title: Targeting inflammatory macrophages with hyaluronan tetrasaccharide: effects on fibroblast collagen degradation and synthesis [1]

city: Kizugawa

first: Eiko

last: Uno

address: 6-5-4 Kunimidai

institute: Rohto Pharmaceutical Co., Ltd.

summary: Hyaluronan (HA) provides moisturizing benefits and exhibits unique biological activities based on its molecular weight. While the anti-inflammatory effects of high-molecular-weight HA have been well studied, the impact of hyaluronan tetrasaccharide (HA4), an ultralow-molecular-weight HA, on the skin immune system is not fully understood. Thus, we investigated how HA4 affects the differentiation of M1 macrophages, which increase during photoaging. As a result, we added HA4 during the M1 macrophage differentiation phase and conducted a gene expression analysis. HA4 partially decreased the transition from M0 to M1 macrophages and reduced the expression of proinflammatory cytokines like IL-6. However, the M2 marker IL-1ra increased, while IL-10 levels remained constant, suggesting that HA4 does not fully polarize macrophages toward the M2 phenotype. Normal human dermal fibroblasts (NHDF) were treated with an M1 macrophage-conditioned medium (M1-CM) and a modified version containing HA4 (M1+HA4-CM). The M1+HA4-CM notably decreased the expression of IL-6 and IL-8, along with the collagen-degrading enzyme MMP1. Collagen synthesis assays showed that HA4 helped restore collagen fiber formation. Moreover, RNA-seq analysis of NHDF treated with the conditioned medium confirmed that M1+HA4-CM amplified the expression of genes related to collagen production while decreasing collagen-degrading enzyme gene expression. Neutralization assays employing a TLR4 antibody suggested that decreasing IL-6 in NHDF by HA4 may be independent of the TLR4 signaling pathway. HA4 is vital in partially suppressing M1 macrophage differentiation and the release of inflammatory factors, as well as regulating collagen remodeling in NHDF. These findings indicate that HA4 holds promise as a molecule for mitigating inflammation-induced collagen degradation by modulating macrophage activity in photoaged skin.

overall_design: RNA-seq profiling was performed using three groups of cells: (1) M0 macrophages derived from THP-1 monocytes, (2) M1 macrophages differentiated from M0 cells by stimulation with LPS and IFN-γ, and (3) M1 macrophages differentiated in the presence of HA4 (M1+HA4).

last: Muto

first: Florence

last: Kim

first: Mihoko

last: Yoshino

first: Yasunari

last: Sato

first: Masao

last: Hashimoto

first: Kenji

last: Watanabe

first: Yoichi

last: Mizukami


title: FLASH Irradiation Modulates Immune Responses and Accelerates Lung Recovery: A Single-Cell Perspective

status: Public on Jun 06 2025

city: Beijing

first: Changzhen

last: Wang

address: No 27. Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

type: Expression profiling by high throughput sequencing

summary: We performed single-cell RNA sequencing to analyze murine lung tissues exposed to either conventional dose rate (CONV) or FLASH radiation therapy (FLASH-RT). This approach elucidated distinct early immune responses in radiation-induced lung injury and revealed protective mechanisms specific to FLASH irradiation. Systematic characterization of over 135,000 cells within the pulmonary microenvironment uncovered critical immune and stromal cell dynamics that differentiate CONV and FLASH-RT responses. These findings provide mechanistic insights into FLASH-RT's biological effects and its potential clinical applications in thoracic oncology.

overall_design: In this controlled experiment, C57BL/6J mice underwent whole-thorax irradiation at a dose of 17.8 Gy administered via either CONV or FLASH-RT. Lung specimens displaying characteristic radiation-induced injury phenotypes were systematically harvested during the acute phase (days 1 and 7 post-irradiation) from experimental cohorts (n=3 per group per time point). Age-matched sham-irradiated control groups underwent identical procedures without radiation exposure. Single-cell suspensions were generated through enzymatic dissociation of collected tissues and subsequently subjected to transcriptomic profiling using the 10x Genomics platform for single-cell RNA sequencing (scRNA-seq).

first: Hao

last: Lu

first: Guofu

last: Dong


title: PAD4 deletion inhibited obstruction-induced kidney inflammation and fibrosis

first: Yuandong

last: Tao

state: --- Select One ---

address: Beijing

institute: Chinese PLA General Hospital

summary: To understand the roles and mechanisms of neutrophil extracellular traps (NETs) in unilateral ureteral obstruction (UUO)-induced renal fibrosis, we performed RNA sequencing of UUO kidneys from wild-type and PAD4-deficient mice. PAD4 deletion led to reduced expression of fibrosis- and injury-associated genes, as well as inflammatory cytokines in UUO kidneys. Enrichment analysis of the downregulated genes in PAD4-deficient mice revealed a drastic decrease in inflammation pathways, such as T cell-associated pathways and cytokine-cytokine receptor interaction.

overall_design: Bulk RNA sequencing was performed in kidneys from wild-type or Padi4-knockout mice that were subject to 10 days of unilateral ureteral obstruction.


title: Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [CUT&Tag]

status: Public on Jun 05 2025

city: Chicago

first: Boyang

last: Gao

state: IL

address: 929 E 57th Street

department: Chemistry

country: USA

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 5-azacytidine (5-azaC) is a DNA hypomethylating agent clinically used to improve outcomes in myeloid malignancies. However, 5-azaC treatment causes gene dysregulation inconsistent with DNA hypomethylation changes. Some patients benefited from 5-azaC treatment did not display notable DNA demethylation. These observations suggest alternative mechanisms of action by 5-azaC. As a ribonuleoside analogue, 5-azaC is more readily incorporated into nascent RNA. Here, we demonstrate that RNA 5-methycytosine (m5C) depletion by 5-azaC treatment, particularly at early time points, is sufficient to induce leukemia cell death. In contrast to its DNA demethylation function, the RNA-dependent process by 5-azaC causes transcriptional repression, disrupting genes involved in cell cycle regulation and DNA repair. Mechanistically, 5-azaC impairs two specific m5C-mediated transcriptional regulatory pathways. First, depletion of m5C in chromatin-associated RNA (caRNA) disrupts the MBD6-mediated H2AK119ub removal. In parallel, this also impairs SRSF2 recruitment and the downstream H3K27ac deposition by p300. Indeed, loss of the caRNA methyltransferase NSUN2 caused prolonged cell cycle, defective DNA repair, and shifted hematopoietic lineage commitment toward erythropoiesis, mirroring the effects of 5-azaC treatment. Furthermore, we performed leukemia cell line screen and identifies that TET2 and IKZF1 depletion can sensitize 5-azaC treatment, consistent with the observed RNA-dependent cytotoxicity of 5-azaC in leukemia cells. In summary, our findings highlight the transcription regulation by 5-azaC through depleting caRNA m5C, providing insights into the mechanism of action for 5-azaC, the prediction of its efficacy, and future directions for therapy developments based on 5-azaC.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MOLM13 and SKM1 CUT&Tag samples were treated with 3 μM 5-azaC for 16 hours; LK cells with 3 μM 5-azaC for 24 hours; SKM1 tetshNSUN2 with Dox-induced KD for 5 days

first: Ying

last: Li

first: Chuan

last: He


title: Biallelic variants in SREK1 downregulating SNORD115/116 cause a novel Prader-Willi-like syndrome

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Up to 10% of patients with severe early-onset obesity carry pathogenic variants in known obesity-related genes, mostly affecting the leptin-melanocortin pathway. Studying children with severe obesity from consanguineous populations provides a unique opportunity to uncover novel molecular mechanisms. Using whole-exome sequencing, followed by a rigorous analytical and filtration strategy, we identified three different homozygous missense variants in SREK1 (encoding Splicing Regulatory glutamic acid and lysine rich protein) in Pakistani children with severe obesity, from three unrelated consanguineous pedigrees. The wild type SREK1 gene of human induced pluripotent stem cell (iPSC)-derived hypothalamic neurons was individually replaced by each of the three variants and the impact of these changes on global gene expression was studied. Neurons expressing the two variants in the SREK1 RNA recognition domain p.P95L and p.T194M, but not the C-terminally located p.E601K, had markedly reduced expression of the small nucleolar RNA clusters SNORD115 and SNORD116, deficiency of which has been implicated in Prader-Willi syndrome (PWS). In addition to hyperphagic obesity the carriers of these two variants had other features of PWS, such as neonatal hypotonia. In conclusion, homozygous variants in SREK1 result in a subtype of severe early onset obesity sharing features with PWS.

overall_design: iPSC derived hypothalamic neurones (WT) or with CRISPER KnockIn mutations T194M, P95L and E601K

first: Anna-Maria

last: Siegert

first: Yi-Chun

last: Tung

first: Sherine

last: Awad

first: Stephen

last: O'Rahilly

first: Giles

last: Yeo


title: Antibiotic adjuvant effects in MRSA USA300

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

institute: High Point University

summary: Methicillin-resistant Staphylococcus aureus (MRSA) is a major threat to human health. Rather than depend on creating new antibiotics (to which bacteria will eventually become resistant), we are employing antibiotic adjuvants that potentiation existing antibiotics. To gain biological insight into how lead compounds potentiate antibiotics and inhibit biofilms, we used RNA-seq on treated MRSA USA300 cultures to examine antibiotic adjuvant affects transcritome-wide.

overall_design: Differential gene expression was examined between MRSA cultures either untreated, treated with oxacillin only, treated with an antibiotic adjuvant (loratadine or compound 8), or cotreated with oxacillin and either loratadine or compound 8. Each of the treatments was performed with biological triplicates.

first: Miller

last: Heather B.


title: Primary human intestinal organoids recapitulate enteric infection of monkeypox virus and enable scalable drug discovery

city: Chengdu

first: Pengfei

address: Chengdu, Sichuan

institute: Sichuan University

summary: Monkeypox virus (MPXV) infection-associated intestinal manifestations including diarrhea and proctitis have been frequently reported during mpox outbreaks. The clade IIb MPXV strain has caused the 2022-2023 global outbreak, whereas the Ia and Ib strains are causing the concurrent outbreaks in Africa. Here, we found clinical evidence that MPXV can directly infect human intestine to induce lesions. Intriguingly, primary organoids cultured from human ileum and rectum support productive infections of MPXV clade IIb, Ia and Ib strains. Upon differentiation, we found that enterocytes and goblet cells but not enteroendocrine cells are capable of supporting viral replication. Given that primary intestinal organoids can be rapidly expanded in large scale, we were able to screen a broad-spectrum antiviral drug library. We identified 12 leading candidates of safe-in-human agents including clinically used drugs such as clofarabine. We extensively validated the anti-MPXV activity of clofarabine in human intestinal and skin organoids, and consistently demonstrated the potent antiviral activity against clade Ia, Ib and IIb strains. These findings are important for better understanding the clinical manifestations of mpox. Primary intestinal organoids-based infection models and the established antiviral drug discovery pipeline bear major implications in responding to the current mpox global health emergency, and sustaining epidemic poxvirus preparedness.

