title: Defining the Effects of PKC Modulator HIV Latency-Reversing Agents on Natural Killer Cells

city: Los Angeles

first: Jerome

last: Zack

address: 615 Charles E Young Drive S., Biomedical Sciences Research Building, Rm 173

department: Molecular Biology, Immunology & Molecular Genetics (MIMG)

institute: University of California, Los Angeles

summary: Latency reversing agents (LRAs) such as protein kinase C (PKC) modulators can reduce rebound-competent HIV reservoirs in small animal models. Furthermore, administration of natural killer (NK) cells following LRA treatment improves this reservoir reduction. It is currently unknown why the combination of a PKC modulator and NK cells is so potent and whether exposure to PKC modulators may augment NK cell function in some way. Here, we compare the transcriptional profiles of PKC-treated NK and CD4+ T cells to assess their generalized cellular effects. Transcriptomic profiles from both cell types displayed signatures of cellular activation and enrichment of genes associated with the NFκB pathway. However, the transcriptomic effects of PKC stimulation on NK cells are much milder than that in CD4+ T cells. This finding, combined with our experimental data testing killing capacity of PKC-stimulated NK cells against K562 cells and infected CD4+ T cells suggests that their contribution in “kick and kill” strategies is primarily due to upregulating HIV expression in CD4+ T cells, rather than directly enhancing the effector functions of NK cells. This suggests that PKC modulators are primarily augmenting the “kick” rather than the “kill” arm of this HIV cure approach.

overall_design: Gene expression profiling analyis of RNA-seq data from primary human NK and resting CD4+ T cells treated with PKC modulators (10nM bryostatin-1, 1μM prostratin, or 10nM of the designed, synthetic bryostatin-1 analog SUW133). Samples were collected after 24 hours of stimulation (n=4-5 donors for each cell type in singlicate).

first: Melanie

last: Dimapasoc

first: Jose

last: Moran

first: Steve

last: Cole

first: Alok

last: Ranjan

first: Rami

last: Hourani

first: Jocelyn

middle: T

last: Kim

first: Paul

last: Wender

first: Matthew

last: Marsden


title: Research on the occurrence and progression of colorectal cancer.

status: Public on Jan 23 2025

city: chongqing

first: Ruyi

last: HANG

address: Yuzhong District

country: China

institute: Army Medical Center of PLA

type: Expression profiling by high throughput sequencing

summary: APX3330 suppresses the occurrence and advancement of colorectal cancer by reducing infiltration of PMN-MDSCs

overall_design: In the AOM/DSS-induced CAC model of C57BL/6 mice, RNA-seq profiling of mice treated with APX3330/saline.

first: Tianyi

last: Chen

last: Hang


title: Transcriptome reveals differential expression of flavor and color in closely related species of tomato

city: 云南省

first: 郭

last: 雅妍

address: 云南省昆明市盘龙区沣源路452号云南农业大学

department: 园林园艺学院

institute: 云南农业大学

summary: Fruit flavor and color are critical quality characteristics of tomatoes. Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analyses were conducted on the closely related yellow-fruited tomato (No.19) and red-fruited tomato (No.20) strains. This analysis aimed to identify key regulatory genes and biosynthetic pathways related to flavor and color development in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the differentially expressed genes, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide insights into the underlying mechanisms of flavor and color development in tomato fruit, offering valuable information for the genetic improvement of tomatoes.

overall_design: RNA-seq analysis of fruits at color break (40 days after anthesis) and maturity (55 days after anthesis) of yellow tomato No. 19 and red tomato No. 20

first: Guo

last: Chunmei

first: Liu

last: Xiuyuan

first: Ding

last: Yinfeng

first: He

last: Zhaoyilan

first: Shi

last: Songmei

last: Yumei

first: Shen

last: Hui

first: Yang

last: Zhengan


title: Wild-Type vs Orai1KO pTH17 and npTh17 cells_ 48h

first: Yousang

last: Gwack

state: CA

address: 10833 Le Conte Ave, 53-159 CHS

department: Physiology

country: USA

institute: Uuniversity of California Los Angeles

summary: Transicriptome comparison between WT and ORAI1 KO pTH17cells at 48 hours during differentiation

overall_design: Naive CD4+ T-cells were isolated and purified from either wild-type or ORAI1 KO mice. Naïve CD4+ T cells were enriched by magnetic sorting from single-cell suspensions generated by mechanical disruption of spleens and lymph nodes of adult mice using MagniSort naïve CD4+ T cell enrichment kit (catalog # 8804-6824-74,ThermoFisher Scientific). For effector T cell differentiation, cells were stimulated with anti-CD3 antibody (1452C11, Bio X Cell) and anti-CD28 antibody (Clone 37.51, Bio X Cell) for 48 hours on a plate coated with rabbit anti-hamster antibody (MP Biomedicals). CD4 + CD25 - T cells were cultured with anti-IL-4 antibody (Peprotech) and 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech), 10 ng/ml IL-23 (R&D Systems) and 10 ng/ml IL-1β (R&D Systems) for pathogenic Th17 differentiation and cultured in T cell medium. For non-pathogenic Th17 cell differentiation,CD4 + CD25 - T cells were cultured with 10 μg/ml anti-IL-4 antibody, 10 μg/ml anti-IFN-γ antibody, 30 ng/ml IL-6 (Peprotech) and 1 ng/ml TGF-β (Peprotech). Cells were taken off the plate on D2 (48hrs) and prepared for bulk RNA sequencing analysis.

first: Beibei

last: Wu

first: Spyridon

last: Hasiakos

first: Jinseok

last: Woo

first: Shawn

last: Cokus

first: Matteo

last: Pellegrini

first: Sonal

last: Srikanth


title: Brain transcriptomics of social challenge and maternal aggression in incubating female tree swallows

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

summary: Aggressive behavior is ubiquitous across many contexts, including defense of territories, mates, and offspring. For decades, researchers have detailed the effect of aggressive behavior on physiology, but our understanding of these mechanisms in females lags behind that of males, despite the fact that female aggression is widespread, particularly in the context of maternal defense (i.e., maternal aggression). Here, we measured effects of a social challenge on brain gene expression in free-living incubating females. We hypothesized that the social challenge would generate at least one of three transcriptomic effects: (1) sensitizing the brain to otherwise low levels of sex steroids, (2) changing other neuroendocrine signaling pathways associated with social behavior (e.g., dopamine), or (3) broad shifts related to metabolism or immune function. We tested these hypotheses in incubating female tree swallows (Tachycineta bicolor), exposing 10 females to a 30-minute simulated territorial intrusion, which elicited maternal aggression. After this challenge, we measured neural gene expression via RNA-seq and compared gene expression to 10 unchallenged controls. We saw no global treatment effect on gene expression. However, within the experimental group, more maternal aggression was correlated with upregulation of genes associated with immune activation and downregulation of genes associated with synaptic plasticity. Though more research is needed to understand the downstream effects of these transcriptional differences, our findings generate key questions about how the brain responds to social challenges across different contexts.

overall_design:
To measure the brain's response to a social challenge, we exposed 10 wild tree swallows to a 30-minute simulated territorial intrusion, which elicited maternal aggression. These experimental females were compared to 10 unchallenged controls.
https://github.com/ejlevy/Tree-Swallow-Maternal-Aggression

first: Emily

middle: J

last: Levy

first: Elizabeth

middle: M

last: George

first: Douglas

middle: B

last: Rusch

first: Aaron

last: Buechlein

first: Kimberly

middle: A

last: Rosvall


title: Combination adjuvant improves influenza virus immunity by downregulation of immune homeostasis genes in lymphocytes

status: Public on Jan 24 2025

city: Irvine

first: Huw

last: Davies

address: 812 Medical Plaza Drive, Med Surge II

department: Department of Physiology & Biophysics

institute: UC Irvine

summary: Adjuvants play a central role in enhancing the immunogenicity of otherwise poorly immunogenic vaccine antigens. Combining adjuvants has the potential to enhance vaccine immunogenicity compared with single adjuvants, although the cellular and molecular mechanisms of combination adjuvants are not well understood. Using the influenza virus hemagglutinin H5 antigen, we define the immunological landscape of combining CpG and MPLA (TLR-9 and TLR-4 agonists, respectively) with a squalene nanoemulsion (AddaVax) using immunologic and transcriptomic profiling. Mice immunized and boosted with recombinant H5 in AddaVax, CpG+MPLA, or AddaVax plus CpG+MPLA (IVAX-1) produced comparable levels of neutralizing antibodies and were equally well protected against the H5N1 challenge. However, after challenge with H5N1 virus, H5/IVAX-1–immunized mice had 100- to 300-fold lower virus lung titers than mice receiving H5 in AddaVax or CpG+MPLA separately. Consistent with enhanced viral clearance, unsupervised expression analysis of draining lymph node cells revealed the combination adjuvant IVAX-1 significantly downregulated immune homeostasis genes, and induced higher numbers of antibody-producing plasmablasts than either AddaVax or CpG+MPLA. IVAX-1 was also more effective after single-dose administration than either AddaVax or CpG+MPLA. These data reveal a novel molecular framework for understanding the mechanisms of combination adjuvants, such as IVAX-1, and highlight their potential for the development of more effective vaccines against respiratory viruses.

overall_design: H5 antigen in different adjuvants (AddaVax, CpG+MPLA, or IVAX), along with H5 in PBS and PBS only, was administered to 3 C57BL/6 female mice via the subcutaneous (subcutaneous) route at the base of the tail. Mice were boosted on day 28, and 3 mice were culled 4 d after the boost for single-cell mRNA sequencing of draining (inguinal) lymph nodes.

