title: Study on the effects and mechanisms of alcohol combined with high-fat diet in promoting enteritis-induced liver injury

city: Nanjing

first: Mingrui

last: Zhao

state: Jiangsu

address: No. 639, Longmian Avenue, Chunhua Street, Nanjing City, Jiangning District, China Pharmaceutical University

institute: China Pharmaceutical University

summary: Inflammatory hepatic injury associated with inflammatory bowel disease (IBD) is a type of liver disease that occurs in patients with IBD. Up to 30% of IBD patients clinically exhibit abnormal liver function tests. With the increasing incidence of IBD due to economic development and lifestyle changes, the number of patients with IBD complicated by liver injury is on the rise. The mechanism of IBD complicated by liver injury is not yet clear, with unhealthy habits and environmental factors possibly being the main triggers. As a country with a high alcohol consumption rate, statistics show that 30.5% of the population in China drinks alcohol. With lifestyle improvements, people often consume high-calorie foods (such as fats) while drinking, and these combined factors are often key triggers for IBD and liver injury. The simultaneous intake of alcohol and high fat content tends to increase the permeability of the intestinal mucosal barrier, disrupt the gut-liver axis, and exacerbate acute liver damage. It is known that alcohol and high-fat diets are significant potential risk factors for promoting inflammatory liver damage, yet their specific molecular mechanisms remain unknown, and there are currently no effective drugs for treating related inflammatory liver damage clinically. Therefore, clarifying whether alcohol combined with a high-fat diet promotes inflammatory liver damage and exploring its specific mechanisms have important clinical implications for the prevention and treatment of such damage. This study uses DSS-induced colitis mice as subjects to investigate whether alcohol combined with a high-fat diet exacerbates inflammatory liver damage. It also integrates multi-omics data to explore the regulatory mechanisms of alcohol and high-fat diet on inflammatory liver damage, aiming to identify potential intervention targets to provide a theoretical basis for related drug development.

overall_design: Mice were administered 2.5% DSS daily to establish a model of colitis. During the modeling period, the weight and Disease Activity Index (DAI) scores of the mice were recorded daily. On day 6, DSS administration was ceased, and the mice were grouped based on average weight and DAI scores. They were then subjected to interventions with either purified high-fat feed or dietary high-fat feed in conjunction with alcohol. During this intervention period, the weight and adverse condition scores of the mice were monitored daily. Liver damage in the colitis mice was assessed using AST/ALT assay kits, and damage to various organs was examined through H&E staining. Damage markers were detected using ELISA and RT-qPCR. Changes in the number of peripheral immune cells in the mice were monitored through blood flow cytometry and routine blood tests. Levels of IL-6, TNF-α, and IL-1β in the mice's blood were measured using ELISA kits. Immune cell levels in the liver were also assessed through flow cytometry, and liver-related inflammatory factors were measured using ELISA. Key signaling pathways were identified through transcriptome sequencing, and common genes within significant pathways were analyzed using GO gene set analysis. Key metabolites were identified through metabolome sequencing, and their levels in liver tissue were measured using ELISA. Correlative analysis between transcriptome and metabolome sequencing was conducted to explore the connections between highly expressed genes in key signaling pathways and critical metabolites. In vitro cell assays were used to validate the role of these metabolites and differential genes in promoting liver damage.

first: Han

last: Li

first: Tianqi


title: Asparagine endopeptidase prompts breast cancer-related pericardial calcification by regulating IGF2 and integrin αvβ5

status: Public on Dec 30 2025

city: Shanghai

first: Xuefeng

last: Wang

address: 320 Yueyang Road

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Cardiac calcification, commonly observed in age-related diseases, impairs heart function. However, its link to malignant tumors is poorly understood. Our study revealed that pericardial metallization occurs in up to 80% of breast cancer patients with pulmonary metastasis. We demonstrate a reciprocal relationship where breast cancer promotes pericardial calcification, which in turn accelerates cancer progression in both human patients and mice. Lung metastases increase macrophage and pre-osteoblast infiltration in the pericardial tissue, triggering inflammation and osteogenesis. Mechanistically, metastatic cancer cells in lungs highly express asparagine endopeptidase (AEP), which cleaves IGF2BP3 to enhance IGF2 level within these cells’ selves. These secreted AEP and IGF2 contribute to pericardial calcification by promoting osteoblast differentiation in heart tissue through activation of integrin αvβ5 and IGF1R respectively. Pharmacological inhibition of integrin αvβ5 and IGF1R effectively suppressed ectopic osteogenesis and disrupts the feedback loop from pericardial calcification to cancer progression. Taken together, these findings underscore the significance of managing pericardial calcification in breast cancer patients and offer potential treatment strategies.

overall_design: Nine samples of mouse pericardium were analyzed by transcriptome sequencing


title: Adaptability of Cobetia marina to growth at different temperatures

city: Valparaíso

first: M.