overall_design: RNA-seq profiling of healthy control of human intestinal organoids, Monkeypox virus infected intestinal organoids harvested at 1, 24, 48 and 96 hours respectively, and intestinal organoids infected with Monkeypox virus treated with 1uM clofarabine for 96 hours.


title: Chromatin Remodelers in Cardiometabolic Heart Failure with Preserved Ejection Fraction

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Cardiometabolic heart failure with preserved ejection fraction (cHFpEF) is highly prevalent and associated with a poor outcome. Pathological gene expressions in heart failure are accompanied by changes in active histone marks without major alterations in DNA methylation.  Whether chromatin modifications participate to obesity-induced HFpEF is largely unknown. We will investigate whether chromatin marks participate to obesity-induced HFpEF in vivo.

overall_design: RNA-seq in cardiomyocytes obtained from Control and HFpEF with and without SET7 knockout hearts were analyzed

first: Sarah

last: Costantino

first: Shafeeq

middle: A

last: Mohammed

first: Marialucia

last: Telesca

first: Francesco

last: Paneni


title: T cell dynamics in the mammary gland during lactogenesis

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: The mammary gland undergoes profound structural and cellular changes during pregnancy and lactation, yet the changes in immunocyte populations are incompletely understood. We identified increases in CD4+ and CD8+ T effector cells in late pregnancy and lactation that are partly dependent on microbial signals. Some of the mammary T effector cells share TCR clonotypes with intestinal T cells suggesting a possible route of migration.

overall_design: RNA seq profiling of sorted immunocytes and epithelial cells from mammary glands of lactating and nulliparus germ free mice. Single cell RNA seq of mammary gland, small intestine, colon, thymus and spleen in lactating and virign mice.

first: Abigail

last: Jaquish

first: Deepshika

last: Ramanan


title: Distinct proliferative and neuronal programmes of ASCL1 chromatin binding and gene activation are cell cycle stage dependent [ATAC]

first: William

last: Beckman

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Cambridge Stem Cell Institute

summary: ASCL1 is a potent proneural factor with opposing functions during development, promoting both neuronal progenitor pool expansion and terminal differentiation. How one factor can execute, and switch between, such contradictory functions remain to be elucidated. Using neuroblastoma cells as a model system, we show that ASCL1 exhibits cell cycle phase dependent binding patterns, where G1 phase enriched binding is associated with the priming of pro-neuronal enhancer loci, while SG2M phase enriched binding occurs at promoters of transcribed pro-mitotic genes. Prolonged G1 arrest activates ASCL1-bound and primed neuronal enhancers to drive terminal cell differentiation of these neuroblastic progenitor cells. These findings further our understanding of a key developmental factor, with implications for reprogramming and pathologies such as neuroblastoma.

overall_design: We performed ATAC-seq on FACS sorted G1 phase or G2M phase SK-N-BE(2)-C cells. We also performed ATAC-seq on parental SK-N-BE(2)-C cells and ASCL1 knockout cells.


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

city: 银川市

first: 天松

last: 王

state: 宁夏回族自治区

address: 兴庆区大新镇胜利街1160号

institute: 宁夏医科大学

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

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

first: Jing

last: Wang

first: Qiaofeng

last: Wan


title: Application of Transcriptomics Dose-Response Modeling to Risk-Based Prioritization of Contaminants Detected in Tributaries of the North American Great Lakes

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

summary: As part of the Great Lakes Restoration Initiative, a series of chemical monitoring and surveillance efforts have detected approximately 550 chemicals in Great Lakes tributaries. Among these, there were 140 chemicals for which no empirical toxicity data were available to support prioritization. The aim of the present study was to generate transcriptomic points of departure (tPODs) for 10 of these compounds and demonstrate how they could be applied in a screening-level prioritization. Organisms representing three different trophic levels of the aquatic food-web (Pimephales promelas – secondary consumer, Daphnia magna-primary consumer, and R. subcapitata-primary producer). were exposed for 24 h to a ½-log dilution series of nominal exposure concentrations typically ranging from 66.7 to 0.021 µM of each chemical. In addition to observations of apical effects such as survival and morphology, whole body transcriptomic responses to each chemical were evaluated with targeted analysis using TempO-seq for P. promelas and D. magna and non-targeted full RNA-seq for R. subcapitata. Benchmark concentrations (BMCs) were calculated for each gene showing a concentration-dependent expression pattern. The tPOD for each chemical-species combination was defined as the 10th percentile of the BMCs. The tPODs ranged from 0.18 to 10.8 µM for P. promelas and 0.32 to 29 µM for D. magna, with the most potent of the chemicals tested being fipronil carboxamide. For R. subcapitata, the tPODs ranged from 0.04 to 1.77 µM, with gabapentin as the most potent chemical tested. Empirically derived tPODs from these data poor chemicals, as well as tPODs from previously tested data rich chemicals, were compared with concentrations detected in the Great Lakes basin. This work demonstrates the potential utility of emerging ecological high-throughput transcriptomics assays to support timely screening and prioritization of data poor environmental contaminants.

overall_design: RNA-seq was performed using mRNA extracted from Raphidocelis subcapitata that were exposed for 24 h to a ½-log dilution series of nominal exposure concentrations (typically ranging from 66.7 to 0.021 µM) of the following 12 chemicals: 1(2H)-Phthalazinone, cis-nonachlordane, Metolachlor OA, 3,4-Dichlorophenyl isocyanate, Gabapentin, Metribuzin-DA, 2-tert-butyl-4-methoxyphenol, Hydrochlorothiazide, 4-chlorophenyl methyl sulfone, Cetirizine Hydrochloride, Fipronil carboxamide, Fexofenadine.

first: Jenna

middle: E

last: Cavallin

first: Kendra

last: Bush

first: Steven

middle: R

last: Corsi

first: Laura

last: DeCicco

first: Kevin

last: Flynn

first: Monique

last: Hazemi

first: Erin

last: Maloney

middle: G

first: Alex

last: Kasparek

first: Daniel

middle: L

last: Villeneuve


title: Brd4 expression in microglia supports microglial activation, T cell recruitment, and demyelination in EAE

city: Bethesda

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD

summary: In EAE, a mouse model of multiple sclerosis, immunization with MOG autoantigen results in the generation of Th1/Th17 T cells in the periphery. MOG antigen-specific T cells then invade into the central nervous system (CNS) resulting in neuronal demyelination. Microglia, specialized innate immune cells in the CNS, have been suggested to participate in the pathogenesis of EAE.  Bromodomain inhibitors have been reported to reduce EAE pathology by inhibiting T cells. However, the contribution of BRD4 in EAE pathology is unknown. In this study, we demonstrate that microglia-specific Brd4 conditional knockout (cKO) mice, displayed markedly reduced EAE pathology.  Brd4cKO microglia failed to express inflammation and activation-related genes and had reduced CNS T cell invasion. Moreover, Brd4cKO microglia: invading T cell interactions were markedly reduced, suggesting that Brd4-dependent microglial genes may play important roles in facilitating T cell restimulation within the CNS. In summary, our results demonstrate a model in which microglial BRD4 plays a key role in supporting neuroinflammation in EAE.

overall_design:
To investigate the role of BRD4 in EAE pathogenesis, we generared Tamoxifen inducible Brd4 KO mice to delete Brd4 in microglia. To induce EAE mice were immunized with MOG. CNS mononuclear cells were isolated from both immunized and naïve mice. Microglia were purified using FACS/Aria.
We performed gene expression profiling from RNA-seq data obtained from four WT and four KO samples each from EAE and naïve mice.

first: Dey

last: Anup

first: Butcher

last: Mathew

first: Ozato

last: Keiko


title: Full transcriptome and proteome analysis of the mechanism of tuberculosis Ag85B-Fc2a in alleviating allergic asthma in mice

first: 天松

last: 王

address: 兴庆区大新镇胜利街1160号

summary: In the early stage, an OVA-induced mouse allergic asthma model was constructed and treated with Ag85B-Fc2a fusion protein, which proved that Ag85B-Fc2a fusion protein could reduce the infiltration of inflammatory cells in the lungs and had a therapeutic effect on asthma。In order to further explore the mechanism of action, we carried out transcriptomics and proteomic sequencing, screened out related genes and proteins, enriched them, and focused on pathways with significant differences. In the later stage, q-PCR and Western-blot experiments will be performed for verification.

overall_design: There were three groups in this experiment, namely the normal group, the model group, and the treatment group (Ag85B-Fc2a).In order to make the study statistically significant, three samples in each group were labeled with N, M and A in the transcriptome.

first: Tiansong


title: Neurodevelopmental origins of structural and psychomotor defects in CXCR4-linked primary immunodeficiency

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Primary immunodeficiency diseases (PIDDs) encompass a range of congenital disorders that adversely influence both innate and adaptive immune systems. While individuals diagnosed with PIDDs often exhibit elevated levels of emotional distress and neuropsychological challenges - such as depression and anxiety - the neurobiological underpinnings linking genetic alterations in PIDDs to their neurological manifestations have not been so far explored. Here, by mapping the expression of PIDD genes in transcriptional datasets sampling the human brain across multiple areas and ages, we identified a notable regional enrichment in the cerebellum, which encompasses neuronal and glial subtypes, extending beyond the immune cells. Aiming at elucidating the impact of PIDD genetic alterations on brain development, we focus on WHIM syndrome, caused by CXCR4 mutations. Consistently with clinical reports on WHIM patients, magnetic resonance imaging and histological analysis performed on WHIM mouse model showed distinct cerebellar foliation deficits associated with mild motor impairment and anxiety-like behavior from early development. Despite the restricted expression of CXCR4 in rhombic lip-derived progenitors, single-cell profiling uncovered a pervasive transcriptional alteration across various cerebellar cell types, well beyond the cell-autonomous effects of the mutation on the granule lineage. Significant downregulation of genes involved in dendrite branching and axonal elongation molecularly defined the reduced arborization observed in WHIM Purkinje cells, which is associated with altered lobule-specific frequency patterns by high-density multielectrode array recordings. In utero intraventricular administration of CXCR4 antagonist AMD3100 - currently in clinical trials in patients - successfully rescued both morphological and behavioral defects. This unravels a direct effect of the WHIM-associated Cxcr4-Cxcl12 axis on compromised cerebellar assembly of motor and anxiety-associated circuits. Our findings underscore the contribution of the cerebellum to emotional distress while emphasizing the importance of considering neurological implications in the management of PIDDs.

overall_design: Microdissected cerebellar lobules III and IV for Cxcr4+/1013 mice and control littermates at P1 were dissociated to single cell suspension to perform scRNAseq.