first: Emmanuel

middle: P

last: Dollinger

last: Davis


title: Genetic context modulates aging and degeneration in the murine retina

city: Bar Harbor

first: Michael

last: MacLean

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Background Age is the principal risk factor for neurodegeneration in both the retina and brain. The retina and brain share many biological properties; thus, insights into retinal aging and degeneration may shed light onto similar processes in the brain. Genetic makeup strongly influences susceptibility to age-related retinal disease. However, studies investigating retinal aging have not sufficiently accounted for genetic diversity. Therefore, examining molecular aging in the retina across different genetic backgrounds will enhance our understanding of human-relevant aging and degeneration in both the retina and brain—potentially improving therapeutic approaches to these debilitating conditions.  Methods Transcriptomics and proteomics were employed to elucidate retinal aging signatures in nine genetically diverse mouse strains (C57BL/6J, 129S1/SvlmJ, NZO/HlLtJ, WSB/EiJ, CAST/EiJ, PWK/PhK, NOD/ShiLtJ, A/J, and BALB/cJ) across lifespan. These data predicted human disease-relevant changes in WSB and NZO strains. Accordingly, B6, WSB and NZO mice were subjected to human-relevant in vivo examinations at 4, 8, 12, and/or 18M, including: slit lamp, fundus imaging, optical coherence tomography, fluorescein angiography, and pattern/full-field electroretinography. Retinal morphology, vascular structure, and cell counts were assessed ex vivo.  Results We identified common molecular aging signatures across the nine mouse strains, which included genes associated with photoreceptor function and immune activation. Genetic background strongly modulated these aging signatures. Analysis of cell type-specific marker genes predicted age-related loss of photoreceptors and retinal ganglion cells (RGCs) in WSB and NZO, respectively. Fundus exams revealed retinitis pigmentosa-relevant pigmentary abnormalities in WSB retinas and diabetic retinopathy (DR)-relevant cotton wool spots and exudates in NZO retinas. Profound photoreceptor dysfunction and loss were confirmed in WSB. Molecular analyses indicated changes in photoreceptor-specific proteins prior to loss, suggesting photoreceptor-intrinsic dysfunction in WSB. In addition, age-associated RGC dysfunction, loss, and concomitant microvascular dysfunction was observed in NZO mice. Proteomic analyses revealed an early reduction in protective antioxidant processes, which may underlie increased susceptibility to DR-relevant pathology in NZO.  Conclusions Genetic context is a strong determinant of retinal aging, and our multi-omics resource can aid in understanding age-related diseases of the eye and brain. Our investigations identified and validated WSB and NZO mice as improved preclinical models relevant to common retinal neurodegenerative diseases.

overall_design: 1/2 Retinas were processed for RNA-sequencing from 9 strains of mice, of both sexes and at 3 ages. We used the resulting data to identify strain-, age- and strain-by-age effects across the samples.

first: Olivia

last: Marola

first: Travis

middle: L

last: Cossette

first: Cory

last: Diemler

first: Amanda

last: Hewes

first: Alaina

last: Reagan

first: Jonathan Nyandu

last: Kanyinda

first: Daniel

last: Skelly

first: Gareth

middle: R

last: Howell


title: Maternal high-fat diet aggravates the development of atherosclerosis in offspring via epigenetic memory (ATAC-Seq CUT&Tag)

city: tianjin

first: kan

last: li

address: Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China

institute: Tianjin Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maternal exposure to a western-type diet (WD) increases the susceptibility of adult offspring to atherosclerosis. Lining the inner layer of blood vessels, fetus endothelial cells (ECs) become dysfunctional and inflamed in response to risk factors from mother through maternal and fetal blood exchange. However, the mechanism by which maternal WD promotes vascular endothelial dysfunction and atherosclerosis in offspring after adulthood has not been fully clarified. Here, we found that maternal WD exposure sensitized offspring to WD exposure in adulthood of Ldlr-/- mice, significantly increasing atherosclerotic lesions in the aorta and aortic roots, endowed inflammatory memory at the chromatin level and regulated chromatin dynamics by transcription factor AP-1 in mouse aortic ECs. Plasma 27-hydroxycholesterol (27-HC) was significantly increased in maternal blood and transferred into the offspring. Additionally, 27-HC played a crucial role in memory establishment and also acted as a secondary stimulator, amplifying the expression of inflammatory memory factors and enhancing the enrichment of AP-1/p300 and H3K27ac in the binding domain in human ECs. Inhibiting AP-1 binding to chromatin reduced the inflammatory response in human umbilical vein ECs from mother with maternal hypercholesterolemia and the occurrence and development of atherosclerosis in the offspring with maternal WD exposure. Our findings demonstrate that maternal WD aggravating EC dysfunction and atherosclerosis in offspring after adulthood acquires AP-1-associated epigenetic memory to increase chromatin accessibility of inflammatory genes.

overall_design: We isolated and performed SMART-seq, ATAC-seq, and H3K27ac ChIP-seq on mouse aortic ECs (MAECs) from mice in the CDM-CDO / WDM-CDO groups and in the CDM-WDO / WDM-WDO groups that were given WD again for 4 weeks

first: Kan

last: Li

first: Weiqi

last: Qian

first: Fangni

last: Zhang

first: Ding

last: Ai


title: Transcriptional Evidence for Transient Regulation of Muscle Regeneration by Brown Adipose Transplant in the Rotator Cuff

city: St. Louis

first: Gretchen

last: Meyer

state: MO

address: 507 S Euclid Ave

department: Department of Physical Therapy

institute: Washington University School of Medicine in Saint Louis

summary: Chronic rotator cuff injuries can lead to a degenerative microenvironment that favors chronic inflammation, fibrosis, and fatty infiltration. Recovery of muscle structure and function will ultimately require a complex network of muscle resident cells, including satellite cells, fibro-adipogenic progenitors (FAPs), and immune cells. Recent work suggests that signaling from adipose tissue and progenitors could modulate regeneration and recovery of function, particularly pro-myogenic signaling from brown or beige adipose (BAT).  In this study, we sought to identify cellular targets of BAT signaling during muscle regeneration using a rotator cuff BAT transplantation mouse model. Cardiotoxin injured supraspinatus muscle had improved mass at 7 day post-surgery (dps) when transplanted with exogeneous BAT. Transcriptional analysis revealed transplanted BAT modulates FAP signaling early in regeneration likely via crosstalk with immune cells.

overall_design:
To investigate the effect of BAT on muscle regeneration, we collected primary cells isolated from the supraspinatus of 12-week-old male C57BL/6J mouse. Paired samples were collected from the same mouse. The BAT samples were isolated from muscles injected with cardiotoxin and then transplanted with interscapular BAT from 3wks-old mouse. The CTL samples were from muscles injured with cardiotoxin only.
SCs (CD45-/CD31-/Sca1+/a7integrin+) and FAPs (CD45-/CD31-/Sca1+/a7integrin-) were sorted for RNA isolation with a FACSAria II.
We performed differeitial expression gene analysis on the RNASeq results from isolated SCs and FAPs at 2 timepoints.

first: Chang

last: Gui


title: Effect of SCAFs 20h (bulk)

city: Illkirch

first: Matej

last: Durik

state: Alsace

address: 1 rue Laurent Fries

department: Development and stem cells

country: France

institute: IGBMC

summary: The aim is to identify the genes and pathways activated by SCAFs. SCAFs are added to proliferating cells in culture.

overall_design: SCAFs were isolated from GFP labelled senescent IMR90 cells using FACS sorting. As a control, inert plastic beads were isolated using the same procedure. In four independent biological replicates 60 000 IMR90 cells were treated either by 300 000 isolated inert beads as a control (Beads) or with 300 000 isolated SCAFs (SCAFs). Treatment duration was 20 hours.

first: Bill

last: Keyes


title: IL-4 induces CD22 expression to restrain the effector program of self-reactive virtual memory T cells

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: Parasitic helminths induce the production of interleukin (IL)-4 which causes the expansion of virtual memory CD8+ T cells (TVM), a cell subset contributing to the control of viral coinfection. However, the mechanisms regulating IL-4-dependent TVM activation and expansion during worm infection remain ill defined. We used single-cell RNA sequencing of CD8+ T cells to investigate IL-4-dependent TVM responses upon helminth infection in mice. Gene signature analysis of CD8+ T cells identified a cell cluster marked by CD22, a canonical regulator of B cell activation, as a specific and selective surface marker of IL-4-induced TVM cells. CD22+ TVM were enriched for IFN-γ and granzyme A and retained a diverse TCR repertoire, while enriched in CDR3 sequences with features of self-reactivity. Deletion of CD22 expression in CD8+ T cells enhanced TVM responses to helminth infection, indicating that this inhibitory receptor modulates TVM responses. Thus, helminth-induced IL-4 drives the expansion and activation of self-reactive TVM in the periphery that is counter-inhibited by CD22

overall_design:
For 10X single cell RNA sequencing, CD8+ T cells were enriched from spleen samples  from individual mice of one group, followed by hashtagging and pooling of 1 million cells per mouse sample. Groups consisted in WT or E8i-CreIl4ra-lox/lox BALB/c mice, receiving 3 different treatments (PBS ip injection at day -4 and day -2, IL-4c injection at day -4 and day -2, or infected with 200 L3 larvae of H. polygyrus).
For BD Rhapsody sequencing, CD8+ T cells were enriched from mesenteric lymph nodes of 3 E8i-CreIl4ra-lox/lox BALB/c mice at day 15 after infection with 200 L3 larvae of H. polygyrus. After enrichment, CD8+ T cells were stained and FACsorted for CD124+ or CD124- cells. Then, each sorted population was Sample Tagged, and 500,000 cells of the tagged cells were pooled before cell capture.
For bulk RNA-seq and TCR-seq, WT BALB/c mice were treated i.p. with PBS or with IL-4c (day -4 and day -2). At day 0, CD8+ T cells were enriched by bead based negative selection followed by immunostaining in order to sort by FACS CD44low naive T cells or CD44highCD49dlow Tvm from PBS-treated mice (n=4); and CD44low naive T cells or CD44highCD49dlowCD22- Tvm CD44highCD49dlowCD22+ Tvm from IL-4c-treated mice (n=4). 200,000 cells were sorted before cDNA library preparation and sequencing.

first: Bin

last: Yang

first: Guillem

last: Sanchez Sanchez

first: David

last: Vermijlen

first: Benjamin

middle: G

last: Dewals


title: Immune-cell signatures of persistent inflammation-immunosuppression and catabolism syndrome

city: Shanghai

first: Xingfeng

last: Sun

address: Shenyang Road 128#, Yangpu District

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Sepsis is a debilitating disease with a worldwide prevalence. An increasing number of patients with sepsis, especially aged patients, suffer from chronic critical illness and develop persistent inflammation-immunosuppression and catabolism syndrome (PICS). Here, we profiled peripheral blood mononuclear cells in four patients with PICS, two patients with acute sepsis, and three healthy controls using single-cell RNA sequencing and systematic analyses. We found that gene expression patterns and developmental routes in distinct immune cell populations exhibited notable differences between patients with PICS, patients with acute sepsis, and healthy controls.

overall_design: We profile peripheral blood mononuclear cells in four patients with PICS, two patients with acute sepsis (diagnosed with sepsis within 24 hours of ICU admission), and three healthy controls, with single-cell RNA sequencing (scRNA-seq) and systematical analyses.