middle: Alejandro

last: Dinamarca

state: Valparaíso

address: Gran Bretaña 1093

department: Centro de Micro-Bioinnovaci{on

country: Chile

institute: Universidad de Valparaíso

summary: The bacteria Cobetia marina is globally distributed in different oceanic ecosystems and is able to grow in a wide range of temperatures from 0°C to 41°C, with an optimal growth temperature close to 35°C. Its remarkable characteristics include its ability to form biofilm, produce biosurfactants, and use petroleum-derived hydrocarbons as energy and carbon source. In this context, Cobetia marina is a model for biofilm production and the production of diverse biomolecules of relevance for human and animal health, as well as for environmental protection and recovery. This dataset shows the differential expression of genes and gene regulatory circuits that explain the adaptation of Cobetia marina to different temperatures, serving as a model of evolution in response to selection pressures such as temperature changes in the marine environment. In this study, Cobetia marina was grown at 16°C, 35°C, 38°C, and 41°C to establish differential gene expression using high-throughput RNA sequencing.

overall_design: To investigate how temperatures trigger different gene regulatory circuits, mediating the differential adaptation of Cobetia marina strain MM1IDA2H-1, this bacterium was grown at 16°C, 35°C, 38°C, and 41°C. All experiments were carried out using 96-wells microplates. For each experimental condition, 95 cultures were grown until mid-exponential phase, in triplicates. Cells from each replicate were harvested and pooled for RNA extraction. Total RNA was sequenced using an Illumina pair-end protocol (2x 150 bp). Gene expression was quantified, and differential expressions were calculated considering 35 ºC as control condition.

first: M

middle: A

first: Claudia

last: Ibacache-Quiroga

first: Karoll

last: González-Pizarro

first: Ignacio

last: Plaza González

first: Milan

last: Stehlík


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [CUT&Tag]

city: Hefei

first: lingling

last: zhu

address: JinZhai Road

institute: University of Science and Technology of China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Human pluripotent stem cells (hPSCs) provide a valuable platform for studies of human neuronal differentiation, but the mechanisms regulating the timing of this process remain poorly understood. This study compares two differentiation systems with distinct timing of differentiation, transcription factor (TF)-induced forward programming and stepwise cellular differentiation. Our analyses reveal that divergent cellular trajectories drive distinct neurogenesis timing. Multi-omic analysis identifies crucial gene regulatory networks (GRNs) that govern cell fate determination and timing control. Modulation of these GRNs modulates neurogenesis and timing of neuronal maturation. Specifically, OLIG family TFs, enriched in the TF-induced system, promoted cell cycle exit through NOTCH signaling regulation; conversely, ablation of these TFs delayed neurogenesis. In contrast, NEUROD2 overexpression accelerated neuronal maturation through precocious activation of maturation gene modules. Collectively, these findings illuminate characteristics of the cell-intrinsic mechanisms that govern timing of differentiation; the studies also offer a framework for investigation into, and the rational design of, timing-controlled in vitro differentiation strategies.

overall_design: We performed scRNA-seq on cells over the time course of TF-induced forward programming (hPSCs female and male cell lines, with mRNA or dox inducbile NEUROG1, NEUROG2, NEUROD1 overexpression induced neurogenesis) and stepwise cellular differentiation (dual-SMAD inhibition).Taken together, these data indicate that TF-induced forward programming represents a distinct differentiation shortcut from hPSCs to neuronal fate. In order to further decipher the regulatory landscape underlying the drastic cell fate changes, several experiments were performed including high-resolution time-course RNA expression profiling, chromatin accessibility analysis, and TF binding profiling by CUT-TAG (NEUROG1, NEUROG2, and NEUROD1). We next aimed to infer GRNs that may play a crucial role in facilitating rapid neurogenesis (OLIG1, OLIG2, OLIG3) and subsequent neuronal maturation (NEUROD2, MSC). To gain mechanistic insights, scRNA seq of cells induced from OLIG KO cell line, TF binding profiling by ChIP (OLIG2) and CUT-TAG (NEUROD2, MSC) were performed.


title: The Role of CDCP1 in Carotid Artery Stenosis: Implications for Mitochondrial Autophagy and Therapeutic Potential of 8-isopentenylnaringenin

city: Shijiazhuang

first: Xin

last: Ji

address: No. 20, South Second Ring East Road

institute: Hebei Normal University

summary: Carotid artery stenosis (CAS) is a major cause of cardiovascular diseases, such as myocardial infarction and stroke. Mitochondrial dysfunction can trigger the onset of these conditions. CUB Domain Containing Protein 1 (CDCP1) is a transmembrane protein that has been demonstrated to contribute to various tumors and myocardial infarction; however, its role in carotid artery stenosis has not yet been reported. In this study, we investigated how CDCP1 affects cellular activity by regulating mitochondrial autophagy, and we propose that 8-isopentenylnaringenin (8-PN) may promote autophagy and alleviate carotid artery stenosis by reducing the expression of CDCP1. CDCP1 is upregulated in vascular smooth muscle cells within a carotid artery stenosis model, as demonstrated by studies conducted both in vivo and in vitro. Knocking down CDCP1 enhanced mitochondrial autophagy by upregulating ATG4A, leading to a reduction in reactive oxygen species (ROS) release and protection of cell viability. Moreover, both in vitro and in vivo experiments confirmed that 8-PN effectively decreases CDCP1 expression, activates cellular autophagy, and mitigates the progression of carotid artery stenosis. These findings highlight the importance ofCDCP1 in carotid artery stenosis and underscore the capability as a therapeutic option for this condition.