first: Matteo

last: Miotto

first: Giulia

last: Demenego

first: Sara

last: Mancinelli


title: Anti-CD137 drives early epigenetic remodeling of Tex cell associated genes

city: Toulouse

first: Ludovic

last: Martinet

state: Toulouse

address: 2 av Hubert Curien

country: France

institute: INSERM UMR 1037

summary: To understand the mechanism of CD137 induced exhaustion program, we analyzed the splenic CD44hi CD8+ T cell chromatin states along anti-CD137 treatment through assay for transposase-accessible chromatin using sequencing (ATAC-seq)

overall_design: 12 samples; ATAC-Seq


title: Regulation of epigenetics and chromosome structure by human ORC2

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

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

overall_design: Refer to individual Series


title: Eradicating neuroblastomas by an RBM39 degrader in combination with anti-GD2 immunotherapy regardless of cancer cell state alterations

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital


title: Effects of rictor gene deletion on pten-deleted GC B cells

city: Chuncheon

first: Seongwon

last: Pak

address: 12-1, Bonguisan-gil 22beon-gil, Chuncheon-si, Gangwon-do, Republic of Korea

department: Biomedical science

country: South Korea

institute: Hallym university

summary: PI3K/AKT/mTOR/PTEN signaling pathway is well known to regulate metabolism, cell growth and cell survival in all kinds of cells. PI3K phosphorylates PIP2(phosphoinositol-2 phosphate) into PIP3(phosphoinositol-3 phosphate) which acts as docking site for signaling components and activates Akt and mTOR signaling, whereas, Pten is a phosphatase which removes the phosphate from PIP3 and deactivates the singnaling. mTOR signaling encompasses two components namely mTORC1 and mTORC2 complexes and activity of these complexes orchestrated the various biological functions. Several studies have shown that loss of Pten in B cells disrupt the antibody class switching reaction and mTORC1 and mTORC2 has distinct role on the class switching reaction. However, the precise role of mTORC1 and mTORC2 conplexes in the Pten deficient condition is not yet studied. Notably, class switching reaction disrupted by loss of Pten, and that was restored only upon mTORC2 inactivation but not by mTORC1 inactivation in both of in vitro induced-germinal center B cells and plasmablasts culture condition.

overall_design: In order to identify the mechanistic involved in the PI3K/PTEN/mTOR dependent antibody response, we performed the RNA seqeuncing using the in vitro generated germinal center B cells. We isolated Naive B cells(CD43 negative population) from mouse spleen using CD43 (Ly-48) microbeads. Naive B cells from tamoxifen administered Rosa26CreERT2, Rosa26CreERT2:Ptenfl/fl, and Rosa26CreERT2:Ptenfl/fl,Rictorfl/fl mice perfomed in vitro induced-germinal center B cells culture. To obtain the in vitro induced-germinal center B cells, we used CD40LB co-culture system. CD40LB cells that co-express mouse CD40L and BAFF were cultured in 60 mm dish to confluency and treated with 7 μM of mitomycin C for 3 h and washed several times to completely removed the traces of mitomycin C. 2 x 105 purified Naive B cells were co-cultivated with mitomycin C-treated CD40LB cells in with 2 nM IL-4 for 4 day to obtain in vitro induced-germinal center B cells. 4 day cultured sample were colleted and harvested for RNA-seq.

first: Bikash

last: Thapa

first: Yejin

last: Lee

first: Keunwook


title: Eradicating neuroblastomas by an RBM39 degrader in combination with anti-GD2 immunotherapy regardless of cancer cell state alterations [CUT&Tag]

summary: The lineage plasticity of neuroblastoma cells is defined by a mixture of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which presumably contributes to therapy resistance. However, how the neuroblastoma cells switch their cell states during therapy remains largely unknown and how to eradicate neuroblastoma cells regardless of their cell state alterations is a clinical challenge. By using four distinct human and murine neuroblastoma models treated with indisulam, a molecular glue drug serving as a selective RBM39 degrader, we show that cancer cells not only can undergo bidirectional switch of ADRN and MES cell states, but also can acquire additional cell states of melanoma and Schwann cell progenitors, reminiscent of the cellular pliancy of neural crest cells. The lineage alterations of neuroblastoma cells are coupled with epigenetic changes and dependency switch of lineage-specific transcription factors. Nevertheless, indisulam treatment induces an inflamed tumor microenvironment leading to an immune cell infiltration. The combination of indisulam with anti-GD2 monoclonal immunotherapy results in a durable complete response in transgenic neuroblastoma models driven by MYCN and ALK mutant oncogenes, providing a therapeutic rationale to eradicate tumor cells even when they acquire alternative cell lineage(s) in response to treatment.

overall_design: Examination of chromatin changes with various indusilam treated tumor by CUT&TAG

first: Jie

last: Fang

first: Singh

last: Shivendra

first: Jun

last: Yang


title: Methylation Profiling for Pediatric Pineal Parenchymal Tumors

city: Cairo

first: Shahenda

last: El-Naggar

address: 1 Sekket El Emam, El Madbah El Kadeem Yard, Sayeda Zeinab

department: Research Department

country: Egypt

institute: Children’s Cancer Hospital Egypt 57357

type: Methylation profiling by genome tiling array

summary: Pineal parenchymal body tumors are rare central nervous system tumors with a variety of presentations ranging from well-differentiated low-grade tumors to undifferentiated highly aggressive tumors. Recent molecular classification has described the heterogeneity among these tumors, particularly among pineoblastomas (PB) and papillary tumors of intermediate differentiation (PPTID). Herein, we describe the methylation profile for 20 pediatric pineal parenchymal tumors using Illumina Infinium Methylation EPIC BeadChip array and correlate it with the patients’ clinical data. Our findings support that these tumors are diverse, incorporating novel entities with distinct clinical features and the presence of medulloblastomas outside the posterior fossa.

overall_design: Our Study included 20 formalin-fixed-paraffin embedded (FFPE) tumor samples. DNA was isolated with QIAamp DNA FFPE tissue kit (Qiagen) and quantified using the DENOVIX Fluorometer (ds DNA High Sensitivity). DNA quality was determined using the Illumina FFPE QC kit (Illumina Inc.). Bisulfite conversion of the extracted DNA was performed using an EZ DNA methylation kit (D5002, Zymo Research). The bisulfite-converted DNA was restored using the Infinium HD FFPE DNA Restore Kit (WG-321-1002, Illumina Inc.). Restored bisulfite-converted DNA was hybridized to the Illumina Infinium Human Methylation EPIC 850K bead chips and scanned using the Illumina iScan microarray scanner according to the manufacturer's recommendations (Illumina Inc.).

first: Hend

last: Khaled

first: Amal

last: Mosaab

first: Hala

last: Taha

last: Refaat

first: Nada

last: Ashraf

first: Mohamed

middle: S

last: Zaghloul

last: El-Beltagy

first: Manal

last: Zamzam

first: Mark

middle: W

last: Kieran

first: Ahmed

last: El-Hemaly

first: Alaa

last: El-Haddad


title: Single-cell RNA-seq reveals that lack of cell-to-cell communication impairs p53 activation

city: New Haven

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: To dissect the DNA damage response at a single-cell time series, we stimulated HCT-116 cells with the DNA damaging agent doxorubicin (dox) for 0, 4, 8 and 24 hours and performed single-cell RNA-seq using the Fluidigm C1 microfluidics platform. Additionally, to evaluate whether the DNA damage response induced by dox was influenced by cell-to-cell communication, we applied a modified C1 workflow developed by Shalek and colleagues (Shalek, et al. 2014). According to this protocol, cells were captured in the C1 chip, treated with media containing dox or vehicle, and then immediately sealed in individual chambers to prevent intercellular communication for 4 hours (on-chip stimulation, OCS). Following incubation, samples were processed for scRNA-seq as for the previous timecourse experiment.

overall_design: HCT-116 cells were treated with doxorubicin (dox) for 0, 4, 8 and 24 hours and performed single-cell RNA-seq using the Fluidigm C1 microfluidics platform. To model response in absence of paracrine signaling, HCT-116 were also treated with doxorubicin via on-chip stimulation (OCS) and single-cell RNA-seq using the Fluidigm C1 microfluidics performed at the 4h timepoint.

first: Siliva

last: Ottaviani

first: Leandro

last: Castellano


title: Targeting inflammatory macrophages with hyaluronan tetrasaccharide: effects on fibroblast collagen degradation and synthesis [2]

city: Kizugawa

first: Eiko

last: Uno

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical Co., Ltd.

summary: Hyaluronan (HA) provides moisturizing benefits and exhibits unique biological activities based on its molecular weight. While the anti-inflammatory effects of high-molecular-weight HA have been well studied, the impact of hyaluronan tetrasaccharide (HA4), an ultralow-molecular-weight HA, on the skin immune system is not fully understood. Thus, we investigated how HA4 affects the differentiation of M1 macrophages, which increase during photoaging. As a result, we added HA4 during the M1 macrophage differentiation phase and conducted a gene expression analysis. HA4 partially decreased the transition from M0 to M1 macrophages and reduced the expression of proinflammatory cytokines like IL-6. However, the M2 marker IL-1ra increased, while IL-10 levels remained constant, suggesting that HA4 does not fully polarize macrophages toward the M2 phenotype. Normal human dermal fibroblasts (NHDF) were treated with an M1 macrophage-conditioned medium (M1-CM) and a modified version containing HA4 (M1+HA4-CM). The M1+HA4-CM notably decreased the expression of IL-6 and IL-8, along with the collagen-degrading enzyme MMP1. Collagen synthesis assays showed that HA4 helped restore collagen fiber formation. Moreover, RNA-seq analysis of NHDF treated with the conditioned medium confirmed that M1+HA4-CM amplified the expression of genes related to collagen production while decreasing collagen-degrading enzyme gene expression. Neutralization assays employing a TLR4 antibody suggested that decreasing IL-6 in NHDF by HA4 may be independent of the TLR4 signaling pathway. HA4 is vital in partially suppressing M1 macrophage differentiation and the release of inflammatory factors, as well as regulating collagen remodeling in NHDF. These findings indicate that HA4 holds promise as a molecule for mitigating inflammation-induced collagen degradation by modulating macrophage activity in photoaged skin.

overall_design: RNA-seq profiling was performed using three experimental groups of normal human dermal fibroblasts (NHDF): (1) untreated control (no supernatant added), (2) cells treated with supernatant from M1 macrophages (M1), and (3) cells treated with supernatant from M1 macrophages differentiated in the presence of HA4 (M1+HA4).

last: Muto

first: Florence

last: Kim

first: Mihoko

last: Yoshino

first: Yasunari

last: Sato

first: Masao

last: Hashimoto

first: Kenji

last: Watanabe

first: Yoichi

last: Mizukami


title: CELL DIVISION CYCLE 5 regulates floral transition by transcription and splicing regulation of FLC, SEF and MAFs in Arabidopsis

city: Tai’ an

first: Xin

last: Xin

address: 61 Daizong Street

institute: Shandong Agricultural University

summary: Our results establish CDC5 as a bifunctional regulator of flowering, acting both as a splicing factor and a transcriptional activator. This provides valuable insight for future research into plant flowering.