first: Shaoqiang

last: Huang

first: Yijuan

last: Zheng

first: Zhongwei

first: Lei

last: Xiao

first: Jing

last: Zhong

first: Changhong

last: Miao


title: Chromosome X Dosage Modulates Development of Aneuploidy in Genetically Diverse Mouse Embryonic Stem Cells [C3H_scRNA-seq]

status: Public on Jan 22 2025

first: Selcan

last: Aydin

state: Maine

summary: The genetic integrity of pluripotent stem cells (PSC) is integral to their applications in research and therapy, but it is compromised by frequent development of copy number variations. Little is known about the basis of the variable genomic integrity among different PSC lines. Here we identify aneuploidies using RNA-seq and proteomics data from a panel of mouse embryonic stem cell (mESC) lines derived from 170 Diversity Outbred mice. We identified 62 lines with detectable aneuploid subpopulations and a subset of originally XX lines that lost one Chromosome X (XO). Strikingly, a much lower proportion of XX lines were aneuploid, compared to XY or XO lines. Two single-cell RNA-seq data sets demonstrated that aneuploid XY DO mESC also show lower Chromosome X gene expression and that XY mESC accumulate higher aneuploid proportions in culture than isogenic XX lines. Possible mechanisms for this protective effect of X chromosome dosage include our discovery that the lines with two active X Chromosomes have a higher expression of 2-cell-like state genes, and differential expression of X-linked tumor suppressor genes associated with DNA damage response.

overall_design: The samples submitted are from C3H/HeSn-Paf/J mouse embryonic stem cell lines derived from XX, XO, and XY embryos. There are three independently derived lines from each chromosomal sex. All lines were pooled together and submitted for single-cell sequencing at an early passage and after being cultured for 10 more passages to accumulate cells with aneuploidies in the culture.

first: Alexander

last: Stanton

first: Daniel A

last: Skelly

first: Dylan

last: Stavish

first: Kim

last: Leonhard

first: Seth

last: Taapken

first: Erik

last: McIntire

first: Matthew

last: Pankratz

first: Anne

last: Czechanski

first: Tenneille

last: Ludwig

first: Ted

last: Choi

first: Steven P

last: Gygi

first: Ivana

last: Barbaric

first: Steven C

last: Munger

first: Laura G

last: Reinholdt

first: Martin F

last: Pera


title: Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer’s disease neuropathology [RNA-seq]

city: Boston

first: Jean-Pierre

last: Roussarie

state: MA

address: 72 E Concord Street

department: Anatomy & Neurobiology

institute: Boston University School of Medicine

summary: Neurons located in the layer II of the entorhinal cortex (ECII) are the primary site of pathological tau accumulation and neurodegeneration at preclinical stages of Alzheimer's disease (AD). Exploring the alterations that underlie the early degeneration of these cells is essential to develop therapies that delay disease onset. Here we performed cell–type specific profiling of the EC at the onset of human AD neuropathology. We identify an early response to amyloid pathology by microglia and oligodendrocytes. More importantly, we find that the Reelin signaling pathway is already impaired at this early disease stage, particularly in ECII neurons. This indicates that dysregulation of this pathway, with emerging genetic association with AD, plays a pivotal role in the selective vulnerability of the EC and in the onset of AD neuropathology.

overall_design: Study of the gene expression changes undergone by neurons of EC at the onset of AD neuropathology; we compare human postmortem EC without (control C1 to C4) or with incipient AD neuropathology or ADN (AD2 to AD5). All individuals were asymptomatic at death. We profile two neuronal populations: neuronal nuclei (NeuN positive) positive or not for RBFOX1

first: Patricia

last: Rodriguez-Rodriguez

first: Wei

last: Wang

first: Noemi

last: Vidal

first: Ana

last: Milosevic


title: Acute effects of taxifolin food on whole blood gene expression levels after cognitive measure test.

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

country: Japan

institute: Kanagawa Institute of Industrial Science and Technology

summary: Polyphenols are known to improve human immune and cognitive functioning. In this study, we analyzed the effects of a single administration of foods containing taxifolin on whole blood gene expression after cognitive measure test in healthy young adults. A randomized, placebo-controlled, double-blind, crossover-controlled trial was conducted in which a single dose of either a food containing taxifolin (108 mg) or a placebo was administered to 28 human subjects. Cognitive measure test (Serial 3s, Serial 7s, Rapid Visual Information Processing (RVIP)) were performed 90 minutes following administration. They were drawn before food intake and after cognitive measure test. Analysis of whole blood gene expression before and after the test revealed that the expression of foreign body removal-related genes was increased by ingestion of taxifolin, and that most of the expression-variable genes were well expressed in granulocytes. It was suggested that a single intake of taxifolin may enhance the removal of foreign substances by strengthening the innate immune system and suppress the occurrence of injury.

overall_design: A randomized, placebo-controlled, double-blind, crossover trial was conducted on gene expression levels in 28 adults. They ingested either a food containing taxifolin (108 mg) or a placebo. They performed Cognitive measure test (serial 3s, serial 7s, RVIP) four times 90 minutes after ingestion. They were drawn before food intake and after cognitive measure test. For each food intake, comparison was made before the cognitive test (before food intake) and after the cognitive test was completed (after food intake).

first: Asuka

last: KAMEI


title: Chromosome X Dosage Modulates Development of Aneuploidy in Genetically Diverse Mouse Embryonic Stem Cells [D0_scRNA-seq]

first: Selcan

last: Aydin

overall_design: The sample submitted contains embryonic stem cells (ESCs) derived from diversity outbred (DO) mice. The cell lines were derived indepdently and pooled in equal proportion for sequencing. The pooled sample was then divided and sequenced across 4 lanes.

first: Alexander

last: Stanton

first: Daniel A

last: Skelly

first: Dylan

last: Stavish

first: Kim

last: Leonhard

first: Seth

last: Taapken

first: Erik

last: McIntire


title: Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [scRNA-seq]

city: Groton

first: Mark

last: Sheehan

state: CT

address: 274 Eastern Point Rd

department: Drug Safety R&D

institute: Pfizer

summary: Immune checkpoint inhibitors (ICI) targeting CTLA-4 and PD-1 have shown remarkable antitumor efficacy but can also cause immune-related adverse events, including checkpoint inhibitor-induced liver injury (ChILI). This multi-omic study aimed to investigate changes in blood samples from treated cancer patients who developed ChILI. PBMCs were analyzed by transcriptomic and T cell receptor sequencing (bulk and single cell), and extracellular vesicle (EV) enrichment from plasma was analyzed by mass spectroscopy proteomics. Data were analyzed by comparing the ChILI patient group to the control group who did not develop ChILI and by comparing the onset of ChILI to pre-ICI treatment baseline. We identified significant changes in T cell clonality, gene expression, and protein levels in peripheral blood mononuclear cells (PBMCs) or plasma at the time of liver injury. Onset of ChILI was accompanied by an increase in T-cell clonality. Pathway analysis highlighted the involvement of innate and cellular immune responses, mitosis, pyroptosis, and oxidative stress. Single-cell RNA sequencing revealed that these changes were primarily found in select T cell subtypes (including CD8+ effector memory cells), while CD16+ monocytes exhibited enrichment in metabolic pathways. Proteomic analysis of plasma extracellular vesicles showed enrichment in liver-associated proteins among differentially expressed proteins. Interestingly, an increase in PBMC PD-L1 gene expression and plasma PD-L1 protein was also found to be associated with onset of ChILI.

overall_design: 10x Genomics single cell 5' Gene expression and TCR profiling of PBMCs from patients before and after checkpoint inhibitors, including ChILI patients and control patients who did not develop ChILI.

first: Thomas

last: Lanz


title: Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer’s disease neuropathology [scRNA-seq]

overall_design: Study of the gene expression changes undergone by EC cells at the onset of AD neuropathology; we compare human postmortem EC without (control C1 to C5) or with incipient AD neuropathology or ADN (AD1 to AD5). All individuals were asymptomatic at death. Two samples C5 and AD1 were used for cell clustering but not for differential expression analysis because their amyloid levels did not correspond to their respective groups. For excitatory neurons, processed data correspond to our nuclei integrated with nuclei from Leng et al, Nature Neuro, 2021 to increase nucleus counts.


title: Teamwork of clustered low-affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers [ChIP-seq]

city: La Jolla

first: Shandy

last: Shahabi

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

summary: Non-consensus binding sites of transcription factors are often observed within the promoters and enhancers of various genes; however, their effect on transcriptional strength is unclear. Within the promoters and enhancers of NF-κB-responsive genes, we identified clusters of non-consensus κB DNA sites, many exhibiting low affinity for NF-κB in vitro. Deletion of these sites demonstrated their collective critical role in transcription. We explored how these “weak” κB sites exert their influence, especially given the typically low nuclear concentration of NF-κB. Using proteomics approaches, we identified additional nuclear factors, including other DNA-binding TFs, that could interact with κB site-bound NF-κB RelA without binding to DNA directly. ChIP-seq and RNA-seq analyses suggest that these accessory TFs, referred to as the cofactors of NF-κB, facilitate dynamic recruitment of NF-κB to the clustered κB sites. Overall, the occupancy of NF-κB at promoters and enhancers appears to be defined by a collective contribution from all κB sites, both weak and strong, in association with specific cofactors. This congregation of multiple factors within dynamic transcriptional complexes is likely a common feature of transcriptional programs.

overall_design: Gene expression and RelA genome binding/occupancy profiling by high-throughput sequencing in control and knockdown mouse embryonic cell lines.

first: Tapan

last: Biswas

first: Yuting

last: Shen

first: Rose

last: Sanahmadi

first: Yaya

last: Zou

first: Gourisankar

last: Ghosh


title: Teamwork of clustered low-affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers [RNA-seq]


title: Distinct Myeloid Derived Suppressor Cell Populations in Human Glioblastoma

city: Philadelphia

first: Christina

last: Jackson

state: PA

address: 3400 Civic Center Boulevard

department: Neurosurgery

institute: University of Pennsylvania

summary: The diversity of transcriptional programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC) that were unique to IDH wild type glioblastomas (GBM) and absent in IDH mutant low-grade gliomas and IDH mutant grade IV astrocytomas: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. Spatial transcriptomics demonstrated that the E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stem-like tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce specific chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells; in particular the FGFR1 ligand FGF11. This axis is not present in IDH mutant gliomas, associated with hypermethylation and repressed gene expression of the relevant chemokine genes. Our large-scale single-cell analysis elucidated unique MDSC populations that may facilitate GBM progression and mediate tumor immunosuppression.

overall_design:
Patients were prospectively enrolled into this study at Johns Hopkins Hospital. Written informed consent was provided by all participants according to approved Institutional Review Board Protocol. Fresh tumor tissue and blood were collected at the time of surgery following confirmation of primary glial neoplasm on frozen section. None of the patients was treated with chemotherapy or radiation prior to tumor resection. Tumor samples span all glioma stages (Grade II, Grade III, and Grade IV). Patients undergoing anterior temporal lobectomy for seizure control were consented and non-neoplastic tissue from anterior temporal lobectomy resection was collected as control.
>>> Submitter states that raw data are unavailable due to patient privacy concerns.<<<

first: Christopher

last: Cherry


city: Baltimore

first: Srinivasan

last: Yegnasubramanian

address: 1650 Orleans Street

institute: Johns Hopkins University

overall_design: Patients were prospectively enrolled into this study at Johns Hopkins Hospital. Written informed consent was provided by all participants according to approved Institutional Review Board Protocol. Fresh tumor tissue and blood were collected at the time of surgery following confirmation of primary glial neoplasm on frozen section. None of the patients was treated with chemotherapy or radiation prior to tumor resection. Tumor samples span all glioma stages (Grade II, Grade III, and Grade IV). Patients undergoing anterior temporal lobectomy for seizure control were consented and non-neoplastic tissue from anterior temporal lobectomy resection was collected as control. Two patients were analyzed using spatial transcriptomics.

first: Rulin

last: Wang


title: Polystyrene microplastics induce liver fibrosis and lipid deposition in mice through three hub genes revealed by the RNA-seq

city: Wuhan

first: Xuan

last: Niu

state: --- Select One ---

address: 238, Jiefang road

institute: Wuhan university

summary: Microplastics (MPs) have become a serious global environmental threat that causes damage to mammalian organs. In this work, we investigated the potential molecular mechanism underlying the development of liver fibrosis induced by long-term exposure to three different sized PS-MPs (80 nm, 0.5 µm and 5 µm) in mice. Liver fibrosis levels were evaluated in mice after chronic exposure to PS-MPs. Liver inflammation was mainly increased in chronic exposure to 80 nm and 0.5 µm PS-MPs. Liver lipid deposition was significantly enhanced after PS-MP exposure. However, oxidative stress was not changed under PS-MP exposure. GO enrichment and KEGG pathway analyses revealed that the DEGs and shared DEGs were mainly enriched in the metabolism of lipids. The mRNA expression levels of genes related to fatty acid oxidation, synthesis and transport were dramatically induced by PS-MP exposure. Four hub genes, Acot3, Abcc3, Nr1i3 and Fmo2, were identified by CytoHubba analysis of shared DEGs. The mRNA expression levels of three hub genes, Acot3, Abcc3 and Nr1i3, were significantly augmented under chronic PS-MP exposure. Our results suggest that Acot3, Abcc3 and Nr1i3 are potential molecules involved in the development of liver fibrosis under chronic exposure to PS-MPs.

overall_design: Six-week-old ICR male mice were exposed to different diameters of polystyrene microplastics (80 nm, 0.5 µm and 5 µm) at a final concentration of 1 mg/L in drinking water. Total RNA was extracted from the livers of mice after 12 weeks’ exposure. Transcriptome sequencing of RNA was then conducted.

first: Kai

last: Zhu

first: Likun

last: Gao

first: Lizhi

last: Huang

first: Lili

last: Li


title: Capped small RNA sequencing (csRNA-seq) for genome-wide mapping of active transcription start sites and enhancer RNAs from total RNA

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 147, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

summary: Profiling ongoing transcription reveals the complete active transcriptome, including unstable enhancer RNAs, and provides a dynamic view of transcription dynamics, enabling the study of underlying gene regulatory mechanisms. Here, we describe a detailed protocol for capped- small RNA- sequencing (csRNA-seq), a method that uses total RNA to capture actively initiating or ‘nascent’ RNA polymerase II transcripts, including unstable RNAs such as enhancer RNAs, and their transcription start sites (TSSs). csRNA-seq offers several advantages: (1) the decoupling of sample collection and processing; (2) compatibility with diverse sample types, including fresh, frozen, and fixed tissues, as well as various eukaryotic organisms; and (3) scalability. Purified RNA is further non-infectious, can be isolated from inactivated samples—including clinical specimens or pathogenic samples—transported, and studied under standard laboratory conditions. This accessible protocol empowers researchers with minimal experience in nascent transcriptomics to study gene regulation and transcription dynamics.

overall_design: The protocol involves small RNA isolation, 5′-capped RNA enrichment, and library generation, followed by sequencing and data analysis to compare csRNA-seq and input small RNA to identify nascent RNAs.

first: Mackenzie

middle: K

last: Meyer

first: Patricia

last: Montilla-Perez

first: Anna

last: McDonald

first: Oluwadamilola

last: Olanrewaju

first: Eva

last: Rickard

first: Francesca

last: Telese

last: Benner

first: Marina

middle: I

last: Savenkova

middle: H


title: Involvement of p38 MAPK and MAPKAPK2 in promoting cell death and the inflammatory response to ischemic stress associated with necrotic glioblastoma

city: Hershey

first: Wei

address: 500 University Drive

institute: Penn State College of Medicine

summary: The association of necrosis in tumors with poor prognosis implies a potential tumor-promoting role. However, the mechanisms underlying cell death in this context and how damaged tissue contributes to tumor progression remain unclear. Here, we identified p38 mitogen-activated protein kinases (p38) as a key player in promoting cell death and the inflammatory response to ischemic stress associated with necrotic tumors. We found that glioblastoma (GBM) cells expressing patient-derived Kirsten rat sarcoma (KRAS) or phosphoinositide-3-kinase (PI3K) active mutants showed enhanced cell death under ischemia-mimetic conditions in vitro and were more likely to develop into necrotic tumors in vivo. Cell death in both settings depended on p38, which is also required for tumor progression driven by KRAS or PI3K. Under ischemia-mimetic conditions, GBM cells undergo reactive oxygen species (ROS)-dependent cell death. Gene expression in these cells recapitulated multiple features observed in peri-necrotic tumors from patient GBM. Further studies showed the involvement of a positive feedback loop between the p38-MAPK-activated protein kinase 2 (MK2) signaling axis and the unfolded protein response signaling components activating transcription factor 4 (ATF4) and inositol-requiring enzyme 1 (IRE1a) in driving ischemic tumor cell death. This signaling cascade was further potentiated by RAS or PI3K activation under ischemic conditions, contributing to the inflammatory gene expression response. Therefore, our study suggests that p38 could be targeted to relieve the inflammatory response in necrotic tumors and inhibit GBM progression.

overall_design: To further characterize the cellular response to ischemic conditions, we compared the gene expression profile of LN229 cells cultured under ischemic conditions to those cultured under normal conditions using RNA-seq as indicated in the manuscript. We used the p38a inhibitor VX745 or the MK2 inhibitor MK25 in LN229 cells to inhibit p38a or MK2, respectively, and examined the gene expression programs under the ischemic condition using RNA-seq. Compared to control cells treated by DMSO, gene expression in cells treated by VX745 or MK25 showed marked changes.

first: Kim

last: Soo-Yeon

first: Tang

last: Miaolu

first: Chih

last: Stephen

first: Sallavanti

last: Jessica

first: Gao

last: Yan

first: Qiu

last: Zhiqiang

first: Wang

last: Hong-Gang

first: Li

last: Wei


title: Gene expression profiling using RNA-Seq data of 12 mouse syngeneic tumor models treated with lenvatinib

city: Tsukuba

first: Megumi

last: Kuronishi

state: Ibaraki

address: Tokodai 5-1-3

institute: Eisai Co., Ltd.

summary: We performed RNA-Seq analysis using total RNA extracted from tumor tissues of 12 mouse syngeneic tumor models resected from mice orally administered lenvatinib (10 mg/kg once daily), without any treatment (No Treatment) for 7 days (Day 8 NT or Day 8 LEN), or tumor tissues resected from mice when tumor volume reached approximately 100 mm3 (Baseline NT), to investigate the baseline characteristics of 12 tumor models and differentially expressed genes by the drug treatment.

overall_design: Tumors were allowed to grow to approximately 100 mm3 in size (designated Day 1); tumor-bearing mice were then randomly allocated to treatment groups and orally administered lenvatinib (10 mg/kg once daily) for 7 days (Day 8).

first: Yoichi

last: Ozawa

first: Yu

last: Kato


title: HA-PRCC-TFE3 bound regions in HA-PRCC-TFE3 inducible HK-2 cells

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: PRCC-TFE3 is an oncogenic chimeric transcription factor derived from human TFE3-rearranged renal cell carcinoma. To analyze its genome-wide occupancy, we developed HA-tagged PRCC-TFE3-inducible HK-2 cell lines, which expresses HA-tagged TFE3 in a doxycycline-dependent manner. We determined the binding regions of HA-PRCC-TFE3 by ChIPSeq.

overall_design: We performed ChIP-seq analysis with an antibody against HA-tag on HA-PRCC-TFE3-inducible HK-2 cell lines.

first: Takanobu

last: Motoshima

first: Wenjuan

last: Ma

first: Yorifumi

last: Satou


title: Conchiformibius steedae DSM 2580 RNA-Seq

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: mRNA-Seq for differential gene expression analysis and delineation of chromosome interaction domains

overall_design: 3 conditions in biological triplicates (exponential growth (OD600 = 0.2), stationary growth (OD600 = 1), growth on solid medium for 24h)

first: Tobias

last: Viehboeck


title: Functional studies of the rust resistance gene R11 in sunflower (Helianthus annuus) using RNA sequencing (RNA-Seq)

city: Fargo

first: Lili

last: Qi

state: ND

address: 1616 Albrecht Blvd. North

institute: USDA-ARS

summary:
To investigate differntial gene expression patterns associated with R11-mediated resistance at different points after rust inoculation.
Data analysis was performed using RNA-seq data of wild type and two mutant lines at three different time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the rust resistant line R11-HA-R9 and R11-susceptible mutants.