overall_design: RNA-seq profiling of CDCP1 knockdown under Ang II treatment in vascular smooth muscle cells.


title: Transcriptomic analysis of GRHL2 regulated genes in HepG2 cells

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

summary: HepG2 cells were transfected with a plasmid coding for GRHL2 fused to a flag tag or a pcDNA vector and RNA were processed for RNAseq

overall_design: RNAseq analysis in human HepG2 cells with GRHL2 overexpression

first: Ludivine

last: Vasseur

first: Céline

last: Gheeraert


title: Genome-wide maps of chromatin state in HepG2 cells

summary: We generated genome-wide chromatin-state maps of HepG2 cells by using next generation sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histones marks H3K27m3 and H3K27ac in HepG2 cells

first: Clémence

last: Boulet


title: Transcriptomic analysis of GRHL2 regulated genes in BMEL cells

summary: BMEL cells were transfected with a plasmid coding for GRHL2 fused to a flag tag or a pcDNA vector and RNA were processed for RNAseq

overall_design: RNAseq analysis in BMEL cells with GRHL2 overexpression


title: GRHL2 derepression triggers pathophysiological hepatocyte to cholangiocyte transdifferentiation

summary: HepG2 cells were used for GRHL2 ChIP-seq

overall_design: ChIP seq analysis in HepG2 cells with Grhl2 overexpression


title: GRHL2 derepression triggers pathophysiological hepatocyte to cholangiocyte trans-differentiation

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Generation of multi-omic datasets using high-throughput molecular profiling of DNA methylation human data

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

type: Methylation profiling by genome tiling array

summary: Tumor heterogeneity significantly affects cancer progression and therapeutic response, yet quantifying it from bulk molecular data remains challenging. Deconvolution algorithms, which estimate cell-type proportions in bulk samples, offer a potential solution. However, there is no consensus on the optimal algorithm for transcriptomic or methylomic data.  Here, we present an unbiased evaluation framework for the first comprehensive comparison of deconvolution algorithms across both omic types, including reference-based and -free approaches. Our evaluation covers raw performance, stability, and computational efficiency under varying conditions, such as missing or additional cell types and diverse sample compositions. We design a reproducible workflow using containerization and publicly available code to ensure transparency and re-usability. Our results highlight the strengths and limitations of various algorithms, providing practical guidance for selecting the best method based on data type and context. This benchmark sets a new standard for evaluating deconvolution methods and analyzing tumor heterogeneity.

overall_design: This dataset consists of 30 mixtures (and nine pure cell types) constructed to recapitulate the heterogeneity seen in real pancreatic adenocarcinoma (following a Dirichlet distribution model). These mixes contained variable proportion of (i) human tumor cells (from 2 subtypes), (ii) cancer associated fibroblasts, (iii) human tumor derived-endothelial cells and immune cells that were FACS sorted from healthy donors (B, T4, T8 lymphocytes and neutrophils) and differentiated (M2-type macrophages). Cells were mixed and RNA/DNA were simultaneously extracted followed by RNAseq (RNA-seq poly A) and methylome (MethEPIC 850K).

first: Amblard

last: Elise

first: Chuffart

last: Florent

first: Kermezli

last: Yasmina

first: Armenoult

last: Lucile

first: Baures

last: Aurelia

first: Cassard

last: Audrey

first: Ayadi

last: Mira

first: Cros

last: Jerome

first: Blum

last: Yuna

first: Richard

last: Magali


title: Human Aging Lung Cell Atlas

city: New Haven

first: Ruben

last: De Man

state: CT

address: 333 Cedar St

country: USA

institute: Yale School of Medicine

summary: Age is a substantial risk factor and is associated with worse prognosis in nearly all lung diseases. We performed scRNAseq to profile transcriptional changes in the aging human lung at single-cell resolution.

overall_design: Samples were collected from cryopreserved human lung samples and analyzed using scRNAseq.

first: De Man

last: Ruben

first: Rosas

last: Ivan

first: Kaminski

last: Naftali


title: GRHL2 derepression triggers pathophysiological hepatocyte to cholangiocyte transdifferentiation [RNAseq_HepG2_EZHi]

first: Jérôme

last: Eeckhoute

summary: Transcriptome of human HepG2 cells treated or not with Ezh1/2 inhibitors (UNC1999 and Valmetostat Tosylate).