overall_design: Differentially expressed genes between Col-0 and cdc5

first: Shuxin

last: Zhang


title: Sirtuin 4 accelerates heart failure development by enhancing reactive oxygen species-mediated profibrotic transcriptional signaling

first: Sayan

last: Bakshi

department: Department of Pathology

institute: University of Alabama at Birmingham

summary: Sirtuin 4 (SIRT4) is a mitochondrially-localized stress-responsive NAD+-dependent deacylase predominantly regulating energy metabolism and ROS homeostasis. While SIRT4 has been implicated in pathological cardiac hypertrophy, underlying mechanisms remain incompletely understood. Here, we show that myocardial expression of SIRT4 was decreased in individuals with severe dilated cardiomyopathy (-73%) but was relatively higher in subjects with concomitant type 2 diabetes (T2D; +56%). To evaluate consequences and mechanisms of altered myocardial SIRT4 expression, mice with global Sirt4 deletion (Sirt4-/-) or cardiomyocyte-specific Sirt4 overexpression (cSirt4-Tg) underwent transverse aortic constriction (TAC) or sham procedures. Cardiac structure and function were similar in Sirt4-/- and WT mice 12 weeks following TAC, whereas cSirt4-Tg mice displayed aggravated cardiac dilation, dysfunction, and fibrosis following TAC. Transcriptional analysis using RNA sequencing revealed synergistic upregulation of collagens and profibrotic regulators in TAC-treated cSirt4-Tg mice, including transforming growth factor beta (TGF), connective tissue growth factor (CTGF), or follistatin-like 1 (Fstl1). These alterations were reversed by mitochondria-targeted antioxidant treatment using MitoQ, along with attenuation of cardiac dysfunction and remodeling, and reversal of tissue fibrosis. SIRT4 overexpression may drive oxidative stress and fibrotic signaling via synergistically increased NOX4 expression (> 7-fold), and/or direct modulation of SIRT4 targets newly identified by protoarray experiments, including calcitonin gene-related peptide (CGRP) receptor component protein (RCP), cyclophilin A, and interleukin-2 receptor β. Thus, SIRT4 overexpression aggravates cardiac remodeling and dysfunction in response to chronic pressure overload by ROS-mediated enhancement of profibrotic transcriptional signaling, suggesting that relatively higher SIRT4 expression may aggravate heart failure development in individuals with concomitant T2D.

overall_design:
To identify candidate pathways by which mitochondrial ROS may aggravate cardiomyopathy in cSirt4-Tg mice, we performed transcriptomic profiling using RNA sequencing in 6 groups of mice (n=6 in each group)
Comparative gene expression profiling analysis of RNA-seq data in Control and cSirt4-Tg mice after Sham or TAC surgery (Con-Sham, Con-TAC, cSirt4-Tg-Sham, cSirt4-Tg-TAC) and MitoQ supplementation in TAC mice (Con-TAC-MQ and cSirt4-Tg-TAC-MQ).

first: Heiko

last: Bugger


title: Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [RNA-seq]

city: Chicago

first: Boyang

last: Gao

address: 929 E 57th Street

institute: University of Chicago

summary: 5-azacytidine (5-azaC) is a DNA hypomethylating agent clinically used to improve outcomes in myeloid malignancies. However, 5-azaC treatment causes gene dysregulation inconsistent with DNA hypomethylation changes. Some patients benefited from 5-azaC treatment did not display notable DNA demethylation. These observations suggest alternative mechanisms of action by 5-azaC. As a ribonuleoside analogue, 5-azaC is more readily incorporated into nascent RNA. Here, we demonstrate that RNA 5-methycytosine (m5C) depletion by 5-azaC treatment, particularly at early time points, is sufficient to induce leukemia cell death. In contrast to its DNA demethylation function, the RNA-dependent process by 5-azaC causes transcriptional repression, disrupting genes involved in cell cycle regulation and DNA repair. Mechanistically, 5-azaC impairs two specific m5C-mediated transcriptional regulatory pathways. First, depletion of m5C in chromatin-associated RNA (caRNA) disrupts the MBD6-mediated H2AK119ub removal. In parallel, this also impairs SRSF2 recruitment and the downstream H3K27ac deposition by p300. Indeed, loss of the caRNA methyltransferase NSUN2 caused prolonged cell cycle, defective DNA repair, and shifted hematopoietic lineage commitment toward erythropoiesis, mirroring the effects of 5-azaC treatment. Furthermore, we performed leukemia cell line screen and identifies that TET2 and IKZF1 depletion can sensitize 5-azaC treatment, consistent with the observed RNA-dependent cytotoxicity of 5-azaC in leukemia cells. In summary, our findings highlight the transcription regulation by 5-azaC through depleting caRNA m5C, providing insights into the mechanism of action for 5-azaC, the prediction of its efficacy, and future directions for therapy developments based on 5-azaC.

overall_design: RNA-seq of MOLM13 cells treated with 3 μM 5-azaC for 24 hours; SKM1 cells treated with 3 μM 5-azaC for 24 hours; LK cells treated with 3 μM 5-azaC for 24 hours; MOLM13 teton shNSUN2 cells with Dox-induced KD for 5 days; K562 teton shIKZF1 cells with Dox-induced KD for 5 days, followed by 3 μM 5-azaC treatment for 24 hours. Nascent RNA-seq of MOLM13 cells treated with 3 μM 5-azaC for 0, 4, 8 or 16 hours; SKM1 cells treated with 3 μM 5-azaC for 0, 4, 8 or 16 hours. 5-methylcytosine MeRIP-seq of MOLM13 treated with 3 μM 5-azaC for 16 hours; SKM1 treated with 3 μM 5-azaC for 16 hours.

first: Ying

last: Li

first: Chuan

last: He


title: BCAS2 promotes primitive hematopoiesis by sequestering β-catenin within the nucleus

city: Zhan Jiang

first: Guozhu

last: Ning

state: Guangdong

address: Nr. 57 Renmin Dadao Nan, Xiashan  Zhanjiang, P. R. China

institute: Affiliated Hospital of Guangdong Medical University

summary: Breast carcinoma amplified sequence 2 (BCAS2), a core component of the hPrP19 complex, plays crucial roles in various physiological and pathological processes. However, whether BCAS2 has functions other than being a key RNA-splicing regulator within the nucleus remains unknown. Here, we show that BCAS2 is essential for primitive hematopoiesis in zebrafish and mouse embryos. The activation of Wnt/β-catenin signal, which is required for hematopoietic progenitor differentiation, is significantly decreased upon depletion of bcas2 in zebrafish embryos and mouse embryonic fibroblasts (MEFs). Interestingly, BCAS2 deﬁciency has no obvious impact on the splicing efficiency of β-catenin pre-mRNA, while significantly attenuating β-catenin nuclear accumulation. Moreover, we find that BCAS2 directly binds to β-catenin via its coiled-coil domains, thereby sequestering β-catenin within the nucleus. Thus, our results uncover a previously unknown function of BCAS2 in promoting Wnt signaling by enhancing β-catenin nuclear retention during primitive hematopoiesis.

overall_design: RNA-sequencing profiling for wild type and bcas2 +/△14 embryos at 10 ss.

first: Yu

last: Lin


title: KDM6B is a conserved activator at the top of the male sex determination pathway

city: Durham

first: Blanche

last: Capel

state: North Carolina

address: 307 Research Dr Nanaline Duke Bldg Room 456

department: Cell Biology

institute: Duke University

summary: In mammals, commitment to the testis fate is controlled by the gene Sry on the Y chromosome; however, how Sry is regulated is not well understood. In the red-eared slider turtle, Dmrt1 acts as the primary activator of the testis pathway. Removal of the repressive histone modification H3K27me3 from Dmrt1 by the histone demethylase KDM6B is required for its activation. We hypothesized that a similar de-repression mechanism is utilized in mammals to activate the testis pathway. Using a mouse knock-out model for Kdm6b, we found that loss of Kdm6b leads to a delay in Sry activation and the development of an ovotestis. These results implicate KDM6B as a conserved regulator at the top of the sex determination cascade in both reptiles and mammals.

overall_design: RNA-seq profiling of wildtype and Kdm6b-null XX and XY mouse gonads collected at embryonic day (E)11.5.

first: Shannon

last: Dupont

first: Alexandra

last: Garcia-Moreno

first: Eleanore

last: O'Neil


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

first: Xiang

last: Chen

department: Computational Biology

institute: St.Jude Children's Research Hospital

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

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

first: Shivendra

last: Singh

first: Jie

last: Fang

first: Hongjian

last: Jin

first: Lee

last: Velde

first: Andrew

last: Cortes

first: Jiani

first: Sivaraman

last: Natarajan

first: Jun

last: Yang


title: Distinct proliferative and neuronal programmes of ASCL1 chromatin binding and gene activation are cell cycle stage dependent [RNA]

city: Cambridge

first: William

last: Beckman

institute: University of Cambridge

summary: ASCL1 is a potent proneural factor with opposing functions during development, promoting both neuronal progenitor pool expansion and terminal differentiation. How one factor can execute, and switch between, such contradictory functions remain to be elucidated. Using neuroblastoma cells as a model system, we show that ASCL1 exhibits cell cycle phase dependent binding patterns, where G1 phase enriched binding is associated with the priming of pro-neuronal enhancer loci, while SG2M phase enriched binding occurs at promoters of transcribed pro-mitotic genes. Prolonged G1 arrest activates ASCL1-bound and primed neuronal enhancers to drive terminal cell differentiation of these neuroblastic progenitor cells. These findings further our understanding of a key developmental factor, with implications for reprogramming and pathologies such as neuroblastoma.

overall_design: We investigated the response of SK-N-BE(2)-C neuroblastoma cells to palbociclib treatment with or without ASCL1 knockout.


title: Waterpipe (Hookah) Smoking-induced Disordered Biology of the Human Lung

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Background: Waterpipe (hookah, shisha, narghile), a worldwide, commonly used method to smoke tobacco, is considered “safe” by its users because the smoke is “filtered” by water before inhalation. Based on the knowledge that lung cells take the brunt of inhaled smoke, we hypothesized that even mild waterpipe smoking is associated with disordering of lung biology.
Methods: Young (25±4 yr), mild (3.5±2.5 sessions/wk for 4.1±2.5 years) waterpipe smokers with no history of cigarette smoking (n=21) were assessed in comparison to nonsmokers (33±9 yr, n=19) for routine clinical paramters, lung epithelial lining fluid metabolome, small airway epithelial (SAE) cell differential and transcriptome, alveolar macrophage (AM) transcriptome, plasma endothelial cell microparticles (EMPs), cough and sputum scores, lung function, chest HRCT.
Results: Compared to nonsmokers, waterpipe smokers had increased levels of blood carboxy-hemoglobin, an abnormal epithelial lining fluid metabolome profile, increased proportions of SAE secretory and intermediate cells, reduced proportions of ciliated and basal cells, markedly abnormal SAE and AM transcriptomes, elevated levels of EMPs derived from apoptotic pulmo-nary endothelium, more cough and sputum, and lower diffusion capacity (DLCO).
Conclusions: Young, mild-use waterpipe-only smokers have a variety of abnormalities in multiple lung-related biologic and clinical parameters, suggesting that even limited waterpipe use may be linked to lung disease, i.e., waterpipe smoking may be associated with a significant public health risk.

overall_design: Young and mild waterpipe smokers with no history of cigarette smoking (n=21) were assessed in comparison to nonsmokers (n=19): small airway epithelial (SAE) cell transcriptome and alveolar macrophage (AM) transcriptome. Note: AM samples were not obtained for two waterpipe smokers (i.e., no DGM-12277_am or DGM-12481_am samples).

first: Jacqueline

last: Salit

first: Ruba

last: Deeb

first: Anja

last: Krause

first: Renat

last: Shaykhiev

first: Guoqing

last: Wang

first: Robert

middle: J

last: Kaner

first: Thomas

last: Vincent

first: Francisco

last: Agosto-Perez

first: Vignesh

last: Shanmugam

first: Ahmed

middle: M

last: Almulla

first: Hisham

last: Sattar

first: Mai

last: Mahmoud

first: Jason

last: Mezey

first: Steven

last: Gross

first: Michelle

last: Staudt

first: Matthew

last: Walters

first: Ronald

last: Crystal


title: Eradicating neuroblastomas by an RBM39 degrader in combination with anti-GD2 immunotherapy regardless of cancer cell state alterations [RNA-seq]

first: Hongjian

last: Jin

overall_design: To determine the gene expression profile To determine the gene expression and splicing profile with and without GAC and KGA expression in of neuroblastoma cells, BE2C and SKNAS were transduced with Lenti virus control, GAC and KGA to overexpression GCA and KGA.of neuroblastoma cell with,  line BE2C, SKNAS

first: Shivendra

last: Singh

first: Jie

last: Fang

first: Jun

last: Yang


title: Caspase-1-licensed lung epithelial cell pyroptosis drives infiltrating neutrophil necroptosis to dampen immune defense against pulmonary bacterial infection

city: Hangzhou

first: Qinyu

last: Luo

state: Zhejiang

address: Yuhangtang road #866

institute: zhejiang university

summary: Lower respiratorytractinfections, especially those caused by bacteria, are responsible for a large number of deaths each year and are a leading global health issue. Pulmonary bacterial infection causes a severe host response and cell death, such as pyroptosis and necroptosis. However, its pathogenesis is complicated, and whether these different types of cell death communicate with each other and whether these communications are involved in the process of infection remains unknown. Here, we showed that the global deficiency of caspase-1 can protect against lethal pulmonary E. coli infection by reducing the necroptosis of infiltrated neutrophils, which are key players in immune responses in the lung. Mechanistically, neutrophil necroptosis was not directly triggered in a cell-intrinsic manner by invading bacteria. Activation of caspase-1 led to remarkable pyroptotic death of lung epithelial cells, which facilitated the release of intracellular dsRNA. The dsRNA was subsequently taken up by neutrophils and bound to ZBP1 to trigger neutrophil necroptosis. Moreover, blocking dsRNA or depleting ZBP1 ameliorated the pathophysiological process of pulmonary E. coli infection. Overall, our results demonstrated a paradigm of communication between necroptosis and pyroptosis in different cell types cooperated by  microbes and hosts and suggest that therapeutic targeting of the pyroptosis or necroptosis pathway may prevent pulmonary bacterial infection.

overall_design: To exam the difference gene expression of casp1-/- and WT mice lung alveolar neutrophils during E.coli pneumonia, we collected the BALF neutrophils from disease mice and performed gene expression profiling analysis from RNA-seq date acquired from these neutrophils.

first: Qixing

last: Chen


title: Large Clones of Somatic Mutations in the Airway Epithelium of Nonsmokers and Smokers Without Cancer

first: Yael

last: Strulovici-Barel

summary: The human airway epithelium is constantly exposed to the stress of inhaled xenobiotics with the potential to induce somatic mutations

overall_design: To test the hypothesis that humans without cancer have sizeable clones of mutated airway epithelium, bronchoscopy and airway brushing was used to sample 10th-12th order small airway epithelium (SAE) of 91 individuals, including nonsmokers (n=33) and smokers (n=58). Using whole exome sequencing with an average depth of 250x to assess the presence of mutations in the SAE compared to blood DNA, we found that almost all individuals sampled had large clones of SAE with identical somatic mutations, smokers had a higher % of probably deleterious variants. Although no driver mutations were found, all variant detected have been previously identified in by lung cancers. Illumina HiSeq 2500 RNA-Seq SAE expression  for a subset of the 91 subjects, 17 nonsmokers and 42 smokers, was used to examine the SAE expression  of the genes containing deleterious somatic mutations identified in large clones of cells in the small airway epithelium.

first: Juan

last: Rodriguez-Flores

first: Sarah

last: O’Beirne

first: Jacqueline

last: Salit

first: Robert

last: Downey

last: Kaner


title: Dual-RNA-seq of Acinetobacter baumannii ABC141 inside endothelial cells EA.hy926

status: Public on Jun 04 2025

city: Dublin

first: Carsten

last: Kroeger

address: Moyne Institute of Preventive Medicine

department: Microbiology

country: Ireland

institute: Trinity College Dublin

summary: Acinetobacter baumannii poses a substantial global health threat, causing severe multi-drug-resistant infections in hospitalized patients. Circulating clinical isolates present remarkable diversity, with a proportion capable of establishing a transient intracellular niche suitable for persistence, multiplication, and spread. Yet, it remains unknown which bacterial factors mediate the formation and maintenance of this niche, especially within non-phagocytic cells, nor what host responses are elicited. This work demonstrates that the invasive A. baumannii ABC141 strain does not secrete ammonia in endothelial cells as previously shown for other A. baumannii strains multiplying within macrophages but resides in an acidic vacuole devoid of active lysosomal degradative enzymes. Using a Dual-RNAseq approach, we mapped the host and bacterial gene expression during the replicative stage of the infection. An atypical hypoxia cell response was observed without significant induction of the HIF1 pathway, with no metabolic shift or disturbance of mitochondria. Surprisingly, ABC141 efficiently grew in hypoxic conditions in culture and within host cells. In addition, we found a bacterial signature reflective of an adaptation to a nutrient-deprived environment. Our work also highlights a differential role for ABC141 secretion systems, with the T1SS assisting intracellular multiplication and the T2SS required for host cell invasion, implicating for the first time the T2SS in the intracellular lifecycle of invasive ABC141 in endothelial cells.

sample_organism:
Acinetobacter baumannii
Homo sapiens

platform_organism:
Acinetobacter baumannii
Homo sapiens

overall_design: Dual-RNA-seq was performed in human cells EA.hy926 infected with Acinetobacter baumannii ABC141 expressing GFP (cells were infected for 24h) to measure bacterial and human gene expression. Human cells were sorted by FACS for infected cells (using GFP to gate infected cells, Sinf) or left unsorted (Inf). Uninfected cells (sorted (SNeg) and un-sorted (Neg)) served as controls. In addition, A. baumannii ABC141 transcriptome was sequenced from the inoculum before infection of human cells (ABC141).

first: Charline

last: Debruyne

first: Landon

last: Hodge

first: Karsten

last: Hokamp

first: Anna

last: Ershova

last: Kröger

first: Suzana

last: Salcedo


title: Serial Sampling of the Small Airway Epithelium Over 1 Year in the Same Individuals to Identify “Public” Genes Commonly Dysregulated by Smoking [array]

summary:
Background: The small airway epithelium (SAE, >6th generations), the initiation site of smoking-induced airway disorders, is highly sensitive to the stress of smoking. Due to variations over time in smoking habits, the SAE transcriptome fluctuates not only among smokers, but within each smoker.
Averaging the HG-U133 Plus 2.0 transcriptome sampled 4 times in the same individuals over 1 yr enabled the identification of “public” smoking-dysregulated genes, i.e., genes consistently dysregulated within each smoker and shared by most smokers. Using an independent cohort of smokers assessed before and after quitting smoking, it was possible to assess the effect of smoking cessation on the “public” genes over time and identify a subset of genes that remain persistently abnormally expressed despite 12 months of smoking cessation.

overall_design: These  nonsmoker and smoker samples processed on Affymetrix HG-U133 Plus 2.0 mcroarrays were used as the "replication cohort 1" for the consensus genes that were identified in a study of HG-U133 Plus 2.0 expression from small airway epithelium sampled 4 times in the same individuals over 1 yr to identify genes consistently dysregulated within each smoker and shared by most smokers.

first: Sushila

last: Senoy

first: Juergen

last: Schymeinsky

last: Quast

first: Sudha

last: Visvanathan

first: Jay

last: Fine

first: Matthew

last: Thomas

first: Jason

last: Mezey

first: Ronald

last: Crystal


title: Gene expression profile at single cell level of hiPSC-derived lung airways epithelial cells upon knock-out of EHF in normoxia and in hypoxia

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

summary: Cystic Fibrosis (CF) is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene coding for a chloride- and bicarbonate-ion channel. Deficient or dysfunctional CFTR changes ion composition resulting in abnormal mucus, affecting transport and fluid’s homeostasis in multiple epithelia. Lung disease is responsible for the majority of patients’ morbimortality. Intriguingly, more than half of its phenotype is not due to CFTR mutations, but to the environment and genetic modifiers. Genome-Wide Association Studies (GWAS) have identified Single Nucleotide Polymorphisms (SNPs) that could be genetic modifiers. One of the regions outlined (11q13) is located close by an epithelium-specific gene named ETS Homologous Factor (EHF). Here, we hypothesized EHF may be impacted by these variants and may play a crucial role in the airway epithelium. We used human-induced Pluripotent Stem Cells (hiPSC)- derived Airway Epithelial Cells (AECs) to study the knock-out of EHF in normoxia and in hypoxia.

overall_design: Lung airways epithelial cells were generated from hiPSC following our differentiation protocol. At the end point of differentiation, AECs seeded onto ALIs were harvested and analyzed using scRNAseq. We used isogenic background with one clone wild type and one clone homozygous for EHF knock-out.

first: Laetitia

last: Pinte

first: Eleanor

last: Williams

first: Silvia

last: Becca

first: Christopher

last: Gribben

first: Marta

last: Vila Gonzalez

first: Ludovic

last: Vallier


title: Host response to plasmid replication and maintenance

city: Kgs. Lyngby

first: Christoffer

last: Rode

address: Søltofts Plads, Building 220

country: Denmark

institute: Technical University of Denmark

summary: Plasmids are widely used across molecular biology and are becoming increasingly valuable products, but robust plasmid replication is held back by stability issues in the host. This study investigated how Escherichia coli responds to plasmid stress at the transcriptional level by modulating plasmid copy number, plasmid size, selection marker and carbon source. This GEO contains controls from this study alone.

overall_design: RNA-seq profiling of Escherichia coli hosts containing plasmids of variable copy number, size and selection marker, and grown on either glucose or glycerol media.

first: Philipp

last: Becker

first: Bernhard

middle: O

last: Palsson

first: Emre

last: Özdemir

first: Lei

last: Yang


title: Joint representation and visualization of derailed cell states with Decipher

first: Joy

last: Fan

address: 520 West 120th Street

institute: Columbia University

summary: Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.

overall_design: scRNAseq on bone marrow samples for AML and healthy patients with mutations in TET2 and DNMT3a

first: Nazaret

last: Achille

first: Fan

last: Joy Linyue

first: Lavallée

last: Vincent-Philippe

first: Burdziak

last: Cassandra

first: Cornish

last: Andrew

first: Kiseliovas

last: Vaidotas

first: Bowman

last: Robert

first: Masilionis

last: Ignas

first: Chun

last: Jaeyoung

first: Eisman

last: Shira

first: Wang

last: James

first: Hong

last: Justin

first: Shi

last: Lingting

first: Levine

last: Ross

first: Mazutis

last: Linas

first: Blei

last: David

first: Pe'er

last: Dana

first: Azizi

last: Elham


title: IMMUNE DYSREGULATION FOLLOWING INFECTION BY THE NEW CORONAVIRUS SARS-CoV-2 (COVID-19); A NEW DISEASE ENTITY

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

summary: Severe pneumonia by the novel coronavirus (COVID-19 infection) is mediated through immune dysregulation. It was studied if this dysregulation persists after recovery and if it is linked to the manifestation of post-covid syndrome (PCS). Patients who had been hospitalized for COVID-19 pneumonia 3 to 6 months ago during two different time periods and matched comparators were the derivation cohort (n=46, September-October 2020) and the validation cohort (n=484, April-July 2021) respectively. Peripheral blood mononuclear cells (PBMCs) were isolated for culture and cytokine stimulation. Patients provided answers to two health questionnaires allowing classification into PCS and were also subject to lung function tests (LFT). The primary endpoint was the modulation of the production of interleukin (IL)-1b and IL-6 from monocytes and among secondary, the modulation of adaptive immune response and the development of PCS. Increased production of IL-1b (p<0.001) and IL-6 (p<0.001) was found in both study periods compared to control. There was increase of pro-inflammatory Th1 responses over anti-inflammatory Th2 responses and attenuation of the T17 response. PCS was manifested in 22% of patients, grouped into three groups of symptoms. Fatigue was associated with the predominance of Th2 responses and abnormal LFT with overproduction of IL-1b and IL-6. Immune dysregulation is apparent after three months post COVID-19 pneumonia with main features the hyper-production of IL-1β and IL-6 by circulating monocytes, the increase of the Th1/Th2 ratio and the attenuation of T17 response.

overall_design:
The study included 7 COVID patient samples and 7 healthy controls as well as their respective Input samples.

**The raw data and processed data will be made available on the server of the Hellenic Institute for the Study of Sepsis (https://wshiss.com/) due to patient privacy concerns. Username and Password will be provided upon request from the corresponding author at: egiamarel@med.uoa.gr**

first: Evdoxia

last: Kyriazopoulou


title: B-Box protein 28 and BBX29 Interplay with PSEUDO-RESPONSE REGULATORS to Fine-tune Circadian Clock in Arabidopsis

city: Beijing

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

summary: Interplay between BBX28/29 and PRRs fine-tune circadian clock

overall_design: We analyzed the transcriptomic profile of Col-0, BBX28-OE and BBX29-OE using 10-day-old seedlings. Three biological replicates were performed with the tissues harvesting at ZT0.

first: Yingjun

last: Yu


title: Distinct proliferative and neuronal programmes of ASCL1 chromatin binding and gene activation are cell cycle stage dependent [ChIP]

first: William

last: Beckman

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

overall_design: ASCL1 ChIP-seq for asynchronous (vehicle treated), palbociclib treated and thymidine treated SK-N-BE(2)-C neuroblastoma cells.


title: Gonadal gap junctions activate Notch signaling to suppress intestinal innate immunity via p38/PMK-1 and lysosome pathway II

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

institute: Haijun Tu

summary: We showed that the innexin genes encoding gap junction subunits positively regulated GLP-1/Notch signaling to suppress the innate immunity of C. elegans via PMK-1/p38 pathway.

overall_design: Using vector and inx-14 RNAi  in DCL569 ( germline-specific RNAi ) background in the condition of PA14 infection or OP50 fed, then design some different assays to identify the important tips obtained from RNA-seq data analysis.

first: Haijun

last: Tu

first: Xiumei

last: Zhang

first: Yirong


title: Serial Sampling of the Small Airway Epithelium Over 1 Year in the Same Individuals to Identify “Public” Genes Commonly Dysregulated by Smoking [RNA-Seq]

first: Yael

last: Strulovici-Barel

overall_design: These RNA-Seq nonsmoker and smoker samples were used as the "replication cohort 2" for the consensus genes that were identified in a study of HG-U133 Plus 2.0 expression from small airway epithelium sampled 4 times in the same individuals over 1 yr to identify genes consistently dysregulated within each smoker and shared by most smokers.

first: Jacqueline

last: Salit

first: Sushila

last: Senoy

first: Sarah

last: O’Beirne

first: Robert

last: Kaner

first: Juergen

last: Schymeinsky

first: Karsten

last: Quast

first: Sudha

last: Visvanathan

first: Jay

last: Fine

first: Matthew

last: Thomas

first: Jason

last: Mezey

first: Ronald

last: Crystal


title: Single nucleus RNA-sequencing of brain tissue from adult and juvenile three-spined stickleback

city: La Jolla

first: Benjamin

middle: D

last: Gastfriend

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: The three-spined stickleback (Gasterosteus aculeatus) is an important model organism for understanding the genetic basis of adaptation in response to ecological change. We used single nucleus RNA-sequencing (snRNA-seq) to define brain cell type composition and gene expression in adult and juvenile three-spined stickleback. These data will faciliate improved understanding of how the nervous system responds/adapts to environmental factors.

overall_design: snRNA-seq profiling of brain tissue from adult and juvenile three-spined stickleback

first: Diana

last: Rennison

first: Richard

last: Daneman

first: Martin

last: Tresguerres


title: Oral Epithelium Response of Electronic Cigarette Users to Electronic Cigarette

type: Non-coding RNA profiling by high throughput sequencing

summary: Electronic cigarettes (EC) are increasing in popularity, but there is only little information on their biologic effects on the oral epithelium, the initial site exposed to EC smoke. We assessed the oral epithelium response to EC by comparing the histology and RNA transcriptome (mRNA and miRNA) of healthy EC vapers to nonsmokers (NS). mRNA was assessed based on: (1) genome-wide; (2) genes previously identified as dysregulated in the oral epithelium of EC vapers vs NS; (3) immune and inflammatory-related genes previously identified as dysregulated in the nasal epithelium of EC vapers compared to NS; (4) genes previously identified as dysregulated in the small airway epithelium of NS following an acute exposure to EC; and (5) genes related to the initial steps of COVID-19 infection. In addition, miRNA was assessed genome-wide. Comparisons were performed using ANOVA, and Benajmini-Hochberg corrected p <0.05 was considered significant. The histology of the epithelium, lamina propria and basal layer in EC vapers appeared normal. Assessment of mRNA and miRNA, based on all gene lists, did not identify any genes significantly modified in the oral epithelium of EC vapers. Assessment of the oral epithelium of healthy EC vapers by histology, mRNA and miRNA demonstrated no abnormalities in response to EC smoke.

overall_design: Oral biopsies of n=24 electronic cigarette vapers and n=23 nonsmokers were compared by histology and transcriptome (mRNA and miRNA) to assess the effects of electronic cigarette vaping on the oral epithelium.

first: Gwendolyn

last: Reeve

first: Mahboubeh

last: Rostami

first: Renee

middle: F

last: Reich

first: David

last: Behrman

first: Philip

last: Leopold


title: Epigenetic and Post-transcriptional Regulation of LYPD2 Modulates Smoking-associated Phenotype via CHRNA7 and DNMT1 in the Human Airway Epithelium

first: Yael

last: Strulovici-Barel

summary:
Background: The small airway epithelium (SAE, >6th generations), the initiation site of smoking-induced airway disorders, is highly sensitive to the stress of smoking. Lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR, also called PLAUR) superfamily of proteins function in differentiation and inflammation, common phenotypes altered in smoking-related lung diseases including chronic obstructive pulmonary disease (COPD) and lung cancer. In the human small airway epithelial (SAE) transcriptome, LYPD2 (LY6/PLAUR domain containing 2), a gene with unknown function, is the most down-regulated Ly6/uPAR gene in smokers. Based on the knowledge that SLURP1 (secreted LY6/PLAUR domain containing 1), a paralog of LYPD2, modulates inflammatory phenotypes, we hypothesized that LYPD2 plays a role in the smoking-related phenotypes in the airway epithelium.
RNA sequencing, single cell RNA sequencing and immunohistochemistry demonstrated that LYPD is expressed in airway epithelial cells, predominantly in club and intermediate cells. Quantification of LYPD2 expression in the airway epithelium demonstrated a significant suppression of LYPD2 in smokers, overall in the SAE, and specifically in club, mucous and intermedaite cells.  Cigarette smoking extract (CSE) treatment of differentiating airway basal stem/progenitor cells (BC) in air liquid interface culture (ALI) demonstrated significantly down-regulated LYPD2 expression. LYPD2 expression correlated with the expression of tight junction and differentiation-related marker genes in vivo and LYPD2 down-regulation in airway epithelium in vitro resulted in an increased expression of smoking-related inflammatory genes accompanied by decreased airway transepithelial resistance, suppressed junctional gene expression, and diminished gene expression related to normal differentiation.  We show the function of LYPD2 is likely mediated by CHRNA7 and DNMT1, associated with JNK and NF-κB signaling and can be modulated by miR-214-3p and epigenetic mechanisms.

overall_design:
In this study, we identified LYPD2 as a smoking-down-regulated gene in the airway epithelium and explored its previously undiscovered role in regulating airway epithelial inflammation, barrier integrity and mucociliary differentiation. LYPD2, at least partially, functions through CHRNA7 and NF-κB and JNK pathways, likely regulated by miR-214-3p via a post-transcriptional mechanism and DNMT1 via an epigenetic mechanism. Interestingly, LYPD2 feedback regulates DNMT1 leading to the differential methylation of the LYPD2 target gene and miR-214-3p host gene DNM3OS and gene expression changes of these gene, therefore enhancing the abnormal phenotypes induced by the dysregulation of LYPD2. Consistent with the roles of LYPD2, degree of airway inflammation correlates with diminished capacity of differentiation and higher levels of inflammatory cytokine expression from airway epithelium may form a microenvironment facilitating the lung cancer progression.
Small airway epithelial cells and large airway epithelial cells from smokers and non-smokers.

first: Haijun

last: Zhang

first: Jacqueline

last: Salit

last: Walters

first: Yongjiang

last: Tang


title: Utx (Kdm6a) promotes differentiation non-catalytically in somatic self-renewing epithelia [Xenium]

city: Philadelphia

first: Brian

middle: C.

last: Capell

state: PA

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

institute: University of Pennsylvania

summary: To investigate the role UTX (KDM6A) in stratifying epithelia

overall_design: Kdm6a (Utx) was deleted in the keratin-14 expressing tissues of mice via Krt14-Cre recombination

first: Gina

last: Pacella

first: Nina

last: Kuprasertkul

first: Lydia

last: Bao

first: Sijia

last: Huang

first: Carina

last: D'souza

first: Stephen

last: Prouty

first: Amy

last: Anderson

first: Alexandra

last: Maldonado-Lopez

first: Morgan

last: Sinkfield

first: Cyria

last: Olingou

first: John

middle: T

last: Seykora

middle: C


title: Serial Sampling of the Small Airway Epithelium Over 1 Year in the Same Individuals to Identify “Public” Genes Commonly Dysregulated by Smoking

last: Strulovici-Barel

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

overall_design: Refer to individual Series


title: Effect of IRF3 knockdown on gene expression in an HPV16-containing epithelium

city: SHREVEPORT

first: Jason

last: Bodily

state: LA

address: 1501 Kings Highway

institute: LSU Health - Shreveport

summary: The stromal compartment is critical for regulating the growth and differentiation of the epithelium. The life cycle of HPV is tightly linked to epithelial differentiation, and so we investigated the influence of the interferon-related transcription factor IRF3 (expressed in the stroma) on the gene expression in an HPV-containing epithelium. Organotypic cultures were created using shRNAs to knock down IRF3 in the stromal fibroblasts (or non-target controls). HPV16-containing keratinocytes were seeded on the surface and the epithelium was allowed to develop for 14 days. RNA-seq was performed on RNAs from both the epithelial and stromal compartments. We found that knockdown of IRF3 in the stroma did not affet the interferon system at all; rather, gene expression related to epithelial-mesenchymal transition was decreased, and epithelial differentiation markers were increased. These data suggest that IRF3 in stromal cells promotes EMT.

overall_design: Organotypic cultures were created from HPV16-containing keratinocytes, using human foreskin fibroblasts either containing IRF3 knockdown shRNAs or non-target controls. Total RNAs were harvested from both the keratinocytes and fibroblasts (stroma) 14 days following lifting to the air-liquid interface.

first: Raikhy

last: Gaurav

first: Bodily

last: Jason


title: A viral circular RNA in Kaposi’s sarcoma-associated herpesvirus contributes to viral and host gene expression during latent and lytic replication

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 1200 Newell Dr.

institute: University of Florida

summary: Aim: Circular RNA (circRNA) is a class of noncoding, single-stranded RNA generated by backsplicing, a process where the 5’ and 3’ ends of an RNA are covalently joined. Virally encoded circRNAs have been identified in several members of Gammaherpesvirinae, including Kaposi’s sarcoma-associated herpesvirus (KSHV). In KSHV, the viral interferon regulatory factor 4 (vIRF4) region produces two isoforms of circRNA (circ-vIRF4) that are detectable during latency and reactivation. Since these circRNAs are expressed during latency, a period where viral transcription is tightly restricted and tumorigenesis occurs, circ-vIRF4 may contribute to the development of KSHV malignancies. Therefore, the aim of this study is to characterize the function of vIRF4 circRNAs. Methods: A KSHV mutant (Δcirc-vIRF4) was generated in the BAC16 bacmid and transfected into 293T and iSLK cells. Expression of circRNA after mutagenesis was assessed by qualitative and quantitative PCR. Host and viral gene expression in iSLK cells during both viral latency and reactivation were also assessed by RNA-seq. Results: RT-PCR of Δcirc-vIRF4-infected iSLK cells demonstrated no expression of wild type isoforms, but PCR cloning showed that alternative backsplice sites were used to express novel vIRF4 circRNAs, where the most prominent isoform was a 1,020 nt isoform. RNA-seq analyses comparing WT- and Δcirc-vIRF4-infected iSLK cells demonstrated significant differential expression of both host and viral genes during both phases of the viral life cycle. Gene ontology analyses returned terms related to cell adhesion, proliferation, and migration for both datasets, as well as kinase signaling and apoptosis for the lytic dataset. Conclusions: These results show that KSHV can switch to an alternative backsplice site for vIRF4 circRNA production in the absence of a canonical splice site and that circ-vIRF4 contributes to the regulation of both host and viral gene expression through an unknown mechanism.

overall_design: RNA-seq profiling to assess gene expression differences between wild-type and mutant infected cells during either KSHV latency or reactivation

first: Soleil

last: Torres

first: Vaibhav

last: Jain

first: Daniel

last: Stribling

first: Lauren

last: Gay

first: Muhammed

last: Naeem

first: Melody

last: Baddoo

first: Erik

last: Flemington

first: Scott

last: Tibbetts


title: Expression data from Insulin Degrading Enzyme-Knocked Out hepatome human cells

city: Palencia

first: Sergio

last: Díez-Hermano

state: Palencia

address: C/Felipe II, 10, 2C

country: Spain

institute: University of Valladolid

summary:
Insulin-degrading enzyme (IDE) is a protein with proteolytic and non-proteolytic functions that regulates glucose homeostasis.We hypothesize that IDE deficiency alters glucagon signaling and thereby gluconeogenesis. To test this hypothesis we performed microarray studies in HepG2 cells with a complete deficiency of IDE gene. Results show that IDE deficiency led to upregulation of genes involved in cellular functions related to membranes, organelles and signaling receptors.
We used microarrays to find genes whose expression is affected by the absence of IDE gene expression in hetapome human cells

overall_design: We used control human hepatoma cells (HepG2) and HepG2-IDE-KO cells generated using the CRISPR/Cas9 tool. Microarray analyses were performed on the ClariomTM S Array (Thermofisher). Data were acquired on the GeneChipTM 3000 instrument (Affymetrix) and high-throughput automated processing was performed using the GeneTitan™ Microarray System (Thermofisher).

first: G

last: Perdomo

first: S

last: Diez-Hermano


title: Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM

city: changchun

first: Yan

last: Wang

state: jilin

address: 1163 Xinmin Street

institute: Jilin University

summary: Type 2 diabetes mellitus (T2DM) is characterized by beta-cell dysfunction and insulin resistance, but the early molecular drivers remain elusive. The aim of this study was to identify blood long non-coding RNAs (lncRNAs) as a potential systemic biomarkers in patients with new-onset, unmedicated T2DM. We performed transcriptome sequencing of peripheral blood from eight T2DM patients and eight healthy individuals. The intersection of three differential expression analysis methods (Limma, DESeq2 and EdgeR) identified 1,709 lncRNAs with dysregulated expression in peripheral blood, of which , 853 lncRNAs were up-regulated and 856 lncRNAs were down-regulated. Weighted gene co-expression network analysis (WGCNA) identified two modules comprising a total of 1,617 lncRNAs that were significantly negatively associated with T2DM. By integrating differential expression analysis and WGCNA, we screened a total of 257 lncRNAs that were highly correlated with T2DM and exhibited significant changes in expression levels.Our findings provide valuable transcriptomic data for further studies of T2DM, and the screened blood lncRNAs may reflect systemic dysregulation as early biomarkers.

overall_design: We analyzed the expression profiles of long non-coding RNAs in peripheral blood samples from newly diagnosed, untreated type 2 diabetes patients compared to healthy individuals using high-throughput RNA sequencing.

first: Yangming

last: Qu

first: Mingxin

last: Dong

last: Zhao

first: Suli

last: Song

first: Mingyang

last: Huo

last: Lu

first: Baichuan

last: Chen

first: Chengbiao

last: Sun

first: Kaikai

last: Yu

first: Juan

last: Ren

last: Xu

first: Wensen

last: Liu

last: Yao


title: Inhibiting FOXM1 Promotes Polyploidization and Metabolic Maturation in Human iPSC-Derived Hepatocytes by Modulating the Wnt/β-Catenin Pathway [ATAC-seq]

city: Sao Paulo

first: Kayque

last: Alves Telles Silva

address: 106 Matao St.

country: Brazil

institute: University of Sao Paulo

summary: Differentiating induced pluripotent stem cells (iPSCs) into hepatocytes represents a key advancement in regenerative medicine and disease modeling. However, existing protocols mainly produce fetal cells, limiting accurate replication of liver functionality. Topoisomerase II (TOP2) and its transcription factor, forkhead box M1 (FOXM1), are silenced during late liver embryonic development; however, their roles in hepatocyte differentiation remain unexplored. We examined the effects of TOP2 and FOXM1 inhibition on hepatocyte differentiation. Subtoxic TOP2 inhibition reduces nuclear chromatin condensation without causing DNA damage. RNA-seq analysis showed that TOP2 inhibition induced cell cycle arrest in a TOP2A-selective manner with FOXM1 downregulation. ATAC-seq validation demonstrated that TOP2A inhibition decreases chromatin accessibility and modulates the Wnt/β-catenin pathway. Proteomic analysis revealed that FOXM1 inhibition modulated TOP2A expression, replicated TOP2A-mediated cell cycle arrest, and reduced the levels of fetal hepatocyte proteins (HBG1/2, UGT2B7, and AFP). Prolonged FOXM1 inhibition leads to hepatocyte polyploidization, increased CYP450 activity, and improved lipid metabolism. We demonstrated that FOXM1 inhibition is necessary for terminal differentiation of human iPSC-derived hepatocytes. This study suggests a role for FOXM1 and TOP2A in liver development, regeneration, and disease.

overall_design: ATAC-seq profiling of iPSC-derived hepatocytes (control and etoposide-treated) and primary human hepatocytes at day 5 of etoposide treatment.

first: Telles-Silva

last: Kayque Alves


title: The regulatory variant rs1950834 confers the risk of depressive disorder by reducing LRFN5 expression

city: Nanjing

last: Kong

address: 87 Dingjiaqiao Road

institute: Southeast University

summary: Background: Genome-wide association studies have identified 14q21.1 as a robust risk locus for major depressive disorder (MDD). However, the underlying mechanism remains elusive. Here we aim to explore the regulatory function of the rs1950834 on LRFN5 expression in MDD. Methods: CRISPR-Cas9-mediated genome knockout and single-base editing were used to determine the effects of rs1950834 on the binding of transcriptional factors and the expression of the target gene LRFN5. Meta-analysis of multiple transcriptomic datasets was performed to clarify the brain region responsible for LRFN5 downregulation in MDD patients. Adeno-associated virus (AAV)-mediated LRFN5 overexpression or knockdown in the nucleus accumbens (NAc) was used to test their effects on depression-like behaviors and sensitivity to chronic unpredictable mild stress (CUMS). Synaptic structure and functions were monitored by synaptic protein expression assay, Golgi staining, and electrophysiological analysis.  Results: The risk allele (A) of rs1950834 reduced the binding affinity to RNA polymerase II subunit A (POLR2A) and the transcription factor double-strand-break repair protein rad21 homolog (RAD21), leading to decreased expression of LRFN5. LRFN5 expression was downregulated specifically in the NAc of MDD patients as compared to healthy controls. Knockdown of LRFN5 in NAc neurons induced depression-like behaviors and further exacerbated CUMS-induced phenotypes via synaptic damage, but overexpression of LRFN5 in mouse NAc induced resilience to CUMS. Conclusion: These findings reveal that the functional risk single nucleotide polymorphism rs1950834 at 14q21.1 regulates LRNN5 expression and function in NAc, providing a novel perspective for molecular diagnosis and targeted interventions of MDD. Keywords: Major depressive disorder; rs1950834; RAD21; POLR2A; LR

overall_design: Then, utilizing the SK-N-AS cells of rs1950834-AA and rs1950834-GG genotypes, we performed RNA-seq for transcriptomic analysis to further elucidate the pathways regulated by rs1950834.

first: Di

last: Luan

first: Yifan

last: Li

first: Aini

last: Zhang

first: Qingqing

last: Bai

first: Xiongjian

last: Luo

first: Zhijun


title: miR-181a-5p mediates the effects of BMP4 on intestinal cell proliferation and differentiation

city: Lexington

first: Qingding

last: Wang

address: 760 Press Ave

institute: University of Kentucky

summary: The intestinal mucosa undergoes a dynamic process of continual proliferation, differentiation and apoptosis. Delineating the mechanisms involved in intestinal epithelial cell (IEC) differentiation is crucial to our understanding of not only normal gut adaptation but also aberrant intestinal growth. BMP signaling is a crucial regulator of intestinal proliferation and differentiation. However, the molecular underpinnings of the BMP pathway in this context are not entirely known. Here we showed that treatment with BMP4 increased expression of enterocyte markers and decreased proliferation of IECs, and importantly, decreased the expression of miR-181a-5p in mouse and human intestinal organoids. Inhibition of miR-181a-5p, a member of miR-181 with highest expression in intestinal cells, significantly increased enterocyte differentiation as noted by increased expression of enterocyte markers in human and mouse intestinal organoids. In addition, miR-181a-5p miRCURY LNA inhibitor repressed the expression of endogenous miR-181a-5p and decreased intestinal stem cell self-renewal as noted by the decreased expression of Ki67, cyclin D1 and OLFM4 and organoid forming efficiency. In contrast, overexpression of miR-181a-5p mimics decreased the expression of enterocyte markers. Together, we provide evidence showing that miR-181a-5p inhibits intestinal enterocyte differentiation and promotes IEC proliferation.

overall_design: To determine downstream molecules in mediating the effects of mir-181a-5p on intestinal cell proliferation and differentiation, mouse small intestinal organoids were infected with lentivirus expressing miR-181a-5p mimic (MLMIR0085, Sigma) or miRNA mimic control (NCLMIR002, Sigma). The infected organoids were cultured in the presence of puromycin (2 ug/ml) to select for organoids with stable overexpression of miR-181a-5p.

first: Abu Saleh Mosa

last: Faisal

first: Jinpeng


title: The SIRT6-TDO2/KYNA-mTOR Axis Mediates Synaptic Plasticity and Cognitive Impairments in Fetal Growth Restriction Offspring

city: Shanghai

first: Shujuan

last: Chang

address: siping road 1239

institute: tongji university

summary: Fetal growth restriction (FGR) can lead to cognitive impairment in offspring, but the underlying mechanisms remain unclear. This study found that hippocampal excitatory neurons in FGR mice exhibit significantly reduced SIRT6 expression. SIRT6 deficiency upregulates TDO2 via its histone deacetylase activity (independent of ADP-ribosyltransferase function), promoting kynurenic acid (KYNA) accumulation, which suppresses the AKT/mTOR/p70S6K pathway and disrupts synaptic protein synthesis.

overall_design: RNA-seg profiling of the hippocampus at 8 weeks in WT mice and Sirt6 cKO mice

first: Wen

last: Chen

first: Wei

last: Zhu

first: Nana

first: Yuhang

first: Jianguo

first: Jiuhong

last: Kang


title: Purinergic receptors play a key role in shock wave-induced proliferation

city: Vienna

first: Dorota

last: Szwarc-Hofbauer

state: Vienna

address: Höchstädtplatz 5

department: Life Science Engineering

country: Austria

institute: UAS Technikum Wien

summary: Shock wave treatment (SWT) is a non-invasive therapy applied in musculoskeletal and urological disorders, as well as in chronic wound regeneration. As the use of medical SWT broadens, it is important to better understand the molecular mechanisms underlying its success. Here, we identified P2X4 and P2Y2 purinergic receptors to be primarily expressed in C3H/10T1/2 mouse mesenchymal stromal cells and investigated their role in the initiation of the signaling events following SWT using single- and double-receptor knock-out (KO) cell lines. We show that SWT induced the expression of c-Jun and c-Fos within 30 min after stimulation and that the SWT-induced Erk1/2 pathway activation and immediate early gene expression were decreased in P2Y2-, P2X4- and P2Y2/P2X4-deficient cells. Importantly, SWT did not promote proliferation in P2Y2/P2X4-deficient cells, while loss of either one of the receptors significantly reduced the proliferative effect, indicating a cumulative effect of their loss. Finally, our data suggests a more prominent role of the P2Y2 receptor in SWT-induced cellular effects, since primarily its loss contributed to the observed changes. With these findings, we further the understanding of the molecular mechanisms of SWT and propose that the varying expression of purinergic receptors in tissues should be considered when establishing treatment protocols.

overall_design: Differential gene expression analysis of RNA-seq data from C3H/101/2 mouse mesenchymal cells after in vitro shock wave treatment (300 pulses, 0.18 mJ/mm2, 3 Hz; MTS Dermagold 100 device with an OP155 applicator). Samples were collected 30 minutes or 6 hours after treatment in triplicates, with untreated cells serving as controls.

first: Elisabeth

last: Simböck

first: Carina

last: Hromada

first: Michaela

last: Stoiber

first: Janine

last: Tomasch

first: Georg

last: Weitzer

first: Andreas

last: Teuschl-Woller


title: Inhibiting FOXM1 Promotes Polyploidization and Metabolic Maturation in Human iPSC-Derived Hepatocytes by Modulating the Wnt/β-Catenin Pathway [Hi-C]

first: Kayque

last: Alves Telles Silva

overall_design: Hi-C profiling of iPSC-derived hepatocytes (control and etoposide-treated) and primary human hepatocytes (primed) at day 5 of etoposide treatment.

first: Telles-Silva

last: Kayque Alves

first: Fishman

last: Veniamin

first: Gridina

last: Maria

first: Panchenko

last: Daria


title: Alterations in Bile Acid Physiology in Wilson Disease [ChIP-seq]

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: Background & Aims: Wilson disease (WD) is an autosomal recessive disorder that results in excessive hepatic copper causing hepatic steatosis, inflammation, fibrosis, cirrhosis, and liver failure. Previous studies have revealed dysregulation of many FXR metabolic target genes in animal models of WD, including Bsep, the major determinant of bile flow.  Approach & Results: We tested the hypothesis that the FXR-cistrome is decreased in Atp7b-/- mice in accord with dysregulated bile acid homeostasis. RNA-Seq and ChIP-Seq analyses of Atp7b-/- and wild-type (WT) mouse livers confirmed that significantly altered transcripts and FXR-binding events overlapped. Decreased FXR occupancy in Atp7b-/- versus WT mice was observed genes of metabolic pathways and bile acid homeostasis, while enrichment of FXR binding was observed pathways associated with cellular damage, such as the focal adhesion pathway. Consistent with decreased FXR function, serum and liver bile acid concentrations were higher in Atp7b-/- mice than in WT mice. Comparison of bile acid profiles in the serum of WD patients with “liver,” “neurological,” or “mixed” disease vs. healthy controls also revealed increases in specific bile acids in WD-liver vs. healthy controls.  Conclusions:  Atp7b-/- mice and WD patients exhibited changes in serum bile acid speciation, likely due to FXR dysfunction.  These findings provide new insights into possible aberrant bile acid homeostasis in patients with WD.

overall_design: ChIP Sequencing with liver tissue and FXR Antibody (Santa Cruz)

first: Clavia' R

last: Wooton-Kee

first: Islam

last: Mohamed

first: Manal

last: Hassan

first: Kenneth

last: Setchell

first: Monica

middle: N

last: Rivas

first: Ayse

middle: K

last: Coskun

first: Vasanta

last: Putluri

first: Nagireddy

first: Prasun

last: Jalal

first: Michael

last: Schilsky

first: David

last: Moore


title: Reduction in Cord Blood Graft Potency Due to Processing Delay Can be Prevented by Trehalose Supplementation

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: Background and objectives: Maximizing the potency of cord blood (CB) units (CBU) is a goal of all CB banks. Low transplant cell dose in CB transplantation is one of several contributors to the slower engraftment. Processing delays could also be at play since CBU can be stored at room temperature (RT) up to 48 hours before cryopreservation. We hypothesized that prolonged storage at RT reduces the potency and engraftment activities of CBU due to a loss in hematopoietic stem cell (HSC) and progenitor numbers. Materials and Methods: CBU were split in half, with one half processed shortly after collection and the other half after 40 hours of storage at RT. Viabilities and potencies were compared post-thaw, and engraftment activity tested in xenotransplants. Bioinformatic analysis was carried out to identify pathways modulated by prolonged storage at RT. Results: Prolonged storage at RT reduced the viability of CB cells and potency of grafts based on in vitro and in vivo assays. Transcriptomic analyses revealed that paracrine factors released in CBU induce several changes in gene expression programs in CD34+ cells. These included the activation of the senescence gene CDKN1B and down-regulation of cell cycle and autophagy genes. Supplementation of CBU with trehalose prevented the loss in cell viability and potency. The latter was associated with restoration of autophagy and suppression of the senescence gene CDKN1B. Conclusion: These results stress the importance of rapid processing of CBU and support further investigations on trehalose as a natural supplement to protect CBU potency during storage.

overall_design: To identify the molecular programs driven by paracrine factors present in plasma from stored cord blood unit, cord blood CD34+ enriched cells were incubated with plasma derived from baseline (i.e. fresh plasma) and cord blood halves stored for 40 hours at room temperature (i.e., stored plasma) for 0, 20 minutes and 4 hours (n=2). RNA was extracted and the changes in transcriptome were profiled via RNA sequencing. CD34+ cells not exposed to plasma were used as controls to account for baseline gene expression. RNA was isolated using miRNeasy Micro Kit (Qiagen, Toronto, ON, Canada).  cDNA libraries were constructed using TruSeq stranded mRNA protocol (Illumina, San Diego, CA, USA) and sequencing was performed by StemCore Laboratories (Ottawa, ON, Canada) using the Illumina HiSeq 2000, following their standard operating procedures. Reads were assigned to transcripts from the GENCODE v32 assembly (GRCh38) using Salmon v1.0 (https://combine-lab.github.io/salmon/).

first: Suria

last: Jahan

first: Harinad

middle: B

last: Maganti

first: Jaina

last: Patel

first: Roya

last: Pasha

first: Emily

last: Doxtator

first: Javed

last: Manesia

first: Nicolas

last: Pineault