first: Md

last: Shamimuzzaman

first: Guojia

first: William

last: Underwood


title: Deletion of Metal Transporter Zip14 (Slc39a14) Reduces Major Histocompatibility Complex II Expression in Murine Small Intestinal Epithelial Cells

city: Gainesville

first: Robert

middle: John

last: Cousins

state: FL

address: 572 Newell Drive

department: Food Science/Nutrition

institute: University of Florida

summary: Documented worldwide, impaired immunity is a cardinal signature resulting from loss of dietary zinc, an essential micronutrient. A steady supply of zinc to meet cellular requirements is regulated by an array of zinc transporters. Deletion of the transporter Zip14 (Slc39a14) in mice produced intestinal inflammation. Elevated fecal lipocalin-2, calprotectin, IgG levels and dysbiosis support the inflammatory phenotype. Here we show through RNA-sequencing, using purified intestinal epithelial cells (IECs), that Zip14 deletion produces markedly reduced expression of major histocompatibility complex class II (MHCII) molecules and the master MHCII trans-activator (Ciita). qPCR, western analysis and immunohistochemistry confirmed loss of MHCII. Spectrofluorimetry with zinc probe FluoZin-3 showed reduced labile zinc in IECs from knockout mice. Chromatin immunoprecipitation assays, using Ciita antibody and IEC chromatin, suggest decreased transcription accounts for depressed expression of specific MHCII genes. ATAC-sequencing (ATAC-seq) demonstrated that H2-Aa, H2-Ab1 and other MHCII genes result from chromatin remodeling yielding closed chromatin at regulatory regions of these genes. In agreement, ATAC-seq showed peak density of the chromosomal regulatory region of Ciita is consistent with down regulation of specific MHCII genes in IECs with Zip14 loss. Finally, dietary zinc supplementation of knockout mice and zinc supplementation of intestinal organoids in-vitro with Zip14 deletion restored transcript levels. Taken together, our data suggest that cellular zinc delivery, via Zip14, is necessary for proper chromatin occupancy, required for normal MHCII expression and effective immune functions, and to preclude inflammatory disorders of the small intestine.

overall_design: Intestinal epithelial cells were isolated and purified for flow cytometry and cell sorting. The preserved IECs were sent to MedGenome, Foster City, CA, USA). for library preparation and Assay for Transposase-Accessible Chromatin (ATAC) sequencing. Briefly, nuclei were isolated from the IECs and incubated with pre-loaded Tn5 transposase (Cat # FC-121-1030, Illumina, CA, USA) and sequencing adapters. The assembled protein A-Tn5 adapter transposome was activated by Mg2+ to generate adapter-flanked DNA fragments cut near the proteins of interest. The transposed DNA was then extracted, and PCR amplified using NEBNext High-Fidelity PCR Master Mix (Cat # M0541S, New England Biolabs, MA, USA). The library was purified with AMPure XP Magnetic Beads (Cat # A63880, Beckman Coulter, CA, USA), and its quality was assessed using a BioAnalyzer High-Sensitivity DNA Analysis kit (Cat # 5067–4626, Agilent, CA, USA).

first: Jimenez-Rondan

last: Felix

first: Ruggiero

last: Courtney

first: Riva

last: Alberto

last: Fahong

first: Stafford

last: Lauren

first: Cross

last: Tayler

first: Larkin III

last: Joseph

first: Cousins

last: Robert


title: IFNγ regulates ferroptosis in KFs by inhibiting the expression of SPOCD1 through DNMT3A

first: Jingyan

last: Huang

state: China

address: 639 Zhizaoju Road

institute: Shanghai Jiaotong University

summary: Keloid is benign skin tumor, and their curing is relatively difficult due to the unclear mechanism of formation. Inducing ferroptosis of keloid fibroblasts (KFs) may become a new method for treating keloid. Here, we discover interferon (IFN)γ could induce KFs ferroptosis through inhibiting SPOC domain-containing protein 1 (SPOCD1), serving as a mode of action for CD8+T cell (CTL)-mediated keloid killing. Mechanistically, keloid IFNγ deficiency in combination with reduced DNMT3A increase the expression of SPOCD1, thereby promoting KFs’ proliferation and inhibiting its ferroptosis. Moreover, keloid SPOCD1 deficiency attenuates KFs progression and extracellular matrix (ECM) deposition. Reducing IFNγ and SPOCD1 simultaneously can increase the positive rate of reactive oxygen species (ROS) and promote mitochondrial shrinkage. Ex-vivo explant keloid culture has also confirmed that the reduction of SPOCD1 helps to reduce the proliferation rate of KFs, inhibit the angiogenesis of keloid scars, and thus inhibit keloid formation. Thus, IFNγ signaling paired with SPOCD1 is a natural keloid ferroptosis promoting mechanism and a mode of action of CTLs. Targeting SPOCD1 pathway is a potential anti-keloid approach.

overall_design: In order to find the way to cure keloid, we apply RNA sequences to explore the different expression of gene in keloid. And we found the expression of SPOCD1is high in keloid. So, we hypothesis its important role in KFs’ ferroptosis and verified the regulatory effect of IFNγ on it.

first: Xiuxia

last: Wang


title: Dietary fiber promotes antigen presentation on intestinal epithelial cells and development of small intestinal CD4+CD8αα+ intraepithelial T cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To understand how changes in dietary fiber consumption and SFB colonization impact small intestinal epithelial cells (IECs) and consequently intraepithelial lymphocytes.

overall_design: Comparative gene expression analysis of RNA-seq data from intestinal epithelial cells of mice fed a standard chow diet (Control), a low fermentable fiber diet (NFF) or a standard chow diet and colonized with SFB (SFB).

first: Christopher

middle: D

first: Luisa

last: Cervantes-Barragan

first: Naomi

last: Rodriguez-Marino


title: A trigger-inducible split-Csy4 architecture for programmable RNA modulation

city: Hangzhou

first: Lihang

last: Zhang

state: Zhejiang

address: Shilongshan street 18

department: Department of Life science

institute: Westlake University

summary: The CRISPR-derived endoribonuclease Csy4 is a popular tool for controlling transgene expression in various therapeutically relevant settings, but adverse effects potentially arising from non-specific RNA cleavage remains largely unexplored. Here, we report a split-Csy4 architecture that was carefully optimized for in vivo usage. First, we separated Csy4 into two independent protein moieties whose full catalytic activity can be restored via various constitutive or conditional protein dimerization systems. Next, we show that introduction of split-Csy4 into human cells caused a substantially reduced extent in perturbation of the endogenous transcriptome when directly compared to full-length Csy4. Inspired by these results, we went on to use such split-Csy4 module to engineer inducible CRISPR- and translation-level gene switches regulated by the FDA-approved drug grazoprevir. This work provides valuable resource for Csy4-related biomedical research and discusses important issues for the development of clinically eligible regulation tools.

overall_design: In this study, we developed a trigger-inducible split-Csy4 system to efficiently and specifically cleave RNA in mammalian cells. The dataset includes processed RNA-Seq data from HEK-293T cells expressing full-length or split Csy4, and treated with either DMSO or grazoprevir, a small molecule that triggers the reconstitution of split-Csy4. Our findings show that both the split and reconstituted forms of the split-Csy4 system had significantly less impact on the transcriptome of HEK-293T cells compared to the full-length Csy4 nuclease.

first: Xinyuan

last: Qiu

first: Zhengyang

last: Luo

first: Yuting

last: Zhou

first: Lingyun

last: Zhu

first: Jiawei

last: Shao

first: Mingqi

last: Xie

first: Hui


title: Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [bulk RNA-seq]

first: Mark

last: Sheehan

overall_design: Quantseq bulk 3' Gene expression of PBMCs from patients before and after checkpoint inhibitors, including ChILI patients and control patients who did not develop ChILI.

first: Thomas

last: Lanz


title: m6A RNA Methylation Modulates Autophagy by Targeting Map1lc3b in Bisphenol A Induced Leydig Cell Dysfunction

city: Guangzhou

first: Zixin

last: Chen

state: 广东

address: Dongchuan Road

institute: Guangdong General Hospital

summary: Bisphenol A (BPA), a prevalent endocrine disruptor, has been implicated in male reproductive dysfunction, particularly affecting Leydig cells (LCs), which are critical for testosterone production. Here, we explore the impact of BPA on m6A RNA methylation and its regulatory effects on autophagy and LC function. Utilizing both in vivo and in vitro models, we demonstrate that BPA exposure significantly reduces testosterone biosynthesis and upregulates m6A modification in LCs. The m6A 'writer' METTL3 and 'eraser' ALKBH5 were found to play a central role in regulating the m6A levels in Leydig cells upon BPA exposure, and manipulating m6A methylation level mitigates BPA-induced Leydig cell injury.

overall_design: We then performed RNA-seq (also as input) and MeRIP-seq analysis using normal and BPA exposure TM3 Leydig cells.

first: Zhihong

first: Liqian

first: Chunhua

last: Deng


title: DNA methylation profiles of mice embryos (E7.5) of the control group and arsenic group_2nd experiment

first: Keiko

last: Nohara

address: 16-2 Onogawa

institute: National Institute for Environmental Studies

type: Methylation profiling by high throughput sequencing

summary: The control or gestationally arsenic exposed F1 males (C3H strain) and C57BL/6 strain (B6) females were crossed and F2 male embryos were obtained on embryonic day 7.5 (E7.5). The DNA methylomes of the embryos were investigated by RRBS method.

overall_design: Comparative DNA methylation analysis of RRBS data for control group and arsenic group

first: K


title: Transcriptomic analysis of human gastric cancer and normal epithelial tissues

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Small nucleolar RNAs (snoRNAs) are a highly conserved category of non-coding RNAs that play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of snoRNAs in regulating gastric cancer progression remain elusive. We identify SNORA37 as a driver of alternative splicing and gastric cancer progression. To explore the expression profiles of snoRNAs, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling in three pairs of gastric cancer and corresponding normal epithelial specimens. The results showed 15 differentially expressed snoRNAs in gastric cancer tissues, including 9 up-regulated and 6 down-regulated snoRNAs. Meanwhile, 2204 alternative splicing events were also discovered in gastric cancer tissues compared to those in adjacent normal epithelial tissues. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in human gastric cancer tissues, and these findings will help us understand the pathogenesis of cancer progression.

overall_design: Total RNA of tissues was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Wuhan SeqHealth Technology Co., Ltd. (Wuhan, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value less than 0.05.

first: Liduan

last: Zheng


title: ‘Digital Reprogramming’ Decodes Epigenetic Barriers of Cell Fate Changes and Identifies p300 Inhibitors as Facilitators [CUT&RUN]

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

summary: The fate of differentiated cells in our body can be reverted and changed by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling are produced. However, the efficiency of this process is low, partly due to the properties of the somatic donor which stabilize its differentiated fate and compromise reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood.Here, we developed an artificial intelligence-based approach that models reprogramming and identifies the chromatin modification H3K27ac as a novel epigenetic barrier to reprogramming-induced cell fate changes.  Using reprogramming by nuclear transfer to eggs of Xenopus laevis as a model system, we profiled chromatin modifications in cell types alongside gene expression patterns before and after reprogramming. We built computational models that integrate the generated data to accurately predict reprogramming outcomes on a transcriptome level. By leveraging our predictive models, we find that genes resisting inactivation during reprogramming display specific chromatin modification barcodes, including the known reprogramming barrier H3K4me3 alongside a novel candidate barrier, H3K27ac. Reducing H3K27ac levels using p300/CBP inhibitors before reprogramming correlated with an improved downregulation of genes linked to H3K27ac-modified enhancers during reprogramming. Importantly, these effects were accompanied by an improvement in the embryonic development of the resulting NT-embryos. In summary, our study developed ‘Digital Reprogramming”, an artificial intelligence approach capable of predicting resistance to cell-fate reprogramming and implicates H3K27ac as a critical barrier to reprogramming-associated cell fate changes.

overall_design: CUT&RUN experiment against H3K27ac, including neurula-stage Xenopus laevis embryos treated with either DMSO or p300 inhibitors, CBP30 and A-485. As a negative control, IgG was used. 12 H3K27ac samples, 4 IgG samples. A total of 4 biological replicates.

first: Ana

last: Janeva

first: Christopher

last: Penfold

first: Sara

last: Llorente-Armijo

first: Huiwen

last: Li

first: Tomas

last: Zikmund

first: Marco

last: Stock

first: Jerome

last: Jullien

first: Laura

last: Hofmann

first: Tobias

last: Straub

first: Ignasi

last: Forne

first: Axel

last: Imhof

first: Juanma

last: Vaquerizas

first: John

last: Gurdon

last: Hörmanseder


title: ‘Digital Reprogramming’ Decodes Epigenetic Barriers of Cell Fate Changes and Identifies p300 Inhibitors as Facilitators [RNA-Seq]

overall_design: In total 114 samples from mRNA-seq, single or paired-ended from neurula stage 18 endoderm and gastrula stage 11 ectoderm samples; or from neurula stage 18 meso-ectoderm and gastrula stage 11 endoderm samples.


title: Polo-like kinase inhibitors increase AAV production by halting cell cycle progression

city: Berkeley

first: Joshua

last: Tworig

state: CA

address: Weill Hall, Frank Schlessinger Way

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Recombinant Adeno-associated viruses (rAAV) are commonly used in gene therapy for preclinical research and therapeutic applications. Despite its clinical efficacy, the manufacturing of rAAV faces challenges in productivity and quality, leading to limited availability. In this study, we aimed to identify compounds that increase the capacity of cells to produce AAV9 with a high-throughput small-molecule screening strategy. With the Arrayed Targeted Library for AAV Screening platform, we screened a library of 3,300 small molecules and identified several targets, including cell-cycle modulators, G protein-coupled receptor modulators, histone deacetylate inhibitors, Janus kinase inhibitors, and metabolic modulators. Most notably, we identified Polo-like kinase isoform 1 (PLK1) inhibitors as enhancers of AAV production. PLK1 inhibition using HMN-214 increased AAV production, and was largely consistent across HEK293 cell lines, vector payloads and capsid serotypes. Using cell cycle and RNA-sequencing analysis, we show that PLK1 inhibition halts cells in the G2/M phase and blocks their exit from the M to G1 phase. These findings can be used to develop more cost-effective methods to increase AAV yield during production in the manufacturing process.

overall_design: We performed a small molecule screen for enhancers of AAV production in HEK293 cells. We used a triple plasmid transfection for AAV production. After identifying HMN-214 as a top hit, we performed RNA-seq in the presence and absence of this compound, as well as with and without AAV production. We collected total RNA for transcriptome analysis at 3 time points: before treatment (0 hr), 24 hours, and 72 hours after treatment. We carried out differential expression analysis between the HMN-214 treated group at 24 and 72 hours post treatment, and in the presence and absence of AAV production to identify gene products which may support enhanced AAV production when PLK1 is inhibited.

first: Kaylin

last: Fisher

first: Francis

last: Grafton

first: Francesca

last: Ispaso

first: Rupert

last: Durler

first: Florian

last: Sonntag

first: Markus

last: Hörer

first: Andreas

last: Schulze

last: Reid

first: Mohammad

last: Mandegar


title: Multi-omics Analysis Unveils Metabolic Inflexibility Manifesting as Impaired Branched Amino Acid and Enhanced Fatty Acid Degradation in a Mouse Model of Diabetic Cardiomyopathy [ATAC-seq]

first: Li

last: Zhou

address: Tongji Hospital Research Building, Wuxian Road, Caidian District, Wuhan, Hubei Province, People's Republic of China

department: Division of Cardiology, Departments of Internal Medicine

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Diabetic cardiomyopathy (DbCM) is an important clinical syndrome of diabetes and cause great burden to the people's life and health. Understanding its intrinsic epigenetic and metabolic alterations is critical to develop drugs for the treatment of DbCM. Multiple omics technology provides a feasible way for parsing the epigenetic characteristics and metabolic signatures associated with DbCM. The heart isolated from Male db/db mice and db/m mice were used for the analysis of high-throughput sequencing. Non-targeted metabolomics and amino acid-targeted metabolomics analyses were performed to detect the metabolites in plasma and heart tissues. Additionally, RNA-seq, proteomics, and ATAC-seq were employed to elucidate the underlying transcriptional-metabolic regulatory network mechanism in DbCM.

overall_design: the choromatin accessibility profiling of cardiac tissues of 24-week old db/m and db/db mice.


title: Lipid nanoparticles deliver DNA-encoded biologics and induce potent protective immunity

city: Houston

first: Dafei

last: Chai

state: Texas

address: Alkek Building One Baylor Plaza

institute: Baylor College of Medicine

summary: Lipid nanoparticles (LNPs) for mRNA delivery have advanced significantly, but LNP-mediated DNA delivery still faces clinical challenges. This study compared various LNP formulations for delivering DNA-encoded biologics, assessing their expression efficacy and the protective immunity generated by LNP-encapsulated DNA in different models. The LNP formulation used in Moderna’s Spikevax mRNA vaccine (LNP-M) demonstrated a stable nanoparticle structure, high expression efficiency, and low toxicity. Notably, a DNA vaccine encoding the spike protein, delivered via LNP-M, induced stronger antigen-specific antibody and T cell immune responses compared to electroporation. Single-cell RNA sequencing (scRNA-seq) analysis revealed that the LNP-M/pSpike vaccine enhanced CD80 activation signaling in CD8+ T cells, NK cells, macrophages, and DCs, while reducing the immunosuppressive signals. The enrichment of TCR and BCR by LNP-M/pSpike suggested an increase in immune response specificity and diversity. Additionally, LNP-M effectively delivered DNA-encoded antigens, such as mouse PD-L1 and p53R172H, or monoclonal antibodies targeting mouse PD-1 and human p53R282W. This approach inhibited tumor growth or metastasis in several mouse models. The long-term anti-tumor effects of LNP-M-delivered anti-p53R282W antibody relied on memory CD8+ T cell responses and enhanced MHC-I signaling from APCs to CD8+ T cells. These results highlight LNP-M as a promising and effective platform for delivering DNA-based vaccines and cancer immunotherapies.

overall_design: CD45+ cells were isolated from spleens of mice immunized with LNP-M/Ctrl, LNP-M/mRNA-Spike, EP/pSpike, or LNP-M/pSpike). These cells were then subjected to single-cell RNA sequencing (scRNA-seq) to investigate the changes in immune cells within the spleens. Immune and non-immune cells were isolated from tumors of mice treated with LNP-M/pEL285K-mAb or LNP-M/Ctrl. The isolated cells were performed to the scRNA-seq to investigate the differences in tumor-infiltrating T cells within the tumors.

first: Junhao

last: Wang


title: transcriptional change of the lesion site margins after spinal cord injury in canine

city: changsha

first: runlin

last: wen

state: hunan

address: yuelu street

institute: central south university

summary: We conduct complete SCI to canine and transplant stem cell into the lesion, in order to observe the transcriptional change of the lesion site margins,we isolate the margin tissue and performing high-throughput sequencing

overall_design:
After anesthesia, 2 mm spinal cord segments were taken from each canine, sourced from areas 0-2 mm and 2-4 mm away from the lesion border, and total RNA was extracted. RNA high throughput sequencing was performed by Cloud-Seq Biotech
Mid SR mSC: Five days after adding the modified scaffold material to the injury site, isolate tissue samples located 0-2 mm from the injury site
Mid SR: Without adding the modified material, isolate tissue samples located 0-2 mm from the injury site after 5 days
Acute: Five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site
Mid SR 2-4mm: Without adding the modified material, isolate tissue samples located 2-4 mm from the injury site after 5 days
Mid nonSR: Sixty-five days after spinal cord injury (SCI), isolate tissue samples located 0-2 mm from the injury site
Normal: Isolate 2 mm tissue samples from the same anatomical location in normal spinal cord tissue

first: Runlin

last: Wen

first: Xing

last: Li

first: Dingyang

last: Liu


title: Chimeric antigen receptor with novel intracellular modules improves antitumor performance of T cells

city: Xi'an

first: Pengju

state: Shaanxi

address: Changle West Road

department: Immunology

institute: Fourth Military Medical University

summary: The excessive cytokine release and limited persistence represent major obstacles to successful chimeric antigen receptor T (CAR-T) cell therapy in solid tumors. Conventional CARs employ an intracellular domain (ICD) from the ζ chain of CD3 as a signaling module, and it is largely unknown how alternative CD3 chains potentially contribute to CAR design. Here, we obtained a series of CAR-T cells against HER2 and mesothelin using a domain containing one immunoreceptor tyrosine-based activation motif from different CD3 subunits as the ICD of CARs. While these reconstituted CARs conferred sufficient antigen-specific cytolytic activity on equipped T cells, they elicited low tonic signal, ameliorated CAR-T cell exhaustion and facilitated memory differentiation. Intriguingly, the CD3ε-derived ICD outperformed others in generation of CAR-T cells that produced minimized cytokines. Mechanistically, CD3ε-based CARs displayed a restrained cytomembrane expression on engineered T cells, which was ascribed to endoplasmic reticulum retention mediated by the carboxyl terminal basic residues. The present study demonstrated the applicability of CAR reconstitution using signaling modules from different CD3 subunits, and depicted a novel pattern of CAR expression that reduces cytokine release, thus paving a way for generation of CAR-T cells with improved safety and persistence against diverse tumor antigens.

