title: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics

city: Richland

first: Lindsey

last: Anderson

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary: The industrial feasibility of photosynthetic bioproduction using cyanobacterial platforms remains challenging due to insufficient yields, particularly due to competition between product formation and cellular carbon demands. Here we demonstrate that circadian regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942, significantly affecting production efficiency. After entrainment to light-dark cycles, cultures maintained under the constant light revealed distinct temporal patterns in sucrose production, exhibiting three-fold higher productivity during subjective night despite moderate down-regulation of the photosynthetic apparatus. This enhanced productivity coincided with reduced glycogen accumulation and halted cell division, suggesting temporal separation of competing processes. Transcriptome analysis revealed coordinated circadian-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. The subjective night was characterized by altered expression of cell division-related genes and reduced expression of genes involved in glycogen synthesis, while showing upregulation of glycogen degradation pathways, alternative electron flow components, the pentose phosphate pathway, and oxidative decarboxylation of pyruvate. These molecular changes created favorable conditions for product formation through enhanced availability of major sucrose precursors (glucose-1-phosphate and fructose-6-phosphate) and maintained redox balance. Our findings suggest that understanding the circadian regulatory rewiring of carbon metabolism could enable two distinct approaches for improving cyanobacterial bioproduction. First, accounting and leveraging natural circadian rhythms for optimizing cultivation conditions, timing of heterologous pathway induction and harvesting patterns. Second, engineering strains that mimic circadian-driven metabolic shifts through controlled carbon flux redistribution and redox rebalancing to enable efficient cycling between growth, storage accumulation, and production phases.

overall_design: The synchronized cultures were divided to enable parallel sampling for the first two 8-hour periods: subjective day (12:00-20:00) and subjective night (20:00-04:00). For both conditions, samples were collected throughout the 8-hour experimental period, with time 0 corresponding to the start of each period (12:00 for subjective day and 20:00 for subjective night). Sucrose production, biomass (OD750), cell number, and glycogen content were monitored at hours 0, 0.5, 1, 2, 4, 6, and 8. For transcriptome analysis, samples were collected at hours 0, 2, 4, and 8. Both conditions were maintained under continuous light.

first: Pavlo

last: Bohutskyi

first: Zachary

last: Johnson


title: Alzheimer's disease risk ABCA7 p.A696S variant disturbs the microglial response to amyloid pathology in mice

status: Public on Mar 13 2025

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: The adenosine triphosphate–binding cassette transporter A7 (ABCA7) gene is ranked as one of the top susceptibility loci for Alzheimer’s disease (AD). While ABCA7 mediates lipid transport across cellular membranes, ABCA7 loss of function has been shown to exacerbate amyloid-β (Aβ) pathology and compromise microglial function. Our family-based study uncovered an extremely rare ABCA7 p.A696S variant that was substantially segregated with the development of AD in 3 African American families. Using the knockin mouse model, we investigated the effects of ABCA7-A696S substitution on amyloid pathology and brain immune response in 5xFAD transgenic mice. Importantly, our study demonstrated that ABCA7-A696S substitution reduces amyloid plaque–associated microgliosis and increases dystrophic neurites around amyloid deposits compared to control mice. We also found increased X-34–positive amyloid plaque burden in 5xFAD mice with ABCA7-A696S substitution, while there was no evident difference in insoluble Aβ levels between mouse groups. Thus, ABCA7-A696S substitution may disrupt amyloid compaction resulting in aggravated neuritic dystrophy due to insufficient microglia barrier function. In addition, we observed that ABCA7-A696S substitution disturbs the induction of proinflammatory cytokines interleukin 1β and interferon γ in the brains of 5xFAD mice, although some disease-associated microglia gene expression, including Trem2 and Tyrobp, are upregulated. Lipidomics also detected higher total lysophosphatidylethanolamine levels in the brains of 5xFAD mice with ABCA7-A696S substitution than controls. These results suggest that ABCA7-A696S substitution might compromise the adequate innate immune response to amyloid pathology in AD by modulating brain lipid metabolism, providing novel insight into the pathogenic mechanisms mediated by ABCA7.

first: Xiaoye

last: Ma

first: Takahisa

last: Kanekiyo


title: An atypical atherogenic chemokine that promotes advanced athero¬sclerosis and hepatic lipogenesis

city: Munich

first: Omar

last: El Bounkari

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia Research (ISD)

country: Germany

institute: LMU Klinikum

summary: Atherosclerosis is the underlying cause of myocardial infarction and ischemic stroke. It is a lipid-triggered inflammatory condition of arterial vessels driven by cytokines and chemokines. Chemokines that affect both vascular and metabolic pathologies are rare. Here we show that D-dopachrome tautomerase (D-DT)/macrophage migration inhibitory factor-2 (MIF-2), a paralog of the atherogenic cytokine MIF, is a novel atypical chemokine promoting athero-sclerotic plaque formation and hepatic lipid accumulation. Mif-2 deficiency and its pharma-cological blockade in hyperlipidemic atherogenic Apoe-/- mice protected against lesion formation and vascular inflammation in early and advanced atherogenesis. MIF-2 promoted monocyte migration and arrest on aortic endothelial monolayers, promoted B-cell recruitment, and increased foam cell formation. Employing biochemical and cellular assays, we identified CXCR4 as a novel receptor for MIF-2. Notably, Mif-2-/-Apoe-/- mice exhibited decreased plasma lipid levels, smaller livers, and reduced hepatic lipid accumulation compared to Apoe-/- mice. Comparison of the hepatic transcriptome and lipidome between Apoe-/- and Mif-2-/-Apoe-/- mice revealed a notable enrichment of lipogenesis-related pathways, triacylglycerides, diacylglycerides, and cholesterol esters in Mif-2-proficient mice. Mechanistic experiments in hepatocytes suggested that MIF-2 regulates activation of SREBP transcription factors to induce down¬stream lipogenic genes, while upstream, this pathway was mediated by the receptors CD74 and CXCR4, and PI3K/AKT but not AMPK signaling. Proximity ligation and FLIM-FRET multiphoton-microscopy indicated that CXCR4 and CD74 form a MIF-2-inducible heteromeric complex. Lastly, MIF-2 was found upregulated in unstable human carotid plaques from atherosclerotic patients undergoing carotid endarterectomy (CEA), suggesting a role for MIF-2 in advanced stages of athero¬sclerosis. Moreover, plasma concentrations of MIF-2 were increased in patients with coronary artery disease (CAD) and correlated with disease severity. Together, these data identify MIF-2 as a novel atherogenic chemokine and CXCR4 ligand associated with CAD that not only promotes lesion formation and vascular inflammation, but also affects hepatic lipogenesis in a CD74/CXCR4/SREBP-mediated manner. MIF-2 may thus be a novel player in atherosclerotic and metabolic disease.

overall_design: To understand the dual role of MIF-2 in advanced atherosclerosis and lipid metabolism, we compared the effects of Mif-2 deficiency in Apoe-/- mice (DKO) on differential gene expression in the liver compared to Apoe-/- (WT) control mice after 12 weeks of HFD.

first: Simon

last: Ebert


title: SETD3 regulates endoderm differentiation of mouse embryonic stem cells through its effect on the canonical Wnt signaling pathway activity

city: Ankara

first: Nihal

middle: Terzi

last: Terzi Cizmecioglu

state: Select...

address: Universiteler Mah., Dumlupinar Bulvari No:1

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

summary: With self-renewal and pluripotency features, embryonic stem cells (ESCs) provide an invaluable  tool to investigate early cell fate decisions. Pluripotency exit and lineage commitment depend on  precise regulation of gene expression that requires coordination between transcription (TF) and  chromatin factors in response to various signaling pathways. SET domain-containing 3 (SETD3) is  a methyltransferase that can modify histones in the nucleus and actin in the cytoplasm. Through  an shRNA screen, we previously identified SETD3 as an important factor in meso/endodermal  lineage commitment of mouse ESCs (mESC). In this study, we identified SETD3-dependent  transcriptomic changes during endoderm differentiation of (mESCs) using time-course RNA-seq  analysis. We found that SETD3 is involved in timely activation of the endoderm-related gene network.  Canonical Wnt signaling pathway was one of the markedly altered signaling pathways in the absence  of SETD3. The assessment of Wnt transcriptional activity revealed a significant reduction in setd3∆  mESCs coincident with a decrease in nuclear pool of the key TF β-catenin level, though no change  was observed in its mRNA or total protein level. Furthermore, proximity ligation assay found an  interaction between SETD3 and β-catenin. We were able to rescue the differentiation defect by  stably re-expressing SETD3 or activating the canonical Wnt signaling pathway by changing mESC  culture conditions. Our results suggest that alterations in canonical Wnt pathway activity and  subcellular localization of β-catenin might contribute to the endoderm differentiation defect of  setd3∆ mESCs.

overall_design: To investigate the function of SETD3 in the regulation of endoderm differentiation, we established an  SETD3 knock-out mouse embryonic stem cell (mESC) line using CRISPR-Cas9.  Then, we differentiated the wild-type and SETD3 knock-out mESCs to definitive endoderm for four  days, and performed RNA-sequencing with two mESC lines at four time points.

first: Emre

last: Balbasi

first: Ceren

last: Alganatay

first: Nurcan

last: Tuncbag

first: Dersu

last: Sezginmert


title: Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb

status: Public on Mar 12 2025

city: Philadelphia

first: Jonathan

middle: A

last: Raper

state: Pennsylvania

address: 105 Johnson Pavilion

department: Department of Neuroscience

institute: University of Pennsylvania

summary: To understand how neural circuits are assembled, it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single-cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance-related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non-clustered delta-protocadherin family of adhesion molecules. We found that two members of the delta1-protocadherin family, pcdh7b and pcdh11, are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus, but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast, two members of the delta2-protocadherin family, pcdh10b and pcdh17, are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1-protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus, while delta2-protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus.

overall_design: Roughly 2000 zebrafish embryos we sacraficed at 36, 48 and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.

first: Daniel

middle: T

last: Barnes


title: Activation of the ERRα Transcriptional Pathway Alleviates Anthracycline-induced Cardiotoxicity by Improving Mitochondrial Metabolism

city: Beijing

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

country: China

institute: Peking Union Medical College

summary: Anthracycline-induced metabolic remodeling and mitochondrial damage are critical early events that contribute to cardiac dysfunction. However, the gene regulatory pathways governing the derangements in myocardial bioenergetics have not yet been fully delineated. Estrogen-related receptor alpha (ERRα) is a key regulator of energy metabolism, especially in tissues with high energy demands. Here, we demonstrate that ERRα acts as a beneficial modulator of mitochondrial metabolism in anthracycline-induced cardiotoxicity (AIC). ERRα gain-of-function enhances cardiomyocyte metabolism and mitochondrial function, thereby alleviating AIC. Conversely, cardiomyocyte-specific knockdown of ERRα exacerbates mitochondrial bioenergetic collapse and worsens heart failure phenotypes in AIC mice. Additionally, our research identifies a top-ranking isoflavone phytoestrogen as a novel ERRα agonist with favorable pharmacological properties. This compound promotes the transcriptional activity of metabolic genes, representing a significant step toward developing natural ERRα agonists for AIC therapy.

overall_design: RNA-seq profiling of cardiac tissue of miniature pigs from control group, Dox group and Dox+Formononetin group.

first: Guanjing

first: Yan

last: Wei

first: Weili

last: Li

first: Ziyi

last: Yin

first: Yun

last: Chen

first: Qi

last: Qiu

first: Wei

first: Yong


title: Knockdown of GCM1 in BeWo Cells

city: Seattle

first: Alison

last: Paquette

state: WA

address: 1900 Ninth Avenue

department: Center for Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

summary: GCM1 was knocked down in syncytialized and unsyncytialized BeWo cells

overall_design: BeWo cells were treated with  Forskolin to induce syncytialization and/or GCM1 siRNA for knockdown.


title: 3D model of human epidermis exposed to Staphylococci reveals keratinocyte responses unique to atopy-associated S. aureus challenge.

city: Krakow

first: Piotr

last: Brzoza

address: Gronostajowa 7

department: Department of Immunology

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

summary:
The interplay between microbiota and skin cells is a key factor underlying the pathophysiology of this barrier organ. Keratinocytes, the main components of the epidermis, are crucial for skin barrier function, but their responses to different bacteria are not well understood.
We present a high-throughput analysis of the transcriptome of human epidermal-like organoids exposed to two vastly different bacterial skin colonists: Staphylococcus epidermidis and Staphylococcus aureus, which are commonly associated with mostly positive and negative interactions with the host, respectively. We observed partly overlapping but predominantly divergent epidermal changes in response to both bacteria. Among the genes most affected by S. aureus, those related to lipid metabolism were predominant.
This work was supported by grants from the Polish National Science Center (UMO-2014/12/W/NZ6/00454 and 2019/35/B/NZ6/03357) and by a grant for research projects for Young Scientists and PhD students from the Jagiellonian University (N19/MNS/000020). The open-access publication has been supported by the Faculty of Biochemistry, Biophysics and Biotechnology under the Strategic Programme Excellence Initiative at Jagiellonian University in Krakow, Poland.

overall_design: Generated 3D organotypic cultures of human keratinocytes from 3 separate healthy donors were exposed to microbial challange from either live Staphylococcus aureus or Staphylococcus epidermidis bacterial cells, with sterlie PBS as a control. After 24h, RNA was isolated and RNAseq analysis was perfomed studying the differences in expression pattern between tested conditions.

first: Michelle

last: Camacho

first: Maria

last: Tyschenko

first: Agnieszka

last: Morytko

first: Mateusz

last: Kwitniewski

first: Maciej

last: Pastuszczak

first: Paulina

last: Stepinska

first: Marcin

last: Migaczewski

first: Joanna

last: Cichy


title: Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression [scRNA-Seq]

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary:
Purpose: To explore the endogenous expression pattern of Erbb2.
Methods:  Approximately 1000 hearts dissected from 72 hpf Tg(myl7:mCherry) embryos were digested in 0.25% trypsin-EDTA solution for single-cell RNA sequencing.
Results: We found that ventricular Erbb2 expression was highly enriched in subcluster 0 and 2, but weakly expressed in subcluster 3, 10 and 12.
Conclusions: Erbb2 exhibits heterogeneous expression during trabeculation.

overall_design: 72 hpf Tg(myl7:mCherry) zebrafish hearts were collected for single-cell RNA sequencing.

first: Jin-xiu

last: Liang

first: Jia

last: Cheng

first: Pei-dong

last: Han


title: Expression data from lung cancer cell lines

city: Hamamatsu

first: HIROFUMI

last: WATANABE

state: Select State

country: Japan

institute: Hamamatsu University of Medicine

summary: Microarrays were performed to detail the differential gene expression about co-expression patterns of the transcription factors that exert detrimental effects in small cell lung cancer cell lines.

overall_design: RNA was extracted from Lu139-NEUROD1 cells, Lu139-EGFP cells, H524-ASCL1 cells, and H524-EGFP cells with or without doxycycline treatment for 72 hours (triplicate for each cell line).

first: Hirofumi

last: Watanabe

first: Yusuke

last: Inoue


title: Xenium-based spatial transcriptomics of brains following chronic plastic exposure

city: Bonn

first: Maria Francesca

last: Viola

address: Carl Troll Str 32

institute: LIMES Institute

summary: Plastic pollution poses a universal yet understudied environmental risk to the immune system. Once ingested, nano- and microplastic particles (MNPs) can translocate from the gut into internal organs, likely via circulation. In humans, MNPs have been detected in macrophages within carotid artery plaques, suggesting that these highly phagocytic cells, may also serve as key targets for MNPs under homeostatic conditions. Kupffer cells (KCs), the liver-resident macrophages, play a crucial role in liver homeostasis by regulating metabolism, clearing opsonized target cells, and serving as the first line of defence against bacteria. Residing within the liver sinusoids, they continuously monitor the bloodstream, efficiently capturing and eliminating pathogens and circulating particles to maintain immune and metabolic balance5. It remains unknown whether KCs efficiently capture and store MNPs and how this might affect liver function. Here, we utilize a mouse model of chronic plastic exposure to assess how ingested MNP influence KC core functions, and thereby also liver function. We show that KCs are the primary hepatic target of MNPs and that 12 weeks of exposure alters their transcriptome and impairs phagocytic capacity, leading to dysregulated liver metabolism. Microplastics, but not nanoplastics, exposure reduces KC-mediated clearance of circulating cells and bacteria and exacerbates diet-induced obesity. These findings suggest that chronic MNP exposure disrupts tissue-specific macrophage functions in a size-dependent manner, with distinct long-term consequences for liver function and overall health.

overall_design: 8-10 week old male C57Bl6/J mice received weekly oral gavages of either PBS, 100mg/kg 50nm polysterene particles or 500nm polysterene particles. After 12 weeks, mice were euthanised a perfused trans-cardially, the brain was dissected and immediately embedded and snap-frozen in liquid nitrogen.

first: Nikola

last: Makdissi

first: Lisa

last: Steinheuser

first: Nelli

last: Blank-Stein

first: Eliana

last: Franco Taveras

first: Katharina

last: Sieckmann

first: Ronja

last: Cardinal

first: Frederike

last: Graelmann

last: Mauel

first: Nele

last: Kronau

first: Jake

last: Thomas

first: David

last: Bejarano

first: Sandra

last: Högler

first: Joachim

last: L Schultze

first: Christoph

last: Thiele

first: Lukas

last: Kenner

first: Andreas

last: Schlitzer

first: Falk

last: Nimmerjahn

first: Dagmar

last: Wachten

first: Martin

last: Fuhrmann

first: Kevin

last: Thurley

first: Elvira

last: Mass


title: Single-cell transcriptomic based heterogeneity of adipose-derived regenerative cells is independent of gender and BMI

city: Odense M

first: Charlotte Harken

middle: Harken

last: Jensen

address: Campusvej 55

department: Clinical Biochemistry/Clinical Research

country: Denmark

institute: Odense University Hospital/University of Southern Denmark

summary: Adipose-derived regenerative cells (ADRCs) are implicated in fat homeostasis and metabolism, but also provide an ample source of cells with widespread regenerative therapeutic use. Being heterogenous in nature, possibly affecting clinical outcome, the ADRC donor BMI and gender may have a large impact on ADRC composition and quality but this remains largely unexplored. Herein, we provide a comprehensive single-cell RNA sequencing ADRC mapping across two cell trial intervention studies but found no gender- or BMI-related variations, except for a minor female increase in PI16/CD55-expressing stem cells. This provides decision-making support on adipose stem cell donor selection, but also adds to gender-based metabolomics.

overall_design:
ADRCs were isolated from lipoapirates obtained from 14 patients undergoing autologous stem cell therapy in two randomized controlled clinical trials at Odense University Hospital, Denmark. Single cell RNA-sequencing was performed on ADRCs from 7 male patients (M1-M7) treated for erectile dysfunction following radical prostatectomy and 7 female patients (F1-F7) treated for breast cancer related lymphodema. Data were compared with a specific focus on gender and BMI.

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Submitter states that missing raw data for sample ED2_M2 is due to corrupt data.
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first: Frederik

last: Bjerre

first: Jakob

middle: V

last: Nielsen

first: Mark

last: Burton

first: Pratibha

last: Dhumale

first: Mads

middle: G

last: Jørgensen

first: Sabrina

last: Hansen

first: Lars

last: Lund

last: Thomassen

first: Jens

last: Sørensen

first: Ditte

middle: C

last: Andersen

first: Charlotte

middle: H


title: Hyperleukocytosis in a neuroblastoma patient after treatment with natural killer T cells expressing a GD2-specific chimeric antigen receptor and IL15

city: Houston

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

summary: The ability of immune cells to expand numerically after infusion distinguishes adoptive immunotherapies from traditional drugs, providing unique therapeutic advantages as well as the potential for unmanageable toxicities. Here, we describe a case of lethal hyperleukocytosis in a patient with neuroblastoma treated on a phase 1 clinical trial (NCT03294954) with autologous natural killer T cells (NKTs) expressing a GD2-specific chimeric antigen receptor and cytokine IL15 (GD2-CAR.15). This patient was the first to be treated on dose level (DL) 5 and the first patient whose product was restimulated with K562-derived artificial antigen-presenting cells (aAPCs) instead of autologous peripheral blood mononuclear cells (PBMCs). Twelve previously treated patients on DLs 1 through 4 did not experience significant toxicity. Our root-cause analysis revealed no genetic alterations of known clinical significance and excluded the possibility of clonal expansion due to insertional retroviral mutagenesis. The use of aAPCs instead of PBMCs for CAR-NKT restimulation induced a hyperproliferative state associated with a distinct gene expression profile that likely contributed to an explosive lymphocyte expansion event and uncontrolled toxicity in the patient. These findings warrant the implementation of measures to control immune cell activation during manufacture of cell therapy products.

overall_design: scRNA-seq from patient' samples.

first: Gengwen

last: Tian

first: Amy

middle: N

last: Courtney

first: Hangjin

last: Yu

first: Saleh

last: Bhar

first: Xin

last: Xu

first: Gabriel

last: Barragan

first: Claudia

last: Martinez Amador

first: Nisha

last: Ghatwai

first: Deborah

last: Schady

first: David

last: de la Cerda

first: Donald

last: Williams Parsons

first: Erica

middle: J

last: Di Pierro

first: Andras

last: Heczey

first: Leonid

middle: S

last: Metelitsa


title: LARP6 promotes carcinogenic features of triple negative breast cancer cell line by directly modulating alternative splicing of associated genes [RNA-Seq]

city: YinChuan

first: Li

last: Guo

address: Victory Street

institute: Ningxia Medical University

summary: Purpose: Triple-negative breast cancer (TNBC) has the highest mortality rate of all breast cancer subtypes and currently lacks effective targeted therapies. LARP6 is an RNA-binding protein associated with cancer promotion, but its mechanism of action in TNBC remains unclear. Methods: Firstly, Western blot (WB) was used to detect the expression level of LARP6 protein in TNBC cell lines. The effects of LARP6 overexpression on TNBC cell proliferation and invasion were determined through Cell Counting Kit-8 (CCK-8) and Transwell experiments. Next, RNA sequencing (RNA-seq) and improved RNA immunoprecipitation and sequencing (iRIP-seq) were performed to analyze LARP6-bound and regulated differentially expressed genes (DEGs) and alternative splicing (AS) events in MDA-MB-231 cells. Finally, RT-qPCR and RIP-qPCR were used for confirmation. Result：Our study found that the overexpressed LARP6 TNBC cell lines significantly promoted thetumor cell proliferation and invasion of cancer (P<0.05). RNA-seq showed that LARP6 overexpression alteredaffected the expression levels of 171 genes, whileand combined with iRIP-seq, it revealedshowed that only EGR1 and LARP6 were bounddirectly bind to by the LARP6 protein, indicating. This shows that LARP6 hasis a weak ability to bind to and regulate differential expression of in regulating genes expression. However, the number of regulatedrelated alternative splicing evensgenes (RASEGs) was upwards ofreached more than 1000, and the correspondingthese genes (RASGs) were mainly enriched in important pathways such as DNA repair and cellular response to DNA damage stimulus. In addition, bassaed on  binding peak calling of iRIP-seq in both IP samples,Through analysis of binding peaks, we found that there were 321 overlapping binding peaks in both IP samples between IP1 and IP2 samples awere identified, in whichnd the genes they were mainly concentrated in the post-transcriptional regulatory pathway, and it was also found that LARP6 might tend to bind motif. The top 5 binding motifs were obtained using HOMER, among which CGACGAG was the binding motifsequence that appeared simultaneously in both IP groups. The intersection of binding peak-related genes andwith RASGs suggestedrevealed that LARP6 could bind to 16 genes and regulate their alternative splicing, thus playing an important role in TNBC progression. directly bind to LARP6, most of which were related to cell proliferation, invasion and drug resistance. Conclusion: We revealed the mechanism that LARP6 promotes TNBC by directly regulating the AS of related genes, which provides a new clue for the targeted therapy of TNBC.

overall_design: In order to clarify the mechanism of LARP6 promoting triple negative breast cancer, RNA-seq and iRip-seq techniques were used to determine the RNA binding targets and motifs of LARP6 in MDA-MB-231 cells, which is helpful to understand the regulation mechanism of LARP6RNA splicing level in triple negative breast cancer and provides a basis for further understanding the role of LARP6 in various biological processes.

first: Yaobang

last: Liu

first: Hong

last: Li

first: Shuxun

last: Yan

first: Jinping


title: Unravelling the influence of wild olive (Olea europaea L. subsp. europaea var. sylvestris) genotype on the tolerance level to Verticillium wilt.

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

summary: The wild olive tree (Olea europaea L. subsp. europaea var. sylvestris) plays a crucial role in the future of olive cultivation, facing challenges such as climate change and emerging diseases. The selection of resistant varieties is among the most sustainable methods for controlling Verticillium wilt. We compared the transcriptomes from two oleaster cultivars with markedly different responses to V. dahliae, AC15 and AC18, susceptible and tolerant, respectively. The differences in the gene expression profile found between AC15 and AC18 stems may determine susceptibility to the disease in the stem tissue. These differences are reflected in the lignin composition of the cell wall.

overall_design: Two certified varieties of wild olive were selected for the development of this study, one that has been classified as tolerant, AC18, and AC15 as susceptible. Total RNA from stems was isolated and purified from three independent biological replicates using an automated extraction system Maxwell® 16 Lev Plant RSC Instrument (manufactured by Promega Corporation, Wisconsin, USA) using a Maxwell® RSC RNA FFPE kit (AS1440, Promega, Wisconsin, USA).

first: Beatriz

last: Mascuñano

first: Juan

last: Muñoz-Blanco


title: Wildtype and methyl-deficient Puf4 RIP-seq in Cryptococcus neoformans

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main Street Suite 5240

department: Microbiology and Immunology

institute: University at Buffalo

summary: Puf4 is a pumilio/fbf domain containing RNA binding protein. Our previous work revelated that Puf4 modulates ER stress and anrifungal resistance in C. neoformans. Our recent work showed that Puf4 is targeted by arginine methyltransferases. We investigated the RNA binding network of wildtype Puf4 as well as two mutants that have methyl-deficient (arginine to lysine) mutations.

overall_design: Cells were grown overnight to OD600 of 1.5-1.8 in 2 L YPD at 30˚C. Wildtype Puf4-FLAG and RtoK mutants where Arg462 or Arg783/Arg785 are mutated were analyzed. Puf4 was immunoprecipitated using FLAG beads and RNA was extracted using low ph phenol chloroform. Untagged cells were included as a negative control to assess non-specific binding.

first: Murat

last: Kalem


title: RNA Cytidine Acetyltransferase NAT10 Maintains T Cell Pathogenicity in Inflammatory Bowel Disease

city: Shanghai

first: Haixin

state: Shanghai

address: 36 Yunxin Rd

department: Shanghai Tenth People's Hospital, School of Medicine

institute: Tongji University

summary: The enzyme N-acetyltransferase 10 (NAT10), known as the exclusive catalyst for N4-acetylcytidine (ac4C) modification, has been associated with various cellular processes, including tRNA acetylation, 18S rRNA biogenesis, mRNA stability, and translational efficiency. Despite extensive investigation into its molecular mechanisms in vitro, the physiological function of NAT10 under normal conditions has remained largely undefined. In this study, we found that the deficiency of NAT10 led to a disruption of T cell development at steady state, and identified a pivotal role for NAT10 in preserving the pathogenicity of naïve CD4+ T cells to induce adoptive transfer colitis. Mechanistically, the lack of NAT10 triggers the diminished stability of the anti-apoptotic gene Bag3, initiating a cascade of events that includes the upregulation of apoptosis-related genes and an accelerated rate of apoptosis in T cells. Our findings reveal a previously unrecognized role of the NAT10-ac4C-Bag3 axis in maintaining T cell homeostasis in vivo.

overall_design: We isolated naïve CD4+ T cells from 3 WT and 3 Nat10 cKO mice for RNA-sequencing.

first: Xuemin

last: Cai

first: Xinhui

last: Yang

first: Xiaohan

last: Song

first: Yuxin

last: Kong

first: Mei

first: Qielan

last: Wu

first: Ping

last: Wang

first: Jing

last: Zhou

first: Hua-Bing


title: LARP6 promotes carcinogenic features of triple negative breast cancer cell line by directly modulating alternative splicing of associated genes [RIP-Seq]

first: Li

first: Yaobang

first: Kai

last: Zhang


title: Comparison of 3' GEM-X and PIPseq V on human immune cells

city: New York

first: Caleb

last: Lareau

state: New York

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

institute: Memorial Sloan Kettering

summary: Single cell technologies are rapidly evolving. Here, we benchmarked two state-of-the-art profiling techniques, 10x Genomics 3' GEMX and Illumina PIPseq V, for performance, including cell type ID and cluster inference. Our results provide insights into the future of single-cell technologies

overall_design: PBMCs from a healthy human donor were split and processed in parallel with two technologies for scRNA-seq, 3' GEM-X and PIPseq v5

first: Lareau

last: Caleb

first: Chaligne

last: Ronan

first: Kumpaitis

last: Karolis


title: Beclin 1 of megakaryocytic lineage cells is locally dispensable for platelet hemostasis but functions distally in bone homeostasis

city: Su Zhou ; Jiang Su

first: Fang

middle: Yi

last: Xuan

address: No.199, Ren Ai Road

institute: Soochow university

summary: Becn1 deficiency in the megakaryocytic lineage reduces sex hormone-binding globulin (SHBG), thus releasing testosterone into the blood and ultimately leading to increased bone mass and improved bone quality.

overall_design: In order to explore the effect of Becn1 on megakaryocytes in mice.We then performed gene expression profiling analysis using data obtained from RNA-seq of megakaryocytes in Becn1f/f and Becn1f/f ;Pf4-iCre mice.

first: Lei

last: Li

first: Chen

last: Zhao

first: Ruizhi

first: Yixuan

last: Fang

first: Jianrong


title: microRNA sequencing of MSC-derived Extracellular vesicles

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Human bone marrow-derived MSCs were stimulated with Bronchoalveolar lavage fluid (BALF) from healthy individuals or patients with ARDS, Cystic Fibrosis, Cystic Fibrosis positive for Aspergillus or untreated untreated MSC. Extracellular vesicles were isolated from MSC conditioned medium following minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles (J Extracell Vesicles. 2014 Dec 22:3:26913. doi: 10.3402/jev.v3.26913. eCollection 2014). In Phase 1 of this study, differential expression as well as discriminant analysis was used to identify 14 microRNAs that were differentially expressed in MSC-derived EVs from MSCs exposed to BALF from ARDS patients compared to healthy controls. The effect of EVs on cellular physiology and was demonstrated in vitro by demonstration that wwo miRNAs involved in regulation of the cystic fibrosis transmembrane conductance regulator (CFTR), miRNA-145-5p and miRNA-138-5p, were also significantly increased in ARDS BALF-exposed hMSCs EVs. Functionally, EVs from hMSCs exposed to either ARDS or HV BALF had differential on CFTR Cl- secretion by cultured primary human bronchial epithelial cells, an effect predicted to reduce mucociliary clearance.

overall_design: Translational study to demonstrate the acute respiratory distress syndrome (ARDS) inflammatory environment alters mesenchymal stromal cell (MSC) gene and protein expression as well as the microRNA (miRNA) content of MSC-extracellular vesicle (EVs). RNA was isolated from each EV preparation as described in the manuscript submitted and only samples that passed quality control with an A260/A280 above 1.80 were used for RNA sequencing (control=16; ARDS=12; HV=14). A total of 35 ul (35 ng/µl) of eRNA (EV preparation-derived RNA) was used for miRNA sequencing performed using the HTG EdgeSeq miRNA Whole Transcriptome Assay (miRNA WTA, as per manufacturer’s instructions as published). The miRNA library was sequenced on a NextSeq (Illumina, Inc., San Diego, CA) using a V3 150-cycle kit with two index reads. PhiX (Roche, Mississauga, ON, CAN). Data were returned from the sequencer in the form of demultiplexed FASTQ files, with one file per original well of the assay. The HTG EdgeSeq Parser (v. 5.0.535.3181, HTG Molecular, Tucson, AZ, USA) was used to align the FASTQ files to the probe list to collate the data. Raw read counts for the 42 samples were imported into R to perform differential expression analyses with the R package DESeq2 28. Variance stabilization transformation was used to prepare data for analyses. Significance analyses of microarrays (SAM) was run using one class analysis approach to identify miRNAs over-represented in EVs derived from control hMSCs 29 based on the normalized data using variance stabilization transformation. The delta value was set to 7 (the best delta parameter value selected by the software with the lowest False Discovery Rate (FDR]) using 1000 permutations, FDR cut-off was 0.001 (%).

first: C

first: S

middle: R

last: Enes

first: D

last: Weiss


title: Analysis of Metabolically Stressed Primary Hepatocytes with IL-1β Recombinant Protein for 24 Hours

city: Cheongju

first: JeongSu

last: Park

address: 194-21 Osong-saeng-myung-1 Ro

department: College of Pharmacy

country: South Korea

institute: Chungbuk National University

summary: RNA-seq analysis of primary hepatocytes isolated from C57BL/6N mice, stimulated with IL-1β recombinant protein to examine the transcriptional response to inflammatory signaling.

overall_design: Primary hepatocytes were isolated from C57BL/6N mouse livers. Liver perfusion was performed using 75 ml of an enzyme buffer solution containing collagenase type 1 (650 µg/ml; Worthington, Cat. LS004197) and collagenase P (50 µg/ml; Roche, Cat. 11213865001). Upon confirming successful cannulation, a cut was made at the hepatic portal vein for drainage of the perfusate. The liver was then dissected, finely minced, and filtered through a 100 µm filter. Hepatocytes were washed twice with enzyme buffer solution and subsequently resuspended in complete M199 medium. Cells were seeded in 12-well plates and incubated for 3 hours. Following this, the medium was changed, and cells were treated with IL-1β recombinant protein for 24 hours. RNA was isolated for sequencing from 2 untreated control samples (Control1, 2, 3) and 2 IL-1β treated samples (Treatment1, 2, 3).

first: Yoon Seok

last: Roh


title: Decoding muscle-resident Schwann cell dynamics during neuromuscular junction remodeling [spinal crush]

city: Ann Arbor

first: Susan

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

summary: This investigation leverages single-cell RNA sequencing (scRNA-Seq) to delineate the contributions of muscle-resident Schwann cells to neuromuscular junction (NMJ) remodeling in models of healthy, partially denervated, and completely denervated muscles. The study identifies several distinct Schwann cell subtypes, notably a novel terminal Schwann cell (tSC) subtype integral to the denervation-reinnervation cycle, distinguished by a transcriptomic signature indicative of cell migration and polarization. It also characterizes three myelin Schwann cell subtypes, which are notably enriched with genes associated with myelin production, in addition to mesenchymal differentiation and collagen synthesis. Importantly, SPP1 signaling emerges as a pivotal regulator of NMJ dynamics, promoting Schwann cell proliferation and muscle reinnervation across the studied nerve injury models. These findings advance our understanding of NMJ maintenance and regeneration and underscore the therapeutic potential of targeting specific molecular pathways to treat neuromuscular and neurodegenerative disorders.

overall_design: S100GFPtg and S100GFPtg Sod1-/- mice were bred at the University of Michigan, were fed normal chow ad libitum, and housed 12:12 hour light-dark cycle under the UofM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). We used 2-month-old male mice from each genotype (n=4 per group). Additionally, we included an S100GFPtg mouse that underwent sciatic nerve crush injury and was harvested at 7 days post-injury (7dpi), referred to as S100GFPtg 7dpi. We simultaneously harvested and processed hind limb muscles (Tibialis Anterior and Gastrocnemius) from all groups. Using Fluorescence-Activated Cell Sorting, we separated GFP+ and GFP- single cells. The sorted cells then underwent 10X Genomics library preparation and sequencing.


title: Gene expression data in total mRNA from human SKMEL28 melanoma cell line transduced with shCont, shp16, shATR

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

summary: p16/CDKN2A is a critical cell cycle regulator and tumor suppressor that is lost in ~50% of all human cancers. Recent studies have identified roles of p16 outside of the cell cycle, including in ATR and mTORC1 activation.

overall_design: To investigate the transcriptional differences upon p16 and ATR loss, we knocked down p16 with or without knockdown of ATR in SKMEL28 human melanoma cell lines. We isolated total mRNA. All samples were done in triplicate. Comparative gene expression profiling analysis for SKMEL28 shGFP (control), shp16, and shp16+shATR.

middle: M

first: Naveen

middle: K

last: Tangudu


title: Neuronal chromatin remodeling factors in the mammalian nervous system [ChIP-Seq]

city: Mississauga

first: Ho Sung

last: Rhee

address: 3359 Mississauga Rd

department: Cell and Systems Biology

institute: University of Toronto

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin remodeling factors play important roles in accessibility formation of regulatory DNA. The mechanism by which chromatin remodeling factors regulate regulatory DNA regions that activate expression of cell type-specific genes during the nervous system development remains unknown. Chromatin remodeling complexes have neuron-specific factors, which are often mutated in patients with neurological disease. Here we demonstrate that neuronal chromatin remodeling factors activate neuronal gene expression during the nervous system development.

overall_design: Examination of ChIP-seq profiles of mouse ES cell-derived neurons by deep sequencing

first: Kaitlin

last: Montanera

first: Alyssa

last: Ialongo

first: Ssu-Yu

last: Yeh


title: Single-cell landscape and regulation of alternative polyadenylation in the brain

city: Hangzhou

first: Jiuhong

state: Zhejiang

address: No. 1369, West Wenyi Road

institute: Zhejiang university

summary: As so far, the trans-regulation of alternative polydenylation (APA) are poorly understood. In this study, we de novo predicted multiple APA regulators based on large-scale single-cell data and detected some potential regulators, including PABPN1, SF3B4, U2AF2, HDAC1 and PCBP2. To further validate the function of these potential regulators, we generated two biological replicates of knock-down lines for each gene in HEK293T, and then carried out RNA-seq experiments  after extracting nuclei to measure the transcriptome-wide APA usage difference.

overall_design: APA profiling analysis of RNA-seq data from HEK293T cells after knocking down APA regulators, including PABPN1, SF3B4, U2AF2, HDAC1 and PCBP2.

first: Carles

middle: A

last: Boix

first: Xushen

last: Xiong


title: Neuronal chromatin remodeling factors in the mammalian nervous system [ChIP-seq]

first: Montanera

last: Kaitlin

first: Ialongo

last: Alyssa

first: Yeh

last: Ssu-Yu

first: Rhee

last: Ho Sung


title: Proteogenomic Characterization of Primary Oral Cancer Unveils Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked to Lymph Node Metastasis [RNA-seq]

city: Hongkong

first: Yu

middle: university of

last: Liu

address: 10 Mui Fong Street

department: Faculty of Dentistry

country: Hong Kong

institute: The university of hongkong

summary: Our genomic analysis identified significant mutations in key genes within the MAPK, TGF-β, and WNT signaling pathways, which are essential for tumor development. The proteogenomic analysis highlighted pathways critical for lymph node dissemination and factors contributing to an immunosuppressive tumor microenvironment. Elevated levels of POSTN were found to reorganize the extracellular matrix (ECM), interact with TGF-β, disrupt cell cycle regulation, and suppress the immune response by reducing VCAM1 activity. Integrated analyses of single-cell and spatial transcriptome data revealed that cancer-associated fibroblasts (CAFs) secrete TGF-β1/2, promoting cancer cell metastasis through epithelial-mesenchymal transition (EMT). Our integrated multi-omics analysis provides a detailed understanding of molecular mechanisms driving lymph node metastasis of OSCC. These insights could lead to more precise diagnostics and targeted treatments.

overall_design: We analyzed a cohort of 46 patients with primary OSCC, including 10 with lymph node metastasis and 36 without. Using a comprehensive multi-omics approach—encompassing genomic, transcriptomic, proteomic, epigenetic, single-cell, and spatial analyses—we integrated data to delineate the molecular landscape of OSCC in the context of lymph node metastasis.

first: Zhenyu

last: Yang

first: Gao

last: Zhang

first: Jingya

last: Pu

first: Yuxiong

last: Su


title: Targeting the splicing factor SNRPB inhibits endometrial cancer progression by retaining the POLD1 intron

city: jinan

first: David

last: Li

address: 44 Wenhua Xi Road,Jinan

institute: Shandong University

summary: Dysregulated alternative splicing has been closely linked to the initiation and progression of tumors. Nevertheless, the precise molecular mechanisms through which splicing factors regulate endometrial cancer progression are still not fully understood. This study demonstrated the elevated expression of the splicing factor SNRPB in endometrial cancer samples. Furthermore, our findings indicated that high levels of SNRPB expression are correlated with a poor prognosis in endometrial cancer patients. Functionally, SNRPB inhibition hindered proliferative and metastatic capacities of endometrial cancer cells. Mechanistically, we revealed that SNRPB knockdown decreased POLD1 expression, and there was retention of POLD1 intron 22 after SNRPB silencing in endometrial cancer cells based on RNA-seq data analysis. The retained intron 22 of POLD1 created a premature termination codon, leading to the absence of amino acids 941 to 1107 and loss of the site of interaction with PCNA, which is essential for POLD1 enzyme activity. In addition, POLD1 depletion decreased the increase in the malignancy of endometrial cancer cells overexpressing SNRPB. Furthermore, miR-654-5p was found to bind to the 3’-UTR of SNRPB directly, resulting in SNRPB expression inhibition in endometrial cancer. Antisense oligonucleotide-mediated SNRPB inhibition led to a decrease in the growth capacity of a CDX model and a PDX model. Overall, SNRPB promotes the efficient splicing of POLD1 by regulating intron retention, ultimately contributing to high POLD1 expression in endometrial cancer. The oncogenic SNRPB/POLD1 axis is an interesting therapeutic target for endometrial cancer, and ASO-mediated silencing of SNRPB may offer a promising therapeutic approach for treating endometrial cancer patients.

overall_design: To study the molecular mechanisms by which SNRPB exerts oncogenic functions, SNRPB expression was silenced using specific siRNA, and then RNA-seq was performed in Ishikawa cells.

first: Yingwei


title: Gene expression profile in 7.5ED embryos, 14.5ED embryos and liver of 7.5 neonates from either control or obese (SL) grandfathers

city: L'Hospitalet

first: Josep

last: Jimenez-Chillaron

state: Barcelona

address: c/ Feixa Llarga s/n, Pavello de Govern, 4a planta, Biophysics Unit

department: Physiological Sciences

institute: University of Barcelona

summary:
We developed a mouse model of childhood obesity. We next explored whether the effects of childhood obesity influence patterns of expression on the grandoffspring.
The main objective of this study is to  find differentially expressed genes in samples of embryos or liver of early post-natal mice derived from obese parents as opposed to the progeny derived from non-obese (control) parental mice.

overall_design: We collected and analyzed the expression profileof embryos (ED7,5; ED14,5) and noenatal liver (PN7.5) in the grandoffpring of control and obese mice.

last: Jiménez-Chillarón


title: Histone lactylation drives liver cancer metastasis by facilitating NSF1 mediated ferroptosis resistance after microwave ablation

city: Sichuan

first: Jia

middle: yan

last: Huang

address: No.37 Guoxue Lane, Wuhou District

department: Ultrasound

institute: West China hospital

summary: Insufficient microwave ablation (IMWA) is linked to aggressive hepatocellular carcinoma (HCC) progression. An increase in lactate level after sublethal heat stress (HS) has been confirmed in HCC. However, the role of lactate-related histone lactylation in the progression of HCC underwent sublethal HS remains unclear. Here, we found that the metastatic potential of HCC is enhanced in a lactate-dependent manner after IMWA. Meanwhile, sublethal HS triggers an upregulation of H3K18la modification, as validated in a cell-derived xenograft mouse model and human HCC samples. By employing an integration analysis of proteomic and transcriptomic profiling, we revealed that HCC cells exhibit an upregulation of intracellular iron ion homeostasis and develop resistance to platinum-based drugs after exposure to sublethal HS. We subsequently integrated proteomic and transcriptomic data with H3K18la-specific chromatin immunoprecipitation (ChIP) sequencing to identify candidate genes involved in sublethal heat treatment-induced HCC cell metastasis. Mechanically, the upregulation of H3K18la modification enhances the transcriptional activity of NFS1, a key player in iron-sulfur clusters biosynthesis, thereby reducing the susceptibility of HCC to ferroptosis post IMWA. Knocking down NFS1 diminished the metastatic potential of sublethal heat-treated HCC cell. Additionally, the deficiency of NFS1 exhibited a synergistic effect with oxaliplatin, leading to a significant inhibition of the metastatic capability of HCC cells both in vitro and in vivo, regardless of HS treatment. In conclusion, our study reveals the oncogenic role of Histone lactylation in HCC after IMVA, we also bridge histone lactylation with ferroptosis, which provides novel therapeutic targets for HCC following microwave ablation, particularly when combined with oxaliplatin-based chemotherapy.

overall_design: Experimental design1 : To investigate the regulation of Histone lactylation in HCC cell metastasis following insufficient microwave ablation and enhance anti-ferroptosis capability, we established a sublethal heat-treated model using the MHCC-97H cell line treated with water baths at 37℃ and 47℃. Experimental design2 : To investigate the regulatory mechanisms of Histone lactylation in HCC cell metastasis following insufficient microwave ablation, we established a sublethal heat-treated MHCC-97H cell line with targeted gene knockdown using shRNA.


title: RNA Cytidine Acetyltransferase NAT10 Maintains T Cell Pathogenicity in Inflammatory Bowel Disease [ATAC-Seq]

first: Haixin

first: Xuemin

last: Cai

first: Xinhui

first: Xiaohan

last: Song

first: Yuxin

last: Kong

first: Mei

first: Qielan

last: Wu

first: Ping

last: Wang

first: Jing

last: Zhou

first: Hua-Bing


title: Developmental exposure to air pollution particulates increases asthma severity, alters the RNA transcriptome, and DNA methylation in female adult progeny [WGMS]

city: Ultimo

first: Razia

last: Zakarya

state: NSW

address: 15 Broadway

department: SoLS

country: Australia

institute: UTS

type: Methylation profiling by high throughput sequencing

summary: Maternal exposure to particulate air pollution increases the incidence and severity of asthma in offspring, yet the mechanisms for this are unclear. Known susceptibility loci are a minor component of this effect.  We interrogate a mouse allergic airway disease model to assess epigenetic associations between maternal air pollution exposure and asthma-like responses in offspring. Maternal air pollution exposure increased allergic airway disease severity in adult offspring associated with a suppressed transcriptomic response to allergen. Control progeny showed differential expression of 2842 genes across several important pathways, including the SMAD and TGFβR pathways, whilst air pollutant progeny showed an 80% reduction in differentially expressed genes and abrogation of many pathway associations. Whole genome CpG methylome analysis following allergen challenge detected differential methylation regions across the genome. Approximately 20% of differentially expressed genes were associated with differential methylation. Differentially methylated regions were markedly reduced in offspring of air pollution exposed mothers, and this was most evident in intronic regions and some transposable element classes.  This study shows that allergic airways disease in adult offspring of PM2.5 exposed mothers had a markedly repressed transcriptomic response, a proportion of which was associated with identifiable changes in the lung’s methylome. The results point to an epigenetic contribution to the severity of asthma in offspring of mothers exposed to particulate air pollution.

overall_design: Lung homogenates of 13 week old female offspring (+/- OVA challenge) of (+/-) PM2.5 exposed dams examined by RNA-seq and WGMS

first: Brian

last: Oliver

first: Chris

last: O'Neill


title: The Role of Histone Modifications in Chromatin-Mediated Transcriptional Repression in the Protozoan Parasite Trichomonas vaginalis [ChIP-Seq]

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

institute: Yonsei University College of Medicine

summary: Trichomonas vaginalis is an extracellular flagellated protozoan responsible for trichomoniasis, one of the most prevalent non-viral sexually transmitted infections. To persist in the host, T. vaginalis employs sophisticated gene regulation mechanisms to adapt to hostile environmental conditions. Although transcriptional regulation is crucial for this adaptation, the specific molecular mechanisms remain poorly understood. Epigenetic regulation, particularly through histone modifications, has emerged as a key modulator of gene expression. Our previous study demonstrated the role of histone modifications H3K4me3 and H3K27Ac in promoting active transcription. However, the full extent of epigenetic regulation in T. vaginalis remained unclear. In this study, we extend these findings by exploring the repressive role of two additional histone H3 modifications, H3K9me3 and H3K27me3. Genome-wide analysis reveals that these modifications are negatively correlated with gene expression, impacting not only protein-coding genes but also repeat genes and transposable elements. These findings offer new insights into the dual role of histone modifications in both activating and repressing gene expression, providing a more comprehensive understanding of epigenetic regulation in T. vaginalis. This expanded knowledge could inform the development of novel therapeutic strategies targeting the epigenetic machinery of this parasite.

overall_design: Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) was performed to analyze histone modifications, including H3K4me3, H3K27ac, H3K9me3, and H3K27me3, in Trichomonas vaginalis cells.

first: Min-Ji

first: Mikyoung

last: kim

first: Yong-Joon

last: Cho


title: The Role of Histone Modifications in Chromatin-Mediated Transcriptional Repression in the Protozoan Parasite Trichomonas vaginalis [RNA-seq]

overall_design: To investigate histone modifications in the regulation of Trichomonas vaginalis transcriptome, we analyzed mRNA levels through RNA-seq.


title: Immunomodulatory Role of the Stem Cell Circadian Clock in Muscle Repair

city: Chicago

first: Pei

last: Zhu

state: IL

address: 420 E. Superior St

department: Biochemistry and Molecular Genetics

institute: northwestern university

summary: The circadian clock orchestrates vital physiological processes such as metabolism, immune function, and tissue regeneration, aligning them with the optimal time of day. This study identifies an intricate interplay between the circadian clock within muscle stem cells (SCs) and their capacity to modulate the immune microenvironment during muscle regeneration. We uncover that the SC clock provokes time-of-day (TOD)-dependent induction in inflammatory response genes following injury, particularly those related to neutrophil activity and chemotaxis. These responses are driven by rhythms of cytosolic regeneration of the signaling metabolite NAD+. We demonstrate that genetically enhancing cytosolic NAD+ regeneration in SCs is sufficient to induce robust inflammatory responses that significantly influence muscle regeneration. Furthermore, using mononuclear single-cell sequencing of the regenerating muscle niche, we uncover a key role for the cytokine CCL2 in mediating SC-neutrophil crosstalk in a TOD-dependent manner. Our findings highlight a crucial intersection between SC metabolic shifts and immune responses within the muscle microenvironment, dictated by the circadian rhythms, and underscore the potential for targeting circadian and metabolic pathways to enhance tissue regeneration.

overall_design: Mononucleated cells from the tibialis anterior (TA) muscles of both hindlimbs were collected at ZT4 and ZT16 on day 0, 1, and 3 after injury. Single cells were collected through fluorescence-activated cell sorting (FACS), excluding dead cells identified by propidium iodide (PI) staining. Samples from each time point and day were captured in droplet emulsions using a 10x Chromium Controller (10x Genomics), aiming for 10,000 cells per sample, and then sequenced.

first: Eric

last: Pfrender

first: Adam

middle: W

last: Steffeck

first: Collen

last: Reczek

first: Yalu

first: Abhishek

middle: V

last: Thakkar

first: Neha

last: Gupta

first: Ariana

last: Kupai

first: Amber

last: Willbanks

first: Richard

middle: L

last: Lieber

first: Ishan

last: Roy

first: Navdeep

last: Chandel

first: Clara

middle: B

last: Peek


title: Developmental exposure to air pollution particulates increases asthma severity, alters the RNA transcriptome, and DNA methylation in female adult progeny [RNA-Seq]

first: Razia

last: Zakarya

first: Brian

middle: G

last: Oliver

first: Chris


title: Characterization of group I introns in generating circular RNAs as vaccines [SPLASH]

city: Singapore

first: Roland

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: Group I introns can be utilized for efficient circularization of RNA molecules; however different introns show variations in their efficiencies of circularization and immune response inside cells.  Here, we generated circular RNAs using permuted intron-exon (PIE) systems of group I introns from eight different organisms. We observed that group I introns have variable circularization efficiencies, circularize with high accuracies, and form circular RNAs with distinct reactogenicities. Group I introns also exhibit different sequence requirements for their exon1 and exon2 domains, enabling us to engineer elements such as a S1 tag for better purification. Structural probing and mutational analysis in group I introns and their PIE RNAs showed that structural features in P2 and P9 domains are correlated with circularization efficiency and that swapping sequences can restore pairing to improve circularization. Additionally, RNA modifications do not increase protein production but decrease the reactogenicity of circular RNAs. We demonstrated that circular RNAs made by Scytalidium dimidiatum group I intron elicit strong immunogenicity against SPIKE protein and serve as effective RNA vaccines.  Our work deepens the understanding of the properties of group I introns and expands the panel of introns that can be used to generate circular RNAs for vaccines and therapeutics.

overall_design: To determine how the bases are paired to each other in the Po and Gv PIE precursor forms, we performed proximity ligation sequencing using SPLASH on Po and Gv PIE systems.

first: Kuo-Chieh

last: Liao

first: Zebin

last: Hong

first: Antson

last: Tan

first: Aixin

last: Yap

first: Xiang

last: Gao

first: Tzuen Yih

last: Saw

first: Jian

last: Han

first: Youzhi Anthony

last: Cheng

first: Jian An Jovi

last: Lim

first: Su Ying

first: You Zhi Nicholas

last: Cheang

first: Wilfried A

last: Saron

first: Abhay P

last: Rathore

first: Li

last: Zhang

first: Bhuvaneshwari

last: Shunmuganath

first: Rashi

first: Tan Siang Isabelle

last: Ling

first: Xinlei

last: Qian

first: Kiren

last: Purushotorman

first: Paul

last: Macary

first: Ashley

last: St John

first: Yi Yan

last: Yang

first: Sylvie

last: Alonso

first: Haiwei

last: Song

first: Yue

last: Wan


title: Single Cell Spatial Transcriptomics of the Murine Embryonic Palate Links Pax9 to Patterning and Organization of Extracellular Matrix Components

city: Okayama

first: Ziyi

last: Wang

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Molecular Biology and Biochemistry

institute: Okayama University

summary: Despite advances in understanding the morphological disruptions that lead to defects in palate formation, the precise perturbations within the signaling microenvironment of palatal clefts remain poorly understood. To explore in greater depth the genomic basis of palatal clefts, we designed and implemented the first single cell spatial RNA-sequencing study in a cleft palate model, utilizing the Pax9-/- murine model at multiple developmental timepoints, which exhibits a consistent cleft palate defect. A novel platform for true single-cell resolution spatially resolved transcriptomics (Visium HD, 10x Genomics, Inc.) was employed using custom bins of 2x2 µm spatial gene expression data, then validated using Xenium In Situ mRNA spatial profiling and RNAscope Multiplex. Functional enrichment analysis revealed a palate cell-specific perturbation in Wnt signaling effector function in tandem with disrupted expression of extracellular matrix genes in developing mesenchyme. As a key step toward laying the framework for identifying key molecular targets these data can be used for translational studies aimed at developing effective therapies for human palatal clefts.

overall_design: FFPE tissue sections from the embryonic murine secondary palate, ages E12.5 (Pax9-/- vs. WT) and E13.5 (Pax9-/- vs. WT), were placed on Visium HD slide and prepared according to 10X Genomics protocols. After H&E staining, imaging and decrosslinking steps, tissue sections were incubated with mouse specific probes targeting 19,405 genes (10X genomics, Visium Mouse Transcriptome Probe Set v2.0 mm10-2020-A).

first: Jeremie

middle: O

last: Piña

first: Resmi

last: Raju

first: Evan

last: Stipano

first: Aye

middle: C

last: Myo

first: Mitsuaki

last: Ono

first: Parna

last: Chattaraj

first: Masae

last: Furukawa

first: Rena

middle: N

last: D’Souza


title: Denfivontinib activates effector T-cells through NLRP3-inflammasome, yielding potent anticancer effects by combination with pembrolizumab

first: Dongkwon

last: Kim

address: Yonsei ro 50-1

institute: Yonsei university

summary: Various combination therapies have been investigated to overcome the limitations of using immune checkpoint inhibitors. However, determining the optimal combination therapy remains challenging. To overcome the therapeutical limitation, we conducted a translational research to elucidate the mechanisms by which AXL inhibition enhances the anti-tumor effects when combined with anti-PD-1 antibody therapy. Herein, we demonstrated improved antitumor effects through combination treatment with denfivontinib and pembrolizumab which resulted in enhanced differentiation into effector CD4+ and CD8+ memory T cells, accompanied by an increase in IFN-γ expression in the YHIM-2004 xenograft model derived from patients with NSCLC. Concurrently, a reduction in the number of immunosuppressive M2 macrophages and myeloid-derived suppressor cells was observed. Mechanistically, denfivontinib potentiated the NOD-like receptor pathway, thereby facilitating the NLRP3 inflammasome formation. This leads to macrophage activation via the NF-kB signaling pathway activation. We have confirmed that the positive interaction between macrophages and T cells arises from the enhanced antigen-presenting machinery of activated macrophages. Furthermore, the observed tumor effects in AXL knock-out mice confirmed that AXL inhibition by denfivontinib enhances the anti-tumor effects, thus opening new avenues for therapeutic interventions aimed at overcoming limitations in immunotherapy. To demonstrate the extent to which our findings reflect clinical results, we analyzed bulk-RNA sequencing data from 21 NSCLC patients undergoing anti-PD-1 immunotherapy. The NLRP3 inflammasome score influenced enhanced immune responses in patient data undergoing anti-PD-1 immunotherapy, suggesting a role for NLRP3 inflammasome in activating immune responses during treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigate RNA expression level of Tumor sample obtained from humanized mouse model, we engrafted human tumor sample. Therefore, we received RNAseq data from MACROGEN in KOREA

first: DongKwon

first: MiHyun

first: Kyoung-Ho

last: Pyo

first: ByoungChul

last: Cho


title: Chemically induced senescence prompts functional changes in human microglia-like cells

city: Montreal

first: Janelle

last: Drouin-Ouellet

state: Quebec

address: 2940, chemin de Polytechnique Pavillon Jean Coutu

department: Pharmacy

institute: University of Montreal

summary: In response to various stressors, cells can enter a state called cellular senescence which is characterized by irreversible cell cycle arrest and a senescence-associated secretory phenotype (SASP). The progressive accumulation of senescent glial cells in the central nervous system (CNS) with aging suggests a potential role for senescence as driver of aging and inflammation in the brain. As the main immune cell population residing in the CNS, microglia are thought to play a pivotal role in the progression of age-associated neuroinflammation. Furthermore, due to their slow turnover, microglia are highly susceptible to undergoing cellular senescence. However, current understanding of age-related changes in microglia and their impact on brain aging is limited. Due to the challenge in accessing human primary microglia and the lack of models to adequately recapitulate aging, this knowledge is predominantly limited to rodent studies. Here, we chemically induced senescence in a human immortalized microglia cell line with a cocktail of senescence inducing molecules. We demonstrate that chemically induced senescent microglia adopt a pro-inflammatory phenotype, have reduced phagocytic activity and impaired calcium activity. Our results show that chemically induced senescence can mimic features of cellular aging and can provide insight on the impact of aging and cellular senescence on human microglia.

overall_design:
To validate that a cocktail of the three small molecules SBI-026965, Lopinavir and O-151 (SLO) could induce features of aging in human microglia, we treated human immortalized microglia cells HMC3 for 6 consecutive days.
We then performed bulk RNA seq of 3 different experimental groups (vehicle control, SLO full dose, as published in Fathi et al., 2021 (DOI: 10.1111/acel.13541) and SLO 1/2 dose) and validated our findings with an array of experiments evaluating aging features, including nuclear structure, proliferation, p21 expression, beta-galactosidase activity, secretion of proinflammatory molecules, phagocytosis and calcium imaging
Comparative gene expression profiling of our RNA-seq data were conducted for VEH controls and each SLO doses (SLO 1, SLO1/2).

first: Sandrine

last: Armanville

first: Chiara

last: Tocco

first: Zaya

last: Haj Mohamad

first: Darren

last: Clarke

first: Richard

last: Robitaille


title: Breaking Rules: The complex relationship between DNA methylation and X-chromosome inactivation in the human placenta

city: Boston

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

type: Methylation profiling by genome tiling array

summary:
Background: The human placenta is distinct from most organs due to its uniquely low-methylated genome. Previous research has shown that DNA methylation (DNAme) is particularly depleted in the placenta at partially methylated domains and on the inactive X chromosome (Xi) in XX samples. While Xi DNAme is known to be critical for X-chromosome inactivation (XCI) in other tissues, its role in the placenta remains unclear. Understanding X-linked DNAme variation in the placenta may provide insights into XCI and implications for prenatal development and phenotypic sex differences.
Methods: DNAme data were analyzed from over 350 human placental (chorionic villus) samples, along with samples from cord blood, amnion, chorion, and fetal somatic tissues. We characterized X chromosome DNAme variation in the placenta relative to sample variables including cell composition, maternal age, placental weight, and fetal birth weight, and compared these patterns to other tissues. We also evaluated the relationship between X-linked DNAme and previously reported XCI gene expression status in placenta.
Results: Our findings confirm that the placenta exhibits significant depletion of DNAme on the Xi compared to other tissues. Additionally, we observe that X chromosome DNAme profiles in the placenta are influenced by cell composition, particularly trophoblast proportions, with minimal variation across gestation. Notably, low promoter DNAme is observed at most genes on the Xi, regardless of XCI status, challenging known associations in somatic tissues between low promoter DNAme and XCI escape.
Conclusions: This study provides evidence that the human placenta has a distinct Xi DNAme landscape, which may inform our understanding of sex differences during prenatal development. Future research should explore the mechanisms underlying the placenta's unique X-linked DNAme profile and the factors involved in XCI maintenance.

overall_design:
DNAme data for 28 chorionic villous (placental) samples, taken from the fetal-facing side of the placenta and combined before running on either of the Illumina Infinium HumanMethylation450 or MethylationEPIC arrays in Vancouver, Canada. DNAme data from raw IDAT files were read into R, and betas were extracted using the preprocessRaw function from minfi. Methylated intensity, unmethylated intensity, and detection p values were calculated for all probes, separately in the samples run on the 450K array (n=3) and the EPIC array (n=28). The raw data (meth/unmeth/detp) is available, as ae the full beta value matrices after using preprocessRaw for both 450K and EPIC samples.

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IDAT files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable SNP genotyping data for open access.
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first: Amy

last: Inkster

first: Allison

last: Matthews

first: Tanya

last: Phung

first: Seema

last: Plaisier

first: Melissa

last: Wilson

first: Carolyn

middle: J

last: Brown

first: Wendy

middle: P

last: Robinson


title: Clinical value of MGMT promoter methylation score in IDHmt low-grade glioma for predicting benefit from TMZ treatment

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

summary: Background: Diffuse IDH mutant low-grade gliomas (LGG) (WHO grade 2) typically affect young adults. The outcome is variable, ranging from 5 to over 20 years. The timing and choice of initial treatments after surgery remain controversial. In particular, radiotherapy is associated with early and late cognitive toxicity. Over 90% of IDHmt LGG exhibit some degree of promoter methylation of the repair gene O(6)-methylguanine-DNA methytransferase (MGMTp) that when expressed blunts the effect of alkylating agent chemotherapy such as temozolomide (TMZ). However, the clinical value of MGMTp methylation predicting benefit from TMZ in LGG is unclear.  Methods: Patients treated in the EORTC-22033 phase III trial comparing TMZ versus radiotherapy served as training set to establish a cutoff based on the MGMT-STP27 methylation score. A validation cohort was established with patients treated in a single center first-line TMZ after surgeri(es).  Results: The MGMT-STP27 methylation score was associated with better progression free survival (PFS) in the training cohort treated with TMZ, but not radiotherapy. In the validation cohort an association with PFS after TMZ treatment was observed. A cutoff value was established in the training cohort to guide treatment decisions. Set above the 95% confidence interval of being methylated, it was significantly associated with PFS in the TMZ-treated training cohort, but not in the radiotherapy arm. However, this cutoff could not be confirmed in the test cohort.  Conclusions: While the MGMTp methylation score was associated with better outcome in TMZ treated IDHmt LGG, a cutoff could not be established to guide treatment decisions.

overall_design: Bisulphite converted genomic DNA from the 109 Low Grade Glioma samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Amélie

last: Darlix

first: Monika

last: Hegi


title: Mitochondrial DNA promotes M2 polarization of tumor associated macrophages and HCC resistance to sorafenib

city: Kaifeng

first: Dengke

last: Bao

state: Henan

address: Jinming Road

department: School of Pharmacy

institute: Henan University

summary: Mitochondrial damage-associated molecular patterns (DAMPs) including mitochondrial DNA (mtDNA), TFAM (transcription factor A, mitochondrial), and ATP, play crucial roles in the regulation of inflammatory environment in human diseases. However, the role of mitochondrial DAMPs in the regulation of tumor microenvironment (TEM) remains unclear. Herein we demonstrate that infiltration of M2 type tumor-associated macrophages (TAMs) was correlated with the resistance of hepatocellular carcinoma (HCC) to sorafenib. We found that cell free mtDNA in the plasma was significantly increased in sorafenib-resistant HCC mice. Sorafenib induced mitochondrial dysfunction and promoted the release of mtDNA into extracellular matrix of HCC. The mtDNAs were retaken by macrophages in the TME of HCC, activated TLR9 signaling on the endosome, and hence promoted the activation of NF-κB and the polarization of TAMs into M2. Application of DNase I to digest mtDNAs or depletion of macrophages with clodronate liposomes reduced the infiltration of M2 macrophage, decreased the growth of HCC, and sensitized the tumors to sorafenib. Furthermore, we showed that blocking the activation of TLR9 enhanced the therapeutic effect of sorafenib in HCC. Together, in the current study, we demonstrate that sorafenib treatment leads to the release of mtDNAs into TME in HCC, which in turn facilitates the polarization of TAMs into M2 macrophages through TLR9 activation and aggravates the resistance of HCC to sorafenib. Our study reveals a novel mechanism underlying circulating mtDAMPs in remodeling HCC microenvironment by reprograming the TAMs and provides a new strategy for improving the therapeutic effect of sorafenib and overcoming its resistance in HCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1-derive macrophage and mtDNA induced M2 polarization.Three independent biological replicates were prepared for RNA isolation and RNA sequencing.

first: Qi

last: Yang

first: Jiaxin

last: Wang

first: Zhixiang

last: Xu


title: Mitochondrial reorganization is rate-limiting for direct cardiac reprogramming

city: Chapel Hill

first: Brian

last: Spurlock

state: NC

address: 111 Mason Farm Road

department: MHI

institute: UNC-CH

summary: Direct cardiac reprogramming of cardiac fibroblasts (CFs) into induced cardiomyocytes (iCMs) has emerged as a promising potential therapeutic for preserving cardiac function after ischemic injury. Remaining barriers to clinical translation include low conversion efficiency and relative immaturity of iCMs. A major phenotypic distinction between CFs and native CMs is the latter’s reliance on mitochondrial energetics facilitated by their high mitochondrial fusion (joining) activity relative to fission (dividing) activity. However, how mitochondria reorganize during reprogramming remains understudied. We combined metabolic flux assays with novel microscopy techniques to characterize mitochondrial energetics and morphology over a time course of cardiac reprogramming with Mef2c, Gata4 and Tbx5 (MGT). We found that MGT reprogramming induces increased mitochondrial respiration and fusion. However, this reorganization occurs only at later reprogramming time points. Hypothesizing that mitochondrial reorganization represents a rate-limiting step in reprogramming, we then performed a loss of function screen for a panel of genes known to regulate mitochondrial morphology. We found that the fusion apparatus is essential for successful iCM conversion and identified the fission regulator Mtfr1l as a powerful barrier to reprogramming. Using transcriptomic analysis and concomitant knockdown of the Mtfr1l target Opa1, the effector of inner membrane fusion, we showed that loss of Mtfr1l dramatically improves reprogramming efficiency and the maturity of nascent iCMs by facilitating a metabolic switch toward more interconnected and energetically active mitochondria. This study represents a major step forward in understanding reprogramming mechanisms and is the first report of Mtfr1l as a significant barrier to iCM conversion and maturation.

overall_design: To investigate the mechanisms by which loss of Mtfr1l improves direct cardiac reprogramming, we isolated primary cardiac fibroblasts from neonatal CD1 mice and used shRNAs to knock down Mtfr1l during reprogramming and in CF controls.

first: Yifang

last: Xie

first: Yiran

last: Song

first: James

last: Hua

first: Haley

last: Vaseghi

first: Meenakshi

last: Nishtala

first: Rustem

last: Salmenov

first: Jiandong

last: Liu

first: Li

last: Qian


title: Deletion of absent in melanoma (AIM) 2 gene drives bone marrow adipogenesis

city: New York

first: Shoshana

last: Yakar

address: 345E 24th Street

institute: New York University

summary: Absent in Melanoma (AIM) 2 is a gene that is induced by interferon and acts as a cytosolic sensor for double-stranded (ds) DNA. It forms the AIM2 inflammasome, leading to the production of interleukin (IL)-1β and IL-18. Our previous study demonstrated that mice lacking AIM2 exhibit spontaneous obesity, insulin resistance, and inflammation in adipose tissue. In this study, we aimed to explore the impact of AIM2 gene deletion on the bone marrow microenvironment and bone morphology in adult and aged mice. Utilizing micro-computed tomography (micro-CT), we discovered that female mice lacking AIM2 showed an increase in the total cross-sectional area at 5 months of age, accompanied by an increase in cortical thickness in the mid-diaphysis of the femur  at both 5 and 15 months of age. At 15 months of age, the cortical bone mineral density (BMD) significantly decreased in AIM2 null females compared to wild-type (WT) mice. In AIM2 null mice, both trabecular bone volume and BMD at the distal metaphysis of the femur and the lumbar vertebra-4 significantly decreased at 5 and 15 months of age. Histological examination of femurs from aged mice demonstrated increased bone marrow adiposity in AIM2 null mice, accompanied by a significant increase in CD45-/CD31-/Sca1+/Pdgfa+ adipose progenitor cells, and a decrease in the ratio of CD31-/CD31+ osteogenic progenitor cells, as determined by flow cytometry of bone marrow cells. RNAseq analysis of the bone marrow revealed significant increase in interferon-stimulated genes with Ifi202b as the top upregulated gene in the bone marrow of AIM2 null mice. Our findings suggest that AIM2 deficiency affects bone health by promoting adipogenesis in bone marrow cells and inducing a pro-inflammatory environment, potentially contributing to the decreased bone mineral density.

overall_design: Comparative gene expression profiling analysis and GO analyis of AIM2 gene deletion mouse bone marrow samples with RNA-seq

first: Zhenwei

last: Gong

first: Manisha

last: Dixit

first: Zhiming

last: He

first: Sher

last: Poudel

first: Gozde

last: Yildirim

first: Radhika

last: Muzumdar


title: CX3CR1+ Synovial Macrophages for Barrier Restore in Rheumatoid Arthritis: A New Target for Mesenchymal Stem Cell-Based Therapy?

city: Beijing

first: Ming

last: Hao

address: Shuangqing Rd.

institute: Tsinghua Univ

summary: Objective: In this study, we explored the interaction between Mesenchymal stem cells (MSCs) and synovial CX3CR1+ macrophages with rheumatoid arthritis (RA) model mice during the process of barrier reconstruction, deeply analyzed the therapeutic mechanism of MSCs and the underlying mechanisms of the dynamic state changes of the macrophage barrier. Design: ScRNA-seq analysis was conducted 4 days after MSCs/PBS injection in serum transfer-induced arthritis model mice. The role of mitochondria transfer and transplantation of MSCs were also explored. Bulk RNA-seq analysis was performed after the co-culture of MSCs and synovial CX3CR1+ macrophages in vitro. MSCs were retrieved 0/2/4/7 days after injection for Bulk RNA-seq analysis to explore their fate in vivo. Results: Intra-articular injection of MSCs could help restore CX3CR1+ macrophage barrier and attenuate the pathological process of RA mice. ScRNA-seq analysis revealed that an Atf3high Ccl3high subset of CX3CR1+ macrophages with poor oxidative phosphorylation increased in abundance during RA progression. MSCs reduced this subset's abundance through mitochondria transfer. Mitochondria transplantation by MSCs was also effective in treating RA. Bulk RNA-seq and scRNA- seq analyses revealed multiple interaction mechanisms between MSCs and CX3CR1+ macrophages such as Cd74/Mif axis and GAS6/MERTK axis to restore CX3CR1+ macrophage barrier. Bulk RNA-seq analysis showed that MSCs primarily contribute to tissue repair and immune regulation subsequently. Conclusions: Our results suggest that MSCs enhanced the oxidative phosphorylation capacity of CX3CR1+ lining macrophages through mitochondria transfer and promote barrier restoration. In addition, we elucidated the fate of MSCs and the therapeutic potential of mitochondria in RA treatment.

overall_design:
To investigate the potential interaction between ADSCs and Macrophages, in vito separately-cultured and co-cultured ADSCs and Macrophages were collected for RNA-seq.
To investigate the heterogeneity changes of CX3CR1+ synovial lining macrophages in the barrier disruption and restoration process,  CX3CR1+ macrophages of RA model mice with or without ADSCs treatment were collected for single cell RNA-seq.
To investigate the in vivo fate of ADSCs during RA treatment, injected ADSCs were collected from mice knee joints at different time point after injection for RNA-seq.

first: Lei

last: Wang


title: Analysis of gastrocnemius muscle transcriptome from chow fed control and skeletal muscle HuR knockout mice with and without voluntary wheel running

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: To determine the effects of 10 weeks of voluntary wheel running on skeletal muscle gene expression in mice with and without skeletal muscle HuR knockout, we assessed gastrocnemius muscle in chow-fed control and skeletal muscle HuR knockout mice using RNA-seq

overall_design: Examination of gastroc mRNA profiles in 2 different exercise conditions in control and skeletal muscle HuR knockout mice

first: Jaycob

middle: D

last: Warfel

first: Michael

last: Salbaum

first: Sujoy

last: Ghosh

first: Richard

last: Carmouche

first: Jasleen

last: Kaur

first: Sara

last: Webb


title: Single-cell RNA sequencing reveals T and B cell-related immune features in foot and mouth disease virus-infected mice

city: Lanzhou

first: Jingjing

last: Pei

address: No.1, Xujiaping, Chengguan District, Lanzhou, Gansu Province, P. R. China

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (LVRI, CAAS)

summary: T and B lymphocytes protect against foot and mouth disease virus (FMDV). They are essential for long-term immunity and viral clearance, but their immunological features in FMDV infection remain unknown. Here, we performed single-cell RNA sequencing (scRNA-seq) and conducted integrative analyses to determine cell composition, gene expression, cell-cell communication state, and regulatory network of T and B cells in the spleen of FMDV- and mock-infected mice. Our results revealed variational compositions of immune cells on the subsets level. Additionally, we determined the reshaping of several important pathways in T and B cells, such as the inhibition of antigen-presentation capacity. Finally, the remolding of cell-cell communication and regulatory networks was also characterized during FMDV infection. Overall, our research provides valuable insights and abundant resources for understanding the adaptive immune response in FMD.

overall_design: Three infected and three control spleens of ifnar-/- C57/B6 mice were isolated at 5 days post FMDV or solvet injection and analyzed using scRNAseq.

first: Yang


title: Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

country: France

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

summary: There is growing evidence that a wide range of human diseases and physiological traits are influenced by genetic variation of cis-regulatory elements. We and others have shown that a subset of promoter elements, termed Epromoters, can regulate proximal and distal genes in cis. This opens a paradigm in the study of regulatory variants, as single nucleotide polymorphisms (SNPs) within Epromoters might influence the expression of several (distal) genes at the same time, which could disentangle the identification of disease-associated genes. Here, we built a comprehensive resource of human Epromoters using newly generated and publicly available high-throughput reporter assays. We showed that Epromoters display intrinsic and epigenetic features that distinguish them from typical promoters. By integrating Genome-Wide Association Studies (GWAS), expression Quantitative Trait Loci (eQTLs), and 3D chromatin interactions, we found that regulatory variants at Epromoters are concurrently associated with more diseases and physiological traits, as compared with typical promoters. To dissect the regulatory impact of Epromoter variants, we evaluated their impact on regulatory activity by analyzing allelic-specific high-throughput reporter assays and provided reliable examples of pleiotropic Epromoters. In summary, our study represents a comprehensive resource of regulatory variants supporting the pleiotropic role of Epromoters.

overall_design: CapSTARR-seq experiments using a ref-seq promoter library in GM12878 cells, RPMI cells, and CCRF-CEM cells stimulated or not with interpheron alpha for 6 hours

first: Jing

last: Wan

first: Antoinette

last: van Ouwerkerk

first: Lydie

last: Pradel


title: Serotonin attenuates tumor-necrosis-factor-alpha-induced intestinal inflammation by interacting with human mucosal tissue

city: Brno

first: Ioanna

last: Papatheodorou

address: Studentska

department: Center for Translational Medicine

country: Czech Republic

institute: International Clinical Research Center (ICRC), St.Anne’s Hospital

summary: The intestine houses the largest immune system and is serviced by the largest and most complex peripheral nervous system in the human body. The gut-brain axis orchestrates communication between the central and enteric nervous systems, playing a pivotal role in regulating overall body function and intestinal homeostasis. Using a human 3D in vitro model, we investigated the effect of serotonin, a neuromodulator produced in the gut, on immune cell and intestinal tissue interactions. Our findings revealed that serotonin attenuates the tumor-necrosis-factor-alpha-induced pro-inflammatory response, mostly by affecting the expression of chemokines. Serotonin was found to impact tissue-migrating monocytes’ phenotype and distribution, without direct contact with the cells, by remodeling the intestinal tissue. Collectively, using fully human model of intestine, our results show that serotonin has a crucial role in communication among gut-brain axis components and regulates monocyte migration and plasticity, thereby contributing to gut homeostasis and the progression of intestinal inflammation. In vivo studies focused on role of neuromodulators in gut homeostasis and inflammation have shown controversial results, highlighting importance of development of human experimental models. Moreover, our results emphasize importance of human health research in human-cell-based models and suggests serotonin signaling pathway as new therapeutic target for inflammatory bowel disease.

overall_design:
In order to investigate the effect of serotonin on the mucosal tissue in the context of inflammation, we stimulated 3D human intestinal organoids (IOs) with TNFα and/or serotonin.
Differential gene expression analysis from RNAseq data from IOs stimulated with TNFα and/or serotonin.

first: Veronika

last: Bosáková

first: Filip

last: Kafka

first: Zuzana

last: Tomášiková

first: Marcela

last: Hortová Kohoutková

first: Jan

last: Frič


title: A cardiac fibroblast-enriched micropeptide regulates inflammation

city: Guangzhou

first: Tailai

last: Du

state: Guangdong

address: No.58, Zhongshan 2nd road

department: The First Affiliated Hospital

institute: Sun Yat-sen University

summary: Knockdown of IAMP resulted in significant alterations in the transcriptome. Upon cross-analysis of the transcriptomic changes induced by the two siRNAs, we identified 190 genes that were commonly upregulated and 342 genes that were commonly downregulated in both datasets. KEGG enrichment analysis of these differentially expressed genes revealed that IAMP knockdown led to the upregulation of genes associated with inflammation-related pathways, such as the TNF and IL-17 signaling pathways. Collectively, these data suggest that IAMP functions as an anti-inflammatory factor in cardiac fibroblasts.

overall_design: RNA-seq of adult mouse cardiac fibroblasts treated with IAMP siRNA and stimulated with IL-17 or TGF-β.

first: Youchen

last: Yan

first: Tingting

last: Zhang

first: Xin

last: He

first: Zhan-Peng

last: Huang


title: RNA-seq-based transcriptome profiling of fruit extract of Brucea javanica (FEBJ)  and cynaroside

city: 成都市

first: Di

state: 四川省

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

institute: Chengdu University of Traditional Chinese Medicine

summary: Liver fibrosis is a wound-healing process that occurs in response to chronic liver injury. Traditional Chinese medicine (TCM) has been shown to have a significant effect on treating liver fibrosis. We found that the fruit extract of Brucea javanica (FEBJ) suppressed hepatic stellate cell (HSC) activation and extracellular matrix (ECM) deposition in vitro, and attenuated thioacetamide (TAA)- induced liver fibrosis in zebrafish. Moreover, we identified cynaroside as one of the active compounds of FEBJ that could reproduce its antifibrotic effects in vitro and in vivo. To further investigate the global transcriptome changes of FEBJ and cynaroside, RNA-seq was performed. The results indicated that FEBJ-regulated genes were involved mainly in ECM-remodeling related biological functions, and cynaroside-regulated genes were involved in various biological functions besides ECM-remodeling.

overall_design: LX-2 cells were treated with the fruit extract of Brucea javanica (FEBJ), cynaroside, or DMSO (control group) for 24 hours.

first: Lan

last: Xie


title: Zfp462, as a novel stimulating factor of osteoblast differentiation, is associated with the development of age-related bone formation alteration.

city: Seoul

first: Jinman

last: Kim

address: 88, Olympic-ro 43-gil, Songpa-gu

institute: Asan medical center

summary: Zinc finger protein 462 (Zfp462) is a major chromatin regulator containing multiple Cys2His2-type zinc finger motifs and is known to play an important role in embryonic development and neural cell differentiation. Zfp462 can act as a transcription regulator that controls chromatin structure and modification during the aging process. However, the role of Zfp462's transcription regulator remains unclear. Here we demonstrated that Zfp462 directly binds to Runx2 and enhances the DNA binding and transcriptional activity of Runx2. Zfp462 recruits the histone acetyltransferase MOZ to acetylate histone H3 lysines 9, 14, and 23, and thereby promotes osteoblast differentiation and bone formation. Zfp462-deficient mice in osteoblast-lineage cells has an osteopenia phenotype due to impaired osteoblast differentiation. Zfp462/ZNF462 expression were significantly reduced due to a decrease in histone variant H2A.Z and histone H3 lysine 4 tri-methylation occupancies at the Zfp462/ZNF462 loci in aged mice and human. Together, our data reveal a novel role of Zfp462/ZNF462 as a transcription regulator that increases the expression of bone formation-related genes and suggest its potential as a therapeutic target to treat age-related bone loss.

overall_design: Primary calvarial osteoblast precursors were isolated from the newborn calvariae of Zfp462-/- mice and WT littermates. The isolated calvarial osteoblast precursors were differentiated into osteoblasts by treating with 50 μg/mL ascorbic acid and 10 mM β-glycerophosphate in culture medium for 6 days. Total RNA was isolated from the differentiated osteoblasts using the TRIzol reagent.  The gene expression regulated in Zfp462 knockout osteoblasts was obtained through RNA-seq analysis.

first: Jung-Min

last: Koh