinib reduces macrophage pyroptosis in aplastic anaemia

first: Rong

last: Fu

address: xinxing street

institute: Tianjin Medical University General Hospital

summary: Aplastic anaemia (AA) is a disease that shows complex pathogenesis involving multiple immune factors. While immunosuppressive therapies such as cyclosporine can effectively control AA, they may be ineffective in certain patients or those with relapse. Therefore, new treatments are needed. Among the targets for these treatments, the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway regulates inflammatory cytokines and immune activation. Ruxolitinib, a JAK1/2 inhibitor, reduces T-cell activation and the associated inflammatory response and improves AA disease status in mice. However, its mechanism of action is unclear; thus, further research is needed before its clinical use. We previously showed increased pyroptosis in patients with severe AA (SAA) and that macrophage pyroptosis is an important factor in immune activation. The current study investigated the interaction of ruxolitinib with macrophages and whether the drug could treat SAA by improving pyroptosis levels. We induced differentiation of the THP-1 human monocyte cell line into macrophages in vitro and then induced pyroptosis. After constructing a macrophage pyroptosis model, treatment with different concentrations of ruxolitinib was administered. The results showed that ruxolitinib reduced the levels of pyroptosis and inflammatory-related factors. A mouse model of SAA was validated. In conclusion, ruxolitinib may treatment affects SAA by reducing the level of macrophage pyroptosis.

overall_design: We induced differentiation into THP-1 macrophages using a human mononuclear THP-1 cell line and induced pyroptosis using ATP and LPS. Three cases each were divided into experimental (RUX+) and control (RUX-) groups according to whether or not they were treated with Lukotinib, and RNA transcriptome sequencing was performed.

first: Xintong

last: Xu

first: Congwei

last: Zhong

first: Xiaorui

last: Meng

first: Chunyan

last: Liu


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [snRNA-seq]

first: Pierre-Luc

last: Germain

first: Rebecca

last: Waag

first: Emanuel

last: Sonder

first: Johannes

last: Bohacek


title: Expression data of circTMEM45A knockdown in KYSE-150 cell line

city: Shijiazhuang

first: Jia'xiang

last: Wu

address: Shijiazhuang 050011,China

institute: The Fourth Hospital of Hebei Medical University

summary: The circTMEM45A was knocked down in KYSE-150 cells using siRNA, and the gene expression between the knockdown group and the negative control group was compared to explore the downstream molecular mechanism of circTMEM45A in esophageal cancer.

overall_design: After KYSE-150 cells were transfected with negative control si-NC or si-circTMEM45A, total RNA was extracted from the cells and used for transcriptome sequencing analysis.


title: Single cell and clonal analysis of AL amyloidosis plasma cells and their bone marrow microenvironment

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: AL amyloidosis is a disorder characterized by expansion of clonal plasma cells in the bone marrow and distant end organ damage mediated by misfolded immunoglobulin free light chains. There are currently limited data regarding the functional characteristics of AL amyloidosis plasma cells and their surrounding bone marrow microenvironment. We performed 5’ single cell RNA sequencing on 9 newly diagnosed, treatment naive AL amyloidosis patients and 8 healthy subjects. We identified generalized suppression of normal bone marrow hematopoiesis with distinct expansion of CD16 monocytes and subsets of CD4+ T cells in AL amyloidosis patients. We detected significant transcriptional changes broadly occurring among immune cells with increased interferon α and γ response and decreased TNF-α signaling. T and B cell receptor profiling revealed no overt clonal expansion of B or T cells in AL amyloidosis patients. However, we noted a disproportionate expansion of a distinct population of non-malignant plasma cells in AL amyloidosis patients. Finally, clonal AL amyloidosis plasma cells were identified based on their unique VDJ rearrangement and they showed increased expression of genes involved in proteostasis and antigen processing when compared to autologous, polyclonal plasma cells. Inter-patient transcriptional heterogeneity was evident, with transcriptional states reflective of common genomic translocations easily identifiable. Overall, this study defines the transcriptional characteristics of AL amyloidosis plasma cells and their surrounding bone marrow microenvironment, identifying transcriptional signatures that serve as candidates in early diagnosis in larger studies, and potential molecular targets for therapy.

overall_design:
Bone marrow aspirates were obtained from patients with newly diagnosed AL amyloidosis seen at our center between 2019 and 2023. Healthy samples were obtained from discarded surgical material of patients undergoing primary, elective total hip arthroplasty. On the day of analysis, samples were rapidly thawed in a 37 degree C water bath, transferred to a 15 ml conical tube and washed in RPMI with 50% fetal bovine serum medium (Gibco). Cells were spinned for 5 minutes at 300 rcf and resuspended in PBS without calcium or magnesium (Gibco) with 0.4% BSA (Miltenyi). Cells were counted and viable cells enriched via Dead Cell Removal MicroBeads (Miltenyi) according to the manufacturer's protocol. Cells were resuspended in PBS with 0.4% BSA prior to viability check and encapsulation. Samples with viability less than 70% were not included in downstream processing. 10X Chromium Next GEM Single Cell 5’ reagent kits and BCR/TCR amplification kits were used for joint transcriptional and immune profiling of bone marrow samples. For the CD138+ samples, a combined profiling of BCR and 5’RNA was performed. For CD138- samples, a combined profiling of BCR, TCR, and 5’RNA was performed. The samples were aggregated into a fewer number of fraction-specific pools (details in associated publication) and loaded at a concentration of 20,000 cells per lane. The resulting libraries were sequenced on Illumina NovaSeq S1.

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

middle: A

first: Maria

last: Moscvin

first: Benjamin

last: Evans

first: Tianzeng

last: Chen

first: Samuel

last: Boullt

first: Sean

last: Rowell

first: Srinidhi

last: Raghav

first: Antonia

middle: F

first: Jacob

last: Laubach

first: Allon

last: Klein

first: Giada

last: Bianchi


title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum

city: Cambridge

first: Jens

middle: Bager

last: Christensen

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Understanding the molecular mechanisms driving lineage decisions and differentiation during development is especially difficult in systems with a diverse progenitor pool, such as the mammalian cerebellum. Here, we used single-cell RNA-sequencing (scRNA-seq) to characterise the developmental trajectories of Nestin-expressing progenitors (NEPs) in the neonatal mouse cerebellum. We identified FOXO1 as a key regulator of NEP-to-inhibitory neuron differentiation, acting directly downstream of ASCL1. Genome occupancy and functional genomic experiments using primary NEPs showed that both ASCL1 and FOXO1 regulate neurogenesis genes during in vitro differentiation, while independently regulating proliferation and survival, respectively. Furthermore, we demonstrate that WNT is a regulator of the transition from an ASCL1+ to FOXO1+ state. Finally, we show that the ASCL1-FOXO1 axis and role of WNT signalling is conserved in primary human NEPs. Through understanding how cerebellar interneurons differentiate, our findings may inform therapeutic strategies for cerebellar disorders such as spinocerebellar ataxia, where cerebellar interneurons are overproduced.

overall_design: Targeted DamID of Dam methylase, FOXO1- and ASCL1-Dam during in vitro differentiation of primary nestin-expressing progenitors.

middle: B

first: Alex

last: Donovan

first: Andrea

last: Brand

first: Sumru

last: Bayin


title: Direct cell-to-cell transmission of retrotransposons

first: Dominik

last: Handler

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Comparative small RNA-seq profiling of ovaries from Drosophila flies expressing the retrotransposons 412 and Stalker2 vs. control (Flam-del-412St2;iso-1 vs. FRT;iso-1)

first: Maya

last: Voichek

first: Andreas

last: Bernhard

last: Novatchkova

first: Paul

last: Möseneder

first: Baptiste

last: Rafanel

first: Peter

last: Duchek

first: Kirsten-André

last: Senti

first: Julius

last: Brennecke


title: Direct cell-to-cell transmission of retrotransposons [Minion]

overall_design:
Comparative poly(A)-enriched RNA-seq of ovaries from somatic piRNA pathway knockdown Drosophila flies vs. control (Tj-vretenoGD vs. Tj>arrestinGD)
Comparative poly(A)-enriched RNA-seq of OSCs with Piwi knockdown vs. control

first: Maria


title: Single-cell RNAseq of Basal Cell Carcinoma (BCC) mouse models

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

summary: Single-cell RNA sequencing of mouse tail epidermis from Basal Cell Carcinoma mouse models

overall_design: Gene expression analysis was performed from isolated tail epidermis from BCC mouse models (BCC, SmoM2, Gnas-eKO or PKI mice) with respective control mice (no tumor epidermis, Con)

first: Sarah

last: Krantz


title: Bulk RNAseq of Basal Cell Carcinoma (BCC) mouse models

summary: RNA sequencing (RNAseq) of mouse tail keratinocytes from Basal Cell Carcinoma mouse models

overall_design: Gene expression analysis was performed from isolated tail keratinocytes from BCC mouse models (BCC, SmoM2, Gnas-eKO or PKI mice) with respective control mice (no tumor epidermis, Con)


title: Polystyrene microplastics induce activation and cell death of neutrophils through strong adherence and engulfment

city: Seoul

first: Koung-Min

last: Park

address: 5-26, Sinchon-ro 4-gil

country: South Korea

institute: Yonsei university college of medicine

summary: Ingested microplastics (MPs) can accumulate throughout whole body, which may induce the dysfunction of immune system. However, it remains unclear how MP exposure affects innate immune responses at the cellular level. We found that mouse neutrophils strongly bind and then engulf polystyrene MPs. This interaction leads to proinflammatory state of neutrophils and eventually results in apoptotic cell death through toll-like receptor signaling pathway in a bacteria-recognition mimetic manner. Moreover, our data verified that orally administered polystyrene MPs reach various organs in mice, where they are interacted with and endocytosed by neutrophils. We confirmed that human neutrophils also strongly bind and internalize polystyrene MPs. Additionally, RNA sequencing analysis of polystyrene MPs-exposed human neutrophils showed the upregulation of cell death-related function. Therefore, the accumulated MPs may exacerbate inflammatory immune response by disrupting neutrophil function. These results provide novel insight into the adverse responses of neutrophils induced by MP exposure.

overall_design: Total RNA-seq profiling of neutrophils isolated from healthy human blood and treated or no-treated by polystyrene microplastics.

first: Bora

last: Kim

first: Wonjin

last: Woo

first: Lark Kyun

first: Young-Min

last: Hyun


title: RNAseq for peritoneal macrophages phagocytosing E.coli in the absence or presence of retinoic acid

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

institute: Guangxi University

summary: Peritoneal macrophages comprise two distinct subpopulations: large peritoneal macrophages (LPMs) and small peritoneal macrophages (SPMs), each with unique phenotypic and functional characteristics. This study investigates the role of retinoic acid (RA) in modulating the response of peritoneal macrophages to bacterial infections. Using a murine peritonitis model, we demonstrate that RA enhances the phagocytic capacity of macrophages, delays the decline in phagocytic function, and alters macrophage distribution in the peritoneal cavity. RA treatment induced notable transcriptional changes in both LPMs and SPMs.

overall_design: The E. coli ER2272 strain utilized in the experimental procedure incorporates the fluorescent construct pUC19-tdTomato, in which the pUC19 plasmid is capable of constitutive expression of the fluorescent protein tdTomato. Prior to injection, the E. coli bacteria were cultured overnight in LB medium at 37°C and then mixed with 0.2 ml PBS to create a suspension of 1 × 10⁷ CFU/mouse, which was subsequently injected into the peritoneal cavity. To compared the effect of 24 hours treatment of retinoic acid (RA) on the SPMs and LPMs, we separated the mice into two groups: control and RA treatment. In some cases, RA was injected 24 hours before the E. coli injection.Upon the injection of bacteria containing pUC19-tdTomato, both SPMs and LPMs in the the peritoneal cavity can be detected based on the antibody staining of F4/80 and the phagoytosis of E.coli. SPMs and LPMs from the respective group were isolated from the peritoneal cavity using flow cytometry sorting. Total RNA was extracted from cell pellets using TRIzol reagent according to the manufacturer’s protocol. High-throughput RNA sequencing was performed using Illumina NovaSeq Xplus platform.

first: Jian

last: Song

first: Xi

last: Wang

first: Yujuan

last: Qin


title: The mRNA-Seq data of Zic3 overexpression in chicken limbs

city: Shenyang

first: Bai

last: Shibin

address: 120 Dongling Road

institute: Shenyang Agriculture University

summary: Birds exhibit a remarkable diversity in limb morphology. Zic3, a transcription factor highly expressed in the anterior of the limb, has differential expression among bird species. To study how it regulates digit morphogenesis in birds, we overexpressed the chicken-Zic3 gene in the lateral plate mesoderm (LPM) of developing chicken hindlimbs at Hamburger Hamilton (HH) stage 10 using the RCAS avian retrovirus. At HH30, the autopod was dissected and subjected to transcriptome sequencing (mRNA-Seq), with the corresponding positions of individuals injected with the empty RCAS vector serving as controls. Enrichment analysis of differential genes and GSEA analysis suggest that the Zic3 gene inhibits multiple pathways related to skeletal development, resulting in a delay in digit development.

overall_design: After 5 days of infection (HH30), the entire autopod regions of individuals injected with RCAS-Zic3 were collected under a microscope. The same procedure was applied to the control group, where the corresponding areas of individuals injected with RCAS were collected. Each group included three biological replicates.

first: Shanshan

last: Li

first: Shibin

last: Bai

first: Zhe


title: Bulk RNAseq of Gpr161 epidermal knockout mice.

summary: RNA sequencing (RNAseq) of mouse tail keratinocytes from Gpr161 epidermal knockout mice (K14CRE)

overall_design: Gene expression analysis was performed from isolated tail keratinocytes from Gpr161 epidermal knockout mice or control mice.


title: Glycocalyx micro- and nanodomains in cell-cell and cell-matrix adhesions revealed by sensitive click chemistry

city: Nijmegen

first: Daan

last: Smits

address: Geert Grooteplein 26

department: MBS

country: Netherlands

institute: RadboudUMC

summary: The glycocalyx consists of glycoproteins, glycolipids and extracellular polysaccharides at the cell surface which mediate viscoelastic and electrostatic barrier function. In molecular interactions the glycocalyx is thought to segregate locally to facilitate receptor-ligand binding, yet high-resolution maps of glycocalyx domains in cell-cell and cell-matrix interactions are lacking. We here applied TMTH-sulfoximine (THS)-based biorthogonal chemistry in live-cell culture and demonstrate much-enhanced glycocalyx detection, compared to established  dibenzocyclooctyne-based labeling. Using superresolution microscopy, we identified micron-scale moderately diminished glycocalyx in cell-cell contacts and subtotal depletion in protrusions at the leading and trailing edges and membrane blebs when cells invaded 3D fibrillar matrix. At contacts to collagen fibrils, focal integrin clusters segregated in outward-protrusive nanodomains from glycocalyx (distance: 350 nm), forming adhesion sites of low glycocalyx content. Thus, THS-based next-generation bioorthogonal labelling of live cells identifies micro- and nanodomains with altered glycocalyx density, implicating local glycocalyx downregulation in functional cell-cell and cell-matrix interactions.

overall_design: RNA-sequencing to determine transcriptomic interference by metabolic labelling using Ac4ManNAz (5-day treatment), so comparing treated vs. untreated.

first: Yuri

last: Damen

first: Tianfu

first: Floris

last: van Delft

first: Bauke

last: Albada

first: Peter

last: Friedl


title: Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells [CUT&Tag]

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: The organization of chromatin, governed by physicochemical interactions, nucleosome positioning, and histone modifications, regulates transcription to influence cellular plasticity and cell fate. We explored whether the organization of chromatin into nanoscale packing domains is involved in regulating transcriptional programs that govern stemness and responses to chemotherapy. Specifically, chromatin packing domains are a unit of chromatin structure at the single-cell level playing a critical role in regulating cellular transcriptional plasticity and access to the transcriptional landscape. Using an optical spectroscopic nanosensing technology, partial wave spectroscopic (PWS) microscopy, we show that ovarian cancer-derived cancer stem cells (CSCs) display upregulation of nanoscale chromatin packing domains (P<0.05) compared to non-CSCs cells. CUT&Tag sequencing with antibodies for repressive H3K27me3 and active H3K4me3 and H3K27ac marks identified 4438 H3K27me3 differentially enriched regions (P<0.05), of which 2786 were detected in CSCs, supporting chromatin packing domain upregulation in ovarian CSCs. Additionally, more poised genes with both H3K4me3 and H3K27me3 marks were identified in CSCs (n=2292) vs. non-CSCs (n=932), supporting the increased transcriptional plasticity of CSCs. Corresponding to the distinct organization of chromatin marks in CSCs, comparative transcriptomic analyses yielded a higher intercellular transcriptional heterogeneity in global gene expression at baseline in CSCs vs. non-CSCs.  In response to cisplatin, genes with low baseline expression levels underwent the highest upregulation in CSCs, demonstrating transcriptional plasticity under the stress of chemotherapy. Treatment of CSCs with epigenome targeting drugs downregulating chromatin packing domain formation promoted cellular differentiation. In particular, the Dot1L inhibitor (Dot1Li) downregulated chromatin domains and blocked transcriptional plasticity. This resulted in the reversal of stemness features and inhibition of tumor initiation capacity. The results support that CSCs harbor upregulated chromatin packing domains, contributing to transcriptional and cell plasticity that epigenome modifiers can target.

overall_design: To understand how CSCs activate or repress transcription, we mapped known epigenome regulators or histone modifications (H3K27me3, H3K4me3, and H3K27ac) in OVCAR5 derived ALDH+ cancer stem cells vs. ALDH- non-cancer stem cells by using CUT&Tag-sequencing.

first: Yinu

first: Jane

last: Frederick

first: Luay

last: Almassalha

first: Yaqi

last: Zhang

first: I

last: Ye

first: Alex

last: Duval

first: Paola

last: Gonzalez

first: Karla

last: Medina

first: Joshua

last: Pritchard

first: John

last: Carinato

first: Mazhar

last: Adli

first: Vadim

last: Backman

first: Daniela

last: Matei


title: Osmotic Stress Response Reveals Distinct Genome Architectures in Drosophila and Humans

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: The 3D genome organization is mediated by chromatin architectural elements such as insulator binding proteins and cohesin and serves as a crucial epigenetic regulatory mechanism. In Drosophila, architectural proteins translocate from chromatin to the nucleoplasm in response to hyperosmotic stress forming condensates known as insulator bodies, which exhibit liquid-liquid phase separation (LLPS) features. We harnessed the osmotic stress response to gain insights into the differences in genome organization principles between human and fly genomes across several scales. We found that under identical osmotic stress conditions, CTCF also translocates to the nucleoplasm in human cells but does not form condensates. Using genome-wide chromosome conformation capture (Hi-C), we found that in both human and Drosophila, osmotic stress induces a loss of genome structure, characterized by the loss of compartments and the weakening of TAD boundary strength throughout the genome, as well as a significant increase in cross-compartment interactions in the long-range. In both Drosophila and human genomes, looping interactions are also lost during stress. The genome organization in human cells almost fully recovers after 1 hour in normal media post osmotic stress, regaining full compartment structure, TAD boundary strength and loop formation. Recovery of Drosophila cells after 1 hour in normal media, however, is incomplete as genomes fail to regain normal compartment structure and TAD boundary strength remains significantly reduced. Interestingly, loops are re-formed at this time point. Analysis of these differences revealed that the Drosophila genome does not replicate the canonical A/B compartment organization found in vertebrates. In Drosophila, A compartments engage in A-to-A long-range interactions in a manner similar to that found in the human genome. However, long range B-B interactions are rarely observed. Interestingly, A compartments are specifically enriched in γH2Av and Su(Hw) insulator proteins, suggesting that the LLPS properties of these proteins may be required for compartment formation.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Drosophila S2 cells were sub-cultured for 3 days at 25°C. Human A375 cells were sub-cultured for 3 days prior to experiment. Osmotic stress was induced in the cells by quickly replacing the conditioned media with 250 mM NaCl (from a 5M stock) prepared with complete Schneider’s Drosophila media or DMEM media (for A375 cells) while the control cells were kept in the conditioned media. The cells were kept in the increased NaCl for 1 hour, then for Recovery conditions, cells were returned to original media for 1 hour.  Hi-C experiments were performed on Control, Stress, and Recovery conditions.

first: Bright

last: Amankwaa

first: Christopher

last: Playter

first: Emily

last: Stow

first: Jacob

last: Sanders

first: Tianchun

last: Xue

first: Mariano

last: Labrador


title: Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells [scRNA-seq]

first: Elizabeth

last: Bartom

overall_design: To check whether CSCs are more transcriptionally heterogeneous compared to non-CSCs, we performed scRNA-seq to examine the spread in the transcriptional program utilized by ALDH+CSCs and ALDH-non-CSCs at base level and in response to cisplatin.

first: Yinu

last: Wang

first: Jane

last: Frederick

middle: T

first: Luay

last: Almassalha

first: Yaqi

last: Zhang


title: Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells [RNA]

overall_design: 1. Comparing transcriptomes of ALDH+ CSCs derived from OVCAR5 cells with ALDH- non-CSCs to define CSC and non-CSC associated transcriptomic signatures. 2. Comparing transcriptomes of ALDH+ CSCs derived from OVCAR5 cells with ALDH- non-CSCs at baseline and in response to cisplatin to explore transcriptionally heterogenecity of CSCs vs. non-CSCs in response to chemotherapy. 3. Comparing transcriptomes of ALDH+/- CSCs/non-CSCs treated with DMSO, Dot1Li (500nM, 48 hours), cisplatin (1μM, 24 hours) and Dot1Li+cisplatin to check if DOT1Li can reduce transcriptional malleability and thereby reprogram CSCs to a non-stem state.

middle: M

first: I

last: Ye

first: Alex

last: Duval

first: Paola

last: Gonzalez

first: Karla

last: Medina

first: Joshua

last: Pritchard


title: Reprogramming of 3D genome structure underlying HSPC development in zebrafish [HiC]

city: Guangzhou

first: Feifei

last: Li

state: Guangdong

address: Guangzhou Higher Education Mega Center, Panyu District

institute: South China University of Technology

summary: Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals; however, the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision, its dynamic and role in HSPC development is poorly investigated.Here, we performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish  resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi-scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.

overall_design: To verify the difference of chromosome structure of HPSC in zebrafish's development cycle, we process HiC-seq datas from three different developmental stages.In addition,the HiC-seq data can be a part of co-analysis,reveals the correlation between chromosome structure and function.

first: Min

last: He

first: Xiaoli

first: Wenqing

first: Bingxiang

last: Xu

first: Yibo

last: Lu

first: Jingyi

last: Lai

first: Yiming

last: Ling

first: Huakai

last: Liu

first: Ziyang

last: An


title: melinoe mutant uncovers the role of AtFMN/FHy enzyme as a biochemical hub for flavin synthesis in plants

city: Athens

first: Gerasimos

last: Daras

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary: Riboflavin, or vitamin B2, is the biosynthetic precursor of flavocoenzymes, which are essential for the cell. As the central component of FMN and FAD cofactors, riboflavin controls the function of flavoproteins, being indispensable for growth and cellular metabolism. These cofactors sustain photosynthesis, mitochondrial electron transport, fatty acid oxidation, photoreception and secondary metabolism. While animals depend on exogenous resources, riboflavin is mostly biosynthesized in plants and microorganisms. In the model species Arabidopsis thaliana, the key enzyme AtFMN/FHy has both riboflavin kinase and FMN hydrolase activities. Phylogenetic analysis suggests that AtFMN/FHy proteins occur in algae and land plants. AtFMN/FHy 3D structure displays two distinct domains representing the different enzymatic properties. Here, we report the characterization of a FMN/FHy mutant called melinoe (melin), which displays abnormal plant growth and leaf chlorosis. A nucleotide transition at an intron-exon junction of the FMN/FHy gene of melin homozygous plants results in alternative 3' splicing, skipping twelve amino acids within the FMN phosphatase domain. Leaf variegation was apparent during the entire life cycle of melin homozygous plant that showed a specific gradient pattern of chlorosis beginning from the center of the leaves and extending to the entire leaf lamina. The growth of melin homozygous plants ceased upon transition from the reproductive to the vegetative stage. Biochemical approaches revealed that melin mutant seedlings accumulated riboflavin to exceptionally increased levels. Translational fusion to YFP, showed subcellular localization of FMN/FHy in the cytosol and FMN/FHy was constantly expressed in various organs upon distinct developmental stages. Α holistic transcriptome analysis carried out using Next-generation sequencing of RNA isolated from gradually bleached leaves of fmn/fhy plants and bioinformatics analysis used to identify and implicate genes and signaling pathways involved in flavin metabolism in plants. Overall, the results will shed light on the regulatory role of FMN/FHy in intracellular flavins biosynthesis.

overall_design: Total RNA was extracted  from three distinct leaf stages namely green, pale green and chlorotic variation using the Direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis. RNA-seq libraries were generated using the polyA Strand-Specific Transcriptome Library method of BGI for DNBSEQ platform. Sequencing was performed on DNBSEQ platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample. Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using SOAPnuke (version 1.5.2) with parameters “-l 15 -q 0.2 -n 0.05" and the HISAT2 pipeline (version 2.0.4) with parameters “--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8".

first: Stamatis

last: Rigas


title: Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells

first: Elizabeth

last: Bartom

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

overall_design: Refer to individual Series


title: Reprogramming of 3D genome structure underlying HSPC development in zebrafish [ATAC-seq]

summary: Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals; however, the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision, its dynamic and role in HSPC development is poorly investigated. Here, we performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi-scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.

overall_design: ATAC-seq is processed  to verify the chromatin accessibility, combined with other datas, we can then analyse the function of TFs

last: Zhang


title: CARM1 inhibits ferroptosis in bladder cancer cells by upregulating the expression of ENO1

city: Wuhan

first: Alsiel

last: Tang

address: Zhang zhidong road

department: Urology

institute: Renmin hospital of Wuhan

summary: Coactivator-associated arginine methyltransferase 1 (CARM1) is a protein that helps regulate gene expression. Research has shown that CARM1 is also involved in autophagy, RNA regulation, and cancer development, in addition to its primary role in transcriptional regulation. However, its molecular mechanisms and biological consequences in tumor pathogenesis have not been fully elucidated. Our investigation revealed that the overexpression of CARM1 resulted in the upregulation of α-enolase 1 (ENO1), hence enhancing the proliferation, migration, and invasion of bladder cancer (BC) cells. Our findings suggest that the upregulation of ENO1 expression hinders the occurrence of ferroptosis in BC cells by affecting the ACO1/MFRN1 pathway. Through in vivo and in vitro analyses, we discovered that the CARM1-mediated suppression of ferroptosis in BC cells can be partially reversed by using a specific inhibitor: CARM1-IN-3 dihydrochloride (CI3D). This inhibitor also has the ability to inhibit the growth of BC. Collectively, our data indicate that CARM1 could serve as a new oncogenic component in BC and that suppressing CARM1 activity is a promising viable treatment strategy.

overall_design: Screening for genes with differential expression when overexpressing CARM1

first: Yuqi

first: Weimin

last: Hu

first: Ming

first: Linzhi

first: Yunlong

first: Jinzhuo

last: Ning

first: Fan

last: Cheng