overall_design: To exploit the mechanisms underlying the different phenotypes of CAR-T cells, we detected remarkably different gene expression landscapes between CAR-T cells designed using ICDs from different CD3 subunits by RNA seq.

first: Bo

last: Yan

first: Angang

last: Yang

first: Lintao

last: Jia


title: ‘Digital Reprogramming’ Decodes Epigenetic Barriers of Cell Fate Changes and Identifies p300 Inhibitors as Facilitators [ChIP-Seq]

first: Eva

last: Hoermanseder

overall_design: ChIP-seq experiments from neurula stage 21 Xenopus laevis embryos, either in endoderm or meso-ectoderm tissue. In total, 48 samples.

first: Ana

last: Janeva

first: Christopher

last: Penfold

first: Sara

last: Llorente-Armijo

first: Huiwen

first: Tomas

last: Zikmund

first: Marco

last: Stock

first: Jerome

last: Jullien

first: Laura

last: Hofmann

first: Tobias

last: Straub

first: Ignasi

last: Forne

first: Axel

last: Imhof

first: Juanma

last: Vaquerizas

first: John

last: Gurdon

last: Hörmanseder


title: Gene expression profile at single cell level of primary neuronal culture from cortices of C57Bl6 and hTau mice treated with pathogenic brain-derived Tau oligomers

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: Primary cortical neurons are established tool to study Tau oligomers-mediated toxicity. We used single-cell RNA seq to identify diverisity of gene expression upon Tau oligomers treatment

overall_design: Primary cortical neurons have been isolated from embrionic brains from two mouse models C57 (wt) and hTau and their RNAs analyzed according to the treatement with Tau oligomers

first: Mauro

last: Montalbano

first: Nicha

last: Punagmalai


title: Pembrolizumab plus chemotherapy in frontline treatment of advanced epithelial ovarian cancer: clinical and translational results from a phase II trial

first: Jeffrey

middle: Andrew

last: How

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

institute: The University of Texas MD Anderson Cancer Center

summary: We evaluated the efficacy and feasibility of pembrolizumab combined with chemotherapy in frontline management of advanced high-grade epithelial ovarian cancer (EOC). Additionally, chemotherapy-induced changes in the tumor microenvironment and biomarkers of response were evaluated. In this single-arm phase II trial, eligible patients received up to 4 cycles of neoadjuvant chemotherapy followed by interval cytoreduction; then, adjuvant intravenous carboplatin/weekly paclitaxel/pembrolizumab was given for 3 cycles and maintenance pembrolizumab until progression or toxicity (maximum 20 cycles). The primary endpoint was progression-free survival (PFS). Secondary endpoints included feasibility, toxicity, and overall survival (OS). PD-L1 staining, multiplex immunofluorescence staining, RNA-sequencing, reverse phase protein array analyses were performed on pre- and post-chemotherapy samples. Thirty-one eligible patients were enrolled. Median PFS was 14.88 months overall (95% CI 12.40 – 23.00). Among those with PD-L1 Combined Positive Score (CPS), the median PFS and OS were not reached compared to those with CPS<10 (10.50 and 30.90 months, respectively). All patients who initiated chemotherapy with pembrolizumab therapy completed their planned adjuvant cycles. Treatment discontinuation due to immune-related toxicity occurred in 6 patients (20%). Chemotherapy resulted in an infiltration of anti-tumor immune cells in the tumor microenvironment. Samples of patients with the best PFS demonstrated increased expression of NF-κB, TGF-β, and β-catenin signaling. In conclusion, pembrolizumab with chemotherapy was feasible and resulted in PFS within the historical range for this EOC population. Patients with CPS≥10 may benefit more from this regimen and future studies should investigate this potential biomarker. Funding for this investigator-initiated trial was provided by Merck. Clinicaltrials.gov: NCT02520154.

overall_design: Tumor specimens were collected at two time points: 1) prior to start of neoadjuvant chemotherapy and 2) at time of interval cytoreduction. Pre-neoadjuvant chemotherapy samples were obtained either at the time of diagnostic laparoscopy or via diagnostic biopsies performed by interventional radiology. RNA-seq was performed in the MD Anderson Cancer Genomics Core Laboratory.

first: Minghao

last: Dang

first: Sanghoon

last: Lee

first: Linghua

first: Amir

last: Jazaeri


title: Adult zymosan re-exposure exacerbates the molecular alterations in the brainstem rostral ventromedial medulla of rats with early life zymosan-induced cystitis.

city: Wauwatosa

first: Banani

last: Banerjee

state: WI

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

summary: Recent evidence suggests that the descending modulatory pathways from the brainstem rostral ventromedial medulla (RVM) are important for bladder inflammatory pain.  This study aimed to identify the long-term molecular changes in RVM neurons due to early life cystitis during neuronal development and the effect of reexposure later in adulthood.  RVM tissues from two treatment protocols were used: (1) neonatal zymosan exposures with acute adult rechallenge (RC) and (2) only neonatal zymosan exposures (NRC).  RNAseq analysis showed upregulation of several genes associated with synaptic plasticity (Grin1, Grip2, Notch1, Arc, and Scn2b) in the cystitis groups compared to controls in both protocols.  The RC protocol exhibited a stronger treatment effect with significantly higher fold differences between the groups compared to the NRC protocol (p<0.001, fold differences RC vs NRC).  In microarrays, miR-34a-5p showed cystitis-induced downregulation in both protocols.  Bioinformatics analysis identified multiple 3’UTRs complementary binding sites for miR-34a-5p on Grin2b, Notch1, Grip2, Scn2b, and Arc genes. The enhanced response in the RC protocol indicates a possible priming effect of early life cystitis on rechallenge in adulthood.  These long-term molecular alterations may play a critical role in the development of chronic bladder pain conditions as seen in patients with Interstitial Cystitis/Bladder pain syndrome

overall_design: We carried out unbiased high throughput whole genome sequencing of the synaptoneurosomes (SYNs)  preparations from RVM tissues in both protocols and investigated differential expression of genes associated with synaptic neurotransmission in cystitis groups with and without adult reexposure in comparison to respective saline controls.

first: Bhavana

last: Talluri

first: Sankar

last: Addya

first: Maia

last: Terashvili

first: Bidyut

last: Medda

first: Anjishnu

first: Reza

last: Shaker

first: Jyoti

middle: N

last: Sengupta


title: Primary cilia are shear stress calcium-responsive mechanosensors in the epididymis

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

institute: UMR1078 - Université de Bretagne Occidentale

summary: The epithelium of the epididymis proliferates and differentiates until puberty, to become fully functional when the first wave of spermatozoa initiates its post-testicular maturation process. While the tension exerted by the testicular-derived fluid has been proposed to stimulate the proliferation/differentiation of the epithelium through physical cues, the mechanism involved has never been identified. Here we assessed whether the responsiveness of the epididymal cells to luminal shear stress depends on functional primary cilia. Combining in silico fluidic modeling with in vitro microfluidic strategies, we subjected immortalized distal caput epididymis principal cells (DC2) to a static or fluid shear stress condition. RNA sequencing studies identified 100 genes as being overexpressed in response to shear stress (Fold change >1.5, FDR< 0.05), including Early growth response (EGR) 2/3, Cellular communication network factor (CCN) 1/2, and Fos, also found induced in flow-stimulated renal cells. Enrichment of transcriptional factors involved in proliferative signaling pathways was consistent with the proliferative changes observed in DC2 cells under shear stress conditions. Of interest, DEGs particularly relevant to epididymal physiology and sperm maturation, including Serpine1 and Adamts1, were identified as secreted factors interacting with the maturing spermatozoa. While shear stress triggered a rapid increase of intracellular Ca2+ in DC2 cells, this response was abrogated following the impairment of primary ciliogenesis through pharmacological and siRNA approaches. Embracing physical and biological concepts, our findings identify primary cilia as a fluid-mechanosensor that may contribute to epididymal cell development and proliferation, a requisite to sperm maturation

overall_design:
To investigate the effect of fluid shear stress on Distal Caput Principal Cells (DC2) gene expression, we compared DC2 cells exposed to shear stress of 1 dyn/cm2 (Flow condition) to DC2 in static conditions for 3hours. We then performed gene expression profiling analysis using data obtained from RNA-SEq of 4 different experiments.
Furtermore, to investigate the influence of primary cilia located at the apical pole of Distal Caput Principal Cells (DC2) in their response to fluid shear stress, we inhibited the formation of primary cilia in DC2 cells using ift88 siRNA. Subsequently, we conducted gene expression profiling analysis using RNA-Seq data obtained from four separate cell samples

first: Sepideh

last: Fakhari

first: Clémence

last: Belleannée


title: Antigen-driven CD8+ T cell clonal expansion is a prominent feature of MASH in humans and mice [human]

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

summary: Metabolic dysfunction-associated steatoheptaitis (MASH) is a chronic liver disease caused by prolonged poor diet. During MASH-induced chirrosis in humans and diet-induced MASH in murine models, T cells accumulated in the liver but their function in MASH is unresolved. We aimed to evaluated differences in T cell phenotype and T cell receptor (TCR) repertoire in T cells from the livers of diseased humans and murine models. This set contains human sequencing data.

overall_design: Diseased human liver samples were selected from a bioreposistory of patients who had undergone liver transplantation. Non-diseased human liver samples were purchased from Triangle Research Laboraties with the exception of PBMC samples 2-4, which were sourced from 10x Genomics' online datasets (for patient info, see publication Table 1).

first: Abbigayl

middle: E

last: Burtis

first: Diestiny

last: DeNicola

first: Megan

last: Ferguson

first: Radleigh

last: Santos

first: Clemencia

last: Pinilla

first: Michael

middle: S

last: Kriss

first: David

last: Orlicky

first: Beth

last: Tamburini

first: Austin

last: Gillen


title: Neutrophils restricted contribution of CCRL2 genetic variants to COVID-19 severity

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

country: Italy

institute: University of Verona

summary: The 3p21.31 locus, which locus contains a chemokine receptor (CKR) cluster, is the most robust genomic region associated with COVID-19 severity. We tested expression quantitative trait loci (eQTL) targeting the 3p21.31 CKR cluster linked to COVID-19 hospitalization in Europeans from the COVID-19 HGI meta-analysis. Among these, CCRL2, a key regulator of neutrophil trafficking, was targeted by neutrophil-restricted eQTLs. We confirmed these eQTLs in an Italian COVID-19 cohort. Haplotype analysis revealed a link between an increased CCRL2 expression and COVID-19 severity and hospitalization. By the exposure of neutrophils to a TLR8 ligand, reflecting a viral infection, we revealed specific chromatin domains within the 3p21.31 locus exclusive to neutrophils. In addition, the identified variants mapped within these regions altered the binding motif of neutrophils expressed transcription factors. These results support that CCRL2 eQTL variants contribute to the risk of severe COVID-19 by selectively affecting neutrophil’s function

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for the histone modification H3K27Ac in freshly isolated and R848-stimulated human neutrophils

first: Mattia

last: Laffranchi

first: Marco

last: Cassatella

first: Nicola

last: Tamassia


title: S100A8/A9 promotes dendritic cell-mediated Th17 cell response in SS dry eye

city: Tianjin

first: Mei

last: Sun

state: Tianjin

address: 251 Fukang Road, Xiqing District, Tianjin, China

institute: Tianjin Medical University Eye Hospital

summary: Sjogren's syndrome (SS) dry eye is a chronic autoimmune eyedisease driven by T helper 17 (Th17)cells. S100A8/A9 has emerged as an important proinflammatory alarmin in variousautoimmune and inflammatory diseases. However, the role of S100A8/A9 in the pathogenesis of SS dry eye remains unexplored. Here,we show that the expression levels of S100A8/A9 were elevated in peripheral blood mononuclear cells (PBMCs) of patients with SS dry eye, as well as the lacrimal glands (LGs) of SS dry eye mice. The administration of paquinimod, a specific inhibitor of S100A8/A9, could alleviate the progression of SS dry eye with significant reduction of Th17 cell frequency in LGs, spleen and lymph nodes of SS dry eye mice.Further experiment revealed that S100A8/A9 did not directly affect Th17 generation and function, but upregulated the expression of MHCIl andI123a in DCs to augment Th17 cell response through a Acod1/STAT3-dependent signaling pathway in the context of SS dry eye. Together,these findings unveiled the key role of S100A8/A9 in the pathogenesis of SS dry eye and suggested a potential therapeutic avenue for SS dry eyeand otherTh7 cell-related autoimmune disorders.

overall_design: We isolated bone marrow cells from SS dry eye mice to induce DCs, and stimulated DCs with recombinant S100A8/A9 or Vehicle. Total RNAs of Vehicle- or S100A8/A9-treated DCs were extracted using TRIzol® Reagent (Invitrogen). Then RNA‐sequencing was performed to predict downstream signaling pathways involved in the regulatory effect of S100A8/A9 on DCs.

first: Yankai

last: Wei


title: Maternal high-fat diet aggravates the development of atherosclerosis in offspring via epigenetic memory (SMART-Seq)

city: tianjin

first: kan

last: li

address: Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China

institute: Tianjin Medical University

summary: Maternal exposure to a western-type diet (WD) increases the susceptibility of adult offspring to atherosclerosis. Lining the inner layer of blood vessels, fetus endothelial cells (ECs) become dysfunctional and inflamed in response to risk factors from mother through maternal and fetal blood exchange. However, the mechanism by which maternal WD promotes vascular endothelial dysfunction and atherosclerosis in offspring after adulthood has not been fully clarified. Here, we found that maternal WD exposure sensitized offspring to WD exposure in adulthood of Ldlr-/- mice, significantly increasing atherosclerotic lesions in the aorta and aortic roots, endowed inflammatory memory at the chromatin level and regulated chromatin dynamics by transcription factor AP-1 in mouse aortic ECs. Plasma 27-hydroxycholesterol (27-HC) was significantly increased in maternal blood and transferred into the offspring. Additionally, 27-HC played a crucial role in memory establishment and also acted as a secondary stimulator, amplifying the expression of inflammatory memory factors and enhancing the enrichment of AP-1/p300 and H3K27ac in the binding domain in human ECs. Inhibiting AP-1 binding to chromatin reduced the inflammatory response in human umbilical vein ECs from mother with maternal hypercholesterolemia and the occurrence and development of atherosclerosis in the offspring with maternal WD exposure. Our findings demonstrate that maternal WD aggravating EC dysfunction and atherosclerosis in offspring after adulthood acquires AP-1-associated epigenetic memory to increase chromatin accessibility of inflammatory genes.

overall_design: We isolated and performed SMART-seq, ATAC-seq, and H3K27ac ChIP-seq on mouse aortic ECs (MAECs) from mice in the CDM-CDO / WDM-CDO groups and in the CDM-WDO / WDM-WDO groups that were given WD again for 4 weeks

first: Kan

last: Li

first: Weiqi

last: Qian

first: Fangni

last: Zhang

first: Ding

last: Ai


title: Inferring DNA methylation in non-skeletal tissues of ancient specimens

city: Jerusalem

first: Liran

last: Carmel

address: The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. As DNA methylation is more conserved across species than across tissues, and as ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here, we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue- specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation data sets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the NBPF gene family, which likely played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the paleontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.

overall_design:
DNA methylation maps from four femur head bones from present-day humans were generated using whole-genome bisulfite sequencing (WGBS). Patients were females with osteoarthritis. Sample were extracted during a total hip replacement surgery, and were taken from the healthy part of the bone. We aligned paired-end sequencing reads to hg19 genome assembly using Bismark v0.23.0. We then used bismark_methylation_extractor to extract methylation calls.
We also reconstructed the methylome of a previously sequenced Mesolithic anatomically modern human individual from Stora Karlsö, Sweden (available from the European Nucleotide Archive under accession number PRJEB21940).

first: Yoav

last: Mathov

first: Malka

last: Nissim-Rafinia

first: Chen

last: Leibson

first: Nir

last: Galun

first: Tomas

last: Marques-Bonet

first: Arye

last: Kandel

first: Meir

last: Liebergal

first: Eran

last: Meshorer


title: Effects of defined voluntary running distances coupled with high-fat diet consumption on the murine skeletal muscle transcriptome

city: Grand Forks

first: Shanon

last: Casperson

state: ND

address: 2420 2nd Ave North

institute: USDA/ARS Grand Forks Human Nutrition Research Center

summary: Exercise counters many adverse health effects of consuming a high-fat diet (HFD). However, the complex molecular changes that occur in skeletal muscle in response to exercising while consuming a HFD are not yet known. We investigated the interplay between diverse exercise regimes and HFD consumption for 12 weeks on the adaptation of the skeletal muscle transcriptome. C57BL/6 male mice were randomized into six groups – two sedentary control groups and four exercise groups. An unrestricted running group that averaged 8.3 km/day and exercise groups that were restricted to 75%, 50%, or 25% of unrestricted running that averaged 6.3, 4.2, and 2.1 km/day, respectively. Control groups were fed either an AIN93G diet or a HFD (HFD-C) and the exercise groups were fed the HFD. Total RNA was extracted from flash frozen gastrocnemius muscle for sequencing and transcriptome analyses. A total of 12053 transcripts were differentially expressed in the exercise groups compared to the HFD-C. When comparing the HFD-C and the different exercise groups, exercising at 50% of unrestricted access (HFD-50%) resulted in maximum differentially expressed transcripts. Genes down regulated in HFD-50% group were mostly associated with MAPK and cAMP signaling pathways, whereas up-regulated genes were associated with PPAR and JAK-STAT signaling pathways, along with tryptophan and nitrogen metabolism. These results demonstrate that running distance has a significant impact on the adaptation of the skeletal muscle transcriptome to exercise. Furthermore, transcriptome adaptations were more prominent in response to middle-distance running.

overall_design: Three to four weeks old C57BL/6 male mice were randomly assigned to one of six groups – two sedentary control groups and four exercise groups. One of the sedentary control groups was fed the AIN93G diet (NFD-C) and the other sedentary control group was fed the HFD (HFD-C). The four exercise groups were fed the HFD and had access to an in-cage running wheel equipped with programmable brakes (Model 86120, Scurry Activity Monitoring Systems, Lafayette Instrument, Lafayette, Ind.). One group had unrestricted access to the running wheel and averaged 8.3 km/day (HFD-U). The running distance of the HFD-U was then used to calculate the running distance of the other groups so that running was restricted by 75%, 50%, or 25% with average running distances of 6.3, 4.2, and 2.1 km/day, respectively. Brakes were released at Zeitgeber time 12 (light off) for restricted runners and applied when they met their assigned daily running activities. After 12 weeks the mice were euthanized and both gastrocnemius muscles were collected, flash frozen, and store at -80°C.

first: Afrina

last: Brishti

first: Sarah

last: Johnson

first: Lin

last: Yan


title: Optimization of a Micro-scale Air-Liquid-Interface Model of Human Proximal Airway Epithelium for Moderate Throughput Drug Screening for SARS-CoV-2

city: Los Angeles

first: Chandani

last: Sen

state: California

address: 650 Charles Young Drive South Laboratory of Dr. Brigitte Gomperts, CHS 64-200

department: Pediatrics

institute: University of California, Los Angeles

summary: Respiratory viruses (e.g. influenza, RSV, SARS, MERS etc.)  attack the proximal airway (upper respiratory tract) and cause a wide spectrum of diseases for which we have limited therapies. To date, a few primary human stem cell-based models of the proximal airway have been reported for drug discovery but scaling them up to a high throughput platform remains a significant challenge. Here we present a microscale, primary human stem cell-based proximal airway model of SARS-CoV-2 infection, which is amenable to moderate-to-high throughput drug screening. The model recapitulates the heterogeneity of infection seen among different patients and with different SARS-CoV-2 variants. Using this model, we screened 2100 compounds from targeted drug libraries. We characterized a new small molecule with antiviral properties that is effective against both Wuhan and Omicron variants

overall_design: Primary human airway basal stem cells were cultured  in 96-well ALI plates to develop differentiated mucociliary epthelium. Cells were treated or not with Remdesivir and compound MKGaA#49, then exposed or not to Wuhan variant of SARS-CoV-2 for 72 hours. Cells were then harvested for total RNA sequencing

first: Tammy

middle: M

last: Rickabaugh

first: Abdo

last: Durra

first: Ulrich

last: Betz

first: Vaithilingaraja

last: Arumugaswami

first: Robert

last: Damoiseaux

first: Brigitte

last: Gomperts