overall_design: RNAseq analysis in human HepG2 cells treated or not with Ezh1/2 inhibitors

first: Ludivine

last: Vasseur

first: Céline

last: Gheeraert


title: Generation of multi-omic datasets using high-throughput molecular profiling of transcriptomic human data

first: Florent

last: Chuffart

first: Amblard

last: Elise


title: Gene expression profile at single cell level of mouse hematopoietic stem cells (8-week old)

city: Stanford

first: Irving

last: Weissman

state: CA

address: 265 Campus Dr.

department: Stem Cell Institute

institute: Stanford University

summary: gene expression in bwtween Long-term hematopoietic stem cells and short-term hematopoietic stem cells is different, we utilized the single cell RNA sequencing to compare it.

overall_design: Hematopoietic stem cells were dortef by FACS according to the surface markers (LT-HSC: LSK CD34- CD150+ CD48- Flk2-; ST-HSC: LSK CD34- CD150+ CD48+)

first: Xiang

last: Jinyi

first: Almeida

last: Laura


title: Dominant-negative TP53 mutations potentiated by the HSF1-regulated proteostasis network [1]

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue 68-317A

department: Biology

institute: MIT

summary: Protein mutational landscapes are sculpted by the impacts of the resulting amino acid substitu-tions on the protein’s stability and folding or aggregation kinetics. These properties can, in turn, be modu-lated by the composition and activities of the cellular proteostasis network. Heat shock factor 1 (HSF1) is the master regulator of the cytosolic and nuclear proteostasis networks, dynamically tuning the expres-sion of cytosolic and nuclear chaperones and quality control factors to meet demand. Chronic increases in HSF1 levels and activity are prominent hallmarks of cancer cells. One plausible explanation for this ob-servation is that the consequent upregulation of proteostasis factors could facilitate the acquisition of on-cogenic mutations. Here, we experimentally evaluate the impacts of chronic HSF1 activation on the muta-tional landscape accessible to the quintessential oncoprotein p53. Specifically, we apply quantitative deep mutational scanning to assess how HSF1 activation shapes the mutational pathways by which p53 can escape cytotoxic pressure conferred by the small molecule nutlin-3, which is a potent antagonist of the p53 negative regulator mouse double minute 2 homolog (MDM2). We find that activation of HSF1 broadly and significantly increases the fitness of dominant-negative substitutions within p53. This effect of HSF1 activation was particularly notable for non-conservative, otherwise biophysically unfavorable non-polar to polar or charged amino acid substitutions within buried regions of the p53 DNA-binding domain. These results indicate that chronic HSF1 activation profoundly shapes the oncogenic mutational land-scape, preferentially supporting the acquisition of cancer-associated substitutions that are biophysically destabilizing. Along with providing the first experimental and quantitative insights into how HSF1 influ-ences oncoprotein mutational spectra, these findings also implicate HSF1 inhibition as a strategy to re-duce the accessibility of mutations that drive chemotherapeutic resistance and metastasis.

overall_design: A549 cells expressing a consitutively active form of HSF1 (cHSF1) under a tet-repressor were treated with either DMSO (negative control) or Doxycycline (1 μg/mL dox for 24 h) to activate the heat shock response. Each treatment was performed in biological sextuplicate. Differential gene expression was analyzed, with particular attention to upregulation of genes involved in the heat shock response.

first: Rebecca

middle: M

last: Sebastian

first: Matthew

middle: D

last: Shoulders


title: NTPDase8 protects against liver ischemia-reperfusion injury

city: New York

first: George

last: Hasko

state: NY

address: 622 West 168th Street

department: Department of Anesthesiology

institute: Columbia University

summary: CD39 or NTPDase1 and other nucleoside triphosphate diphosphohydrolases (NTPDases), including NTPDase2, NTPDase3, and NTPDase8, regulate purinergic signaling through tuning the extracellular levels of purine nucleotides and nucleosides. Purinergic signaling can regulate liver ischemia-reperfusion (I/R) injury and CD39 is protective. However, the role of other NTPDases is unkown. In this study, we have investigated the roles of NTPDase2, NTPDase3, and NTPDase8 in liver I/R injury. Global Entpd2-/-, Entpd3-/-, and Entpd8-/- and control wild-type (WT) mice were subjected to a 60 minutes of warm hepatic ischemia, which was followed by a 6-hour reperfusion period. In addition, WT and Entpd8-/- mice underwent global ischemia induced by hemorrhagic shock and resuscitation. Liver and plasma samples were collected to assess the extent and mechanisms of liver injury. Bone marrow chimeric mice derived from Entpd8-/- and WT were generated to understand the role of NTPDase expression on hematopoietic cells in regulating liver injury. While wild-type (WT), Entpd2-/- and Entpd3-/- mice exhibited comparable levels of liver injury following local IR, Entpd8-/- mice had increased liver injury compared to WT mice. This was evidenced by increased levels of plasma transaminases (ALT and AST) and histological evidence of heightened hepatocellular damage. Studies with bone marrow chimeric mice indicated that NTPDase8 on parenchymal liver cells protected against hepatic injury. This was confirmed by single-nucleus RNAseq showing hepatocytes are the dominant cell type expressing NTPDase8 in the liver. Entpd8-/- mice after I/R injury were noted to have higher ATP concentrations in the liver and plasma. The P2 antagonist suramin decreased plasma ALT and AST levels in Entpd8-/- mice indicating that extracellular ATP-mediated purinergic signaling contributes to liver injury in these mice. Finally, Entpd8-/- mice had increased liver injury compared to WT mice also after global IR induced by hemorrhagic shock and resuscitation.These findings highlight the differential roles of NTPDase family members in the liver, with parenchymal/hepatocyte expression of NTPDase8 emerging as a critical suppressor of the inflammatory and metabolic responses to hepatic ischemia-reperfusion insult, even in the presence of vascular NTPDase1 expression.

overall_design: We investigate the role of NTPDase8 on liver ischemia

first: Taha

last: Kelestemur

first: Simon

middle: C

last: Robson

first: Zoltan

middle: H

last: Nemeth

first: Pal

last: Pacher

first: Mehmet

middle: S

last: Aydin

first: Baris

middle: E

last: Suzek

first: Julie

last: Pelletier

first: Robert

middle: F

last: Schwabe

first: Yana

last: Geng

first: Jean

last: Sévigny

first: György

last: Haskó


title: Transcriptomic and Translatomic Responses of Leishmania major to Heat Shock Stress

city: Lubbock

first: Zemfira

middle: N.

last: Karamysheva

state: TX

department: Cellular Biology and Biochemistry

institute: Texas Tech University Health Sciences Center

summary: Leishmania parasites have a complex life cycle, alternating between the insect vector and mammalian host and facing a wide spectrum of environmental conditions. During transition between insect to mammal host, the parasite experiment profound changes in temperature, pH and nutrients availability, causing a global translation repression. However, several genes can scape from this translational repression, allowing the parasite to survive in the mammal host, infect cells from immune system, mainly macrophages, and promoting their differentiation into amastigotes. In this way, the goal of this study is of determine the changes in transcriptome and translatome of Leishmania major parasites under heat shock stress, to identify the genes involved in the survival of the parasite. Translatomic results show a global downregulation of translational machinery and protein synthesis, while an upregulation of genes involved in cellular homeostasis, response to stress, and transmembrane transport was observed.

overall_design: Leishmania major strain Friedlin was divided into two groups: WT, which was the control group, and treated, corresponding to parasites subjected to heat shock by incubating for two hours at 37ºC (by triplicate). Then, parasites were lysed, centrifuged, and the supernatant was transferred into a 10% to 50% glucose gradient for polysome profiling. A lysate aliquot was obtained, stored with TRIzol LS, and used as input. The glucose gradients with the samples were ultracentrifuged at 39,000 rpm for 2 hours at 4°C to separate ribosome-bound mRNA (polysome separation) based on the number of ribosomes they contain. Then, polysomes were fractionated, mixed with TRIzol LS, and stored at -80ºC until processing. Fractions were combined to obtain monosomes (1 ribosome), light polysomes (2-4 ribosomes), and heavy polysomes (5 or more ribosomes associated with a single mRNA). RNA purification of inputs, monosomes, light, and heavy polysomes was performed using the Direct-zol™ RNA MiniPrep kit. Purified RNA was quantified and analyzed by RNA sequencing to determine the gene expression of the parasites during heat shock stress.

first: Cristian C

last: Rodriguez-Almonacid

first: Christian

last: Bustamante

first: Sneider

last: Gutierrez Guarnizo

first: Zemfira N


title: DNA methylation profiling of Nlrp5 +/+, and -/- and germinal vesical murine oocytes

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

type: Methylation profiling by high throughput sequencing

summary: Nlrp5 encodes a core component of the subcortical maternal complex (SCMC) a cytoplasmic protein structure unique to the mammalian oocyte and cleavage-stage embryo. NLRP5 mutations have been identified in patients presenting with early embryo arrest, recurrent molar pregnancies and imprinting disorders. Correct patterning of DNA methylation over imprinted domains during oogenesis is necessary for faithful imprinting of genes. It was previously shown that oocytes with mutations in the human SCMC gene KHDC3L had globally impaired methylation, suggesting a role for the SCMC in the establishment of DNA methylation at imprinted regions. Here, we present a multi-omic analysis of an Nlrp5-null mouse model, which displays a global misregulation of maternal proteins in Nlrp5-null oocytes, likely underlying oocyte developmental incompetence. We also show that de novo DNA methylation is altered in Nlrp5-null oocytes, and that epigenetic modifiers such as DNMT3L are significantly reduced. This provides evidence for mechanisms leading to downstream misregulation of imprinted genes, which in turn, may result in imprinting syndromes, multi-locus imprinting disturbances (MLID), and hydatidiform moles.

overall_design: To determine the effects of an Nlrp5 inactivating mutation on DNA methylation patterning in the murine oocyte, we generated a novel Nlrp5 mutant mouse line using CRISPR/Cas9 gene editing, and performed single cell DNA methylation profiling (scPBAT-seq) on germinal vesicle stage oocytes from female Nlrp5 +/+ and -/- mice. Oocytes were collected at 3 weeks old.

first: Leah

last: Nic Aodha


title: DNA methylation and Transcriptional profiling of Nlrp5 +/+, and -/- and germinal vesical murine oocytes


title: Novel roles for the ectoenzyme CD38 in the maintenance of transcriptional and metabolic homeostasis in astrocytes

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

summary: CD38 is an ectoenzyme that converts NAD+ to NAM and helps to maintain bioenergetic homeostasis. A better understanding of CD38 biology in the brain is needed, considering the evidence for CD38 dysregulation and/or gene variation in neurodegenerative conditions such as Parkinson’s Disease (PD) and Alzheimer’s Disease (AD). Here, we demonstrate enrichment of Cd38 in midbrain astrocytes and describe how CD38 deficiency influences brain metabolism, astrocytic gene expression, and bioenergetics. We demonstrate increased NAD content, decreased NAM content, and increased NAD/NAM in the midbrain and striatum of CD38-deficient (Cd38-/-) mice, indicating the dependence on CD38 for NAD to NAM conversion. RNA-sequencing of isolated astrocytes revealed numerous differentially expressed genes in Cd38+/- and Cd38-/-  mice, with alterations in mitochondrial, metabolic, and senescence-related genes and several genes involved in PD and AD etiology. Interestingly, Seahorse XFe24 mitochondrial functional evaluation in primary astrocyte cultures from Cd38+/+, Cd38+/-, and Cd38-/-   mice revealed enhanced oxygen consumption, with an increase in glycolytic rate with Cd38 deficiency. These findings indicate a novel role for astrocytes in the regulation of CD38-dependent NAD/NAM homeostasis in the brain and provide the framework for future studies evaluating the relationship between CD38 dysfunction, aging, and vulnerability of neuronal populations in neurodegenerative disease. Also, these studies highlight the need to better elucidate the impact of CD38 deficiency on brain metabolism, considering ongoing clinical trials using CD38 inhibitors for the treatment of multiple myeloma and other cancers.

overall_design:
Astrocytes were isolated from Cd38+/+, Cd38+/-, and Cd38-/-  late (n = 3, 3 and 6 respectively) -adulthood male mice after 1 year of age (12-14 months, x̄ = 13.5 months) utilizing a magnetic isolation bead approach (MACS -Miltenyi).   Midbrain regions associated with Parkinson’s disease pathology (striatum, thalamus, and substantia nigra) were microdissected from brain tissue for cell-specific isolation. Tissue dissociation was performed, whereby regions of interest were utilized for MACS. All dissections were performed in modified artificial cerebral spinal fluid (120 mM NaCl, 3 mM KCl, 6 mM 2NaHCO3, 11 mM glucose, 5 mM HEPES, 200 µM CaCl, 1 mM MgCl) containing neuronal activity inhibitors (20 µM CNQX, 20 µM D-AP5, 295-299 mOsm) to reduce glutamate excitotoxicity. Briefly, midbrain tissues were removed then sectioned into 1mm pieces, followed by papain dissociation (Worthington Biochemical Corporation, Catalog# LK003150). A series of centrifugation (4°C, 300 RCF, 3-5 minutes, Eppendorf Catalog# 58048R) and PBS wash steps were performed to retain cell containing tissue pellets. Supernatants were discarded and pellets were resuspended in 0.5% w/v bovine serum albumin (Millipore Sigma, Catalog# A7030) in PBS for filtration (70 µm, Fisher Scientific Catalog# 22-363-548) and attainment of midbrain cellular fractions. Cell fractions were then treated with Miltenyi Biotec Microbeads to remove contaminating endothelial cells (Catalog# 130-097-418) and myelin/oligodendrocytes (Catalog# 130-096-433). Samples were incubated in microbeads for 10 minutes at 4°C followed by filtering through Miltenyi LS columns (Catalog# 130-042-401). Samples were then treated with anti-CD11b  microbeads (Catalog# 130-092-263) for 10 minutes at 4°C to selectively isolate microglia by elution of magnetically captured cells for collection. Finally, astrocytes were positively selected using the Miltenyi ACSA-II microbead kit (Catalog# 130-097-679). Samples were first incubated with an FcR blocking reagent for 10 minutes at 4°C immediately followed by an additional 10-minute incubation at 4°C with anti-ACSA-2 microbeads. After LS column filtration and elution, collected cells were stored in 300 µL Trizol (ThermoFisher Scientific, Catalog# 15596026) and snap frozen before being placed in storage at -80°C.
Astrocytes were removed from -80°C , placed on ice to thaw and then gently lysed by syringe for preparation of RNA isolation (Zymo Research, Catalog# R2062). RNA was extracted according to the Direct-zol RNA Microprep protocols, including DNA-degradation with DNase I. Total RNA was eluted in 10µL of DNAse/RNAse free water. Samples were submitted to Medgenome for rRNA depletion, quality verifications, library construction, and ultra-low input RNA-sequencing. RNA integrity was determined by Qubit fluorometric quantitation and tapestation bioanalyzer analysis. Collected RNA was then converted to cDNA samples by using the Takara SMART-Seq v4Ultra low Input RNA kit. Generated cDNA was checked for quality utilizing Quibit and tapestation measures, whereby libraries with marginal pass and higher quality for were used for pair-ended sequencing on the NovaSeq 6000 platform.

middle: L


title: Transcriptional  profiling of Nlrp5 +/+, -/- and +/- germinal vesical murine oocytes

overall_design: To determine the effects of an Nlrp5 inactivating mutation on transcriptional regulation in the murine oocyte, we generated a novel Nlrp5 mutant mouse line using CRISPR/Cas9 gene editing, and performed single cell transcriptome sequencing (scRNA-seq) on germinal vesicle stage oocytes from female Nlrp5 +/+, -/- and +/- mice. Oocytes were collected at 3 weeks old. Nuclear maturation staging (i.e. non-surrounded nucleous (NSN), or surrounded nucleolus (SN)) was determined post scRNA-sequencing, using a list of NSN-SN differentially expressed genes.


city: Milwaukee

first: Xiaowen

last: Bai

state: WI

address: 8701 Watertown Plank Road

department: Department of Cell Biology, Neurobiology & Anatomy

institute: Medical College of Wisconsin

summary:
Pediatric patients detected were younger than 4 years old with longer exposure of general anesthetics (>3hrs)
Pediatric patients detected were younger than 4 years old with longer exposure of general anesthetics (>3hrs)

overall_design: LncRNA and mRNA profiling of Serum from pediatric patients younger than 4 years old with longer exposure of general anesthetics (>3hrs) were determined.

first: Tarun

last: Pant

first: Congshan

last: Jiang

first: Yasheng

last: Yan

first: Schultz

last: Bailey

first: Daniel

last: Laws

first: Sarah

last: Logan

first: Amina

last: Bedrat

first: Matea

last: Juric

first: Richard

middle: J

last: Berens

first: Susan

middle: P

last: Taylor

first: Amy

last: Henry

first: Zeljko

last: Bosnjak


title: human iPSC derived cerebral organoids: Propofol treated vs. DMSO control

summary:
LncRNA and mRNA profiling of human iPSC derived cerebral organoids (Propofol treated vs. DMSO control) were determined.
LncRNA and mRNA profiling of human iPSC derived cerebral organoids (Propofol treated vs. DMSO control) were determined.

overall_design: Two-condition experiment, Propofol treatment vs. DMSO control. Biological replicates: 4 organoids for both groups.


title: Constitutive Epidermal Osteopontin Expression in Osteopontin-Null Mice Develop Ultraviolet B-Induced Cutaneous Squamous Cell Carcinomas Comparable to Wild-Type Mice

city: Birmingham

first: Pi-Ling

last: Chang

state: Alabama

address: 1675 University Blvd

department: Nutrition Sciences

institute: University of Alabama at Birmingham

summary: Studies of osteopontin (OPN)-null mice have supported the role of OPN as a critical factor in the promotion of skin tumorigenesis. OPN is a highly inducible integrin- and CD44-interacting acidic glycoprotein with pleiotropic functions. In various types of cancer, elevated levels of OPN derived from cancer and from inflammatory cells are secreted into the microenvironment and the bloodstream. To determine whether OPN expressed by keratinocytes without any contribution from activated resident and infiltrating inflammatory cells promotes cutaneous tumor development, transgenic mice with constitutive epidermal expression of OPN in an OPN-null background, tg(K14-OPN) were generated. In photocarcinogenesis studies, tumor multiplicity and the incidence of cutaneous squamous cell carcinoma (cSCC) was similar between tg(K14-OPN) and wild-type (WT) mice. Consistent with our previous findings, constitutive epidermal expression of OPN enhanced the survival of acute ultraviolet B (UVB)-induced cell death compared with OPN-null mice and did not enhance UVB-induced epidermal hyperplasia compared to OPN-null or WT mice. Additionally, tg(K14-OPN) and OPN-null mice irradiated with long-term low dose UVB had significantly lower numbers of mutated p53 keratinocytes than WT mice.  RNA-sequencing data from the epidermis of acute UVB-irradiated tg(K14-OPN) versus OPN-null mice compared to UVB-irradiated WT versus OPN-null mice suggests the importance of inflammation, Wnt, integrin and gonadotropin-releasing hormone receptor signaling in cutaneous tumorigenesis and implicates UVB irradiation and its induction of OPN in driving those pathways.  In summary, the constitutive epidermal expression of OPN in OPN-null mice facilitates the development of cSCC comparable to WT mice.

overall_design:
The purpose of RNA-seq analyses are 1) to validate the expression of OPN driven by keratin 14 (K14) promoter in the epidermis of transgenic mice in OPN-null background, 2) to compare the epidermal expression OPN in tg(K14-OPN) mice with that of WT, and OPN-null mice treated with and without one time exposure to UVB, 3) to determine the global gene expression pattern of nonirradiated and a single UVB-irradiated dorsal skin of tg(K14-OPN), OPN-null and WT mice, and 4) to use PANTHER classification analyses to determine biological pathway similarities between the epidermis of single UVB-irradiated tg(K14-OPN) mice versus OPN-null mice with UVB-irradiated WT mice versus OPN-null mice.
RNA-seq data are from the epidermis of WT, OPN-null and tg(K14-OPN) mice not UVB-irradiated or one-time UVB-irradiated, samples sizes are 2-4 replicates.

first: Chu-Fang

last: Chou

first: Yun

last: Huang

first: Jeremy

middle: B

last: Foote

first: Yu-Hua

last: Hsieh

first: Hui-Chien

last: Kuo

first: David

middle: K

last: Crossman

first: Michael

middle: R

last: Crowley

first: Craig

last: Elmets


title: Unraveling the web of nAMD: A transcriptomic analysis of age-related macular degeneration-associated cytokines in primary human retinal endothelial cells.

city: Baulkham Hills

first: Fergus

middle: Campbell

last: McLellan

state: NSW

address: 13 Delaigh Avenue

department: School of Vision Science

country: Australia

institute: University of New South Wales

summary: Neovascular age-related macular degeneration (nAMD) is a complex, blinding retinal disease underpinned by a dynamic and dysregulated interaction among pathogenic cytokines. The present study investigates the impact of six nAMD-associated cytokines, namely transforming growth factor-beta 1 and 2 (TGF-β1/2), tumour necrosis factor-alpha (TNF-α), thrombin, interleukin-6 (IL-6) and vascular endothelial growth factor (VEGF), on the transcriptome of primary human retinal endothelial cells (HRECs), both individually and as a collective 'cocktail'. HRECS were treated for 24 hours before being harvested for bulk RNA-seq. In performing this study, we have described the different transcriptomic signatures of each cytokine in driving nAMD-associated inflammatory, angiogenic and fibrotic pathways when presented in isolation to primary HRECs. Additionally, this study dissects a novel 'cocktail’ effect in the collective group characterised by further differential expression of genes, some of which were not induced by any of the individual cytokines. We explore the translatability of our study as an in vitro model of nAMD in endothelial cells by mapping the identified differential expression patterns to marker gene sets identified in previously performed scRNASeq of nAMD-affected human donor eyes.

overall_design:
n = 6 replicates of primary human retinal endothelial cells (HRECs) were treated with either no treatment (control), transforming growth factor-beta 1 or 2 (TGF-β1/2), tumour necrosis factor-alpha (TNF-α), thrombin, interleukin-6 (IL-6) or vascular endothelial growth factor (VEGF), individually (all at 10 ng/ml) or as a combination of all 6 treatments with the same concentration as individual treatments (i.e. 10 ng/ml) for 24 hours, RNA extraction was performed at the same time point for all groups, followed by sequencing.
We then performed gene expression profiling on each group with reference to the untreated control.
Mapping of obtained differential expression profiles to open-access RNA-seq datasets was then performed to assess translatability of cytokine-treated HRECs as an in vitro model of retinal neovascularisation.

first: McLellan

last: Fergus

first: Ng

last: Pei Qin

first: Williams

last: Pete

first: Shu

last: Daisy


title: Rescue of Angiopoietin-2 inhibits lymphatic malformation endothelial cell proliferation through antagonism of VEGFR3 signaling

city: Little Rock

first: Ravi

middle: W.

last: Sun

state: Arkansas

address: 4301 W Markham St

department: Department of Otolaryngology - Head and Neck Surgery

institute: University of Arkansas for Medical Sciences

summary: Cystic lymphatic malformations (LMs) are congenital anomalies characterized by the formation of dilated lymphatic channels that can infiltrate adjacent structures and cause significant morbidity. Somatic activating single nucleotide variants in PIK3CA have been identified in the majority of these lesions, yet the precise mechanisms underlying their role in LM progression remain unclear. Here, we investigated the role of Angiopoietin-2 (Ang-2) downregulation downstream of hotspot PIK3CA variants in the pathogenesis of LMs and delineated a novel inhibitory mechanism for Ang-2 in the lymphatic vasculature. Transcriptomic profiling of patient-derived lymphatic malformation endothelial cells (LM-ECs) revealed Ang-2 as one of the most significantly downregulated genes. Lentiviral overexpression of Ang-2 in LM-ECs and normal human dermal lymphatic endothelial cells significantly attenuated their proliferation by inhibiting VEGFR3 signaling via the Akt pathway. Treatment of LM-ECs with the PI3K inhibitor alpelisib, but not the mTOR inhibitor sirolimus (rapamycin), rescued Ang-2 expression and downregulated VEGFR3. Alpelisib in combination with Ang-2 overexpression produced a synergistic reduction in LM-EC proliferation compared to Ang-2 overexpression or alpelisib treatment alone. Finally, Ang-2 overexpression in LM-ECs antagonized lymphangiogenesis in a murine xenograft model of LM. Together, our findings suggest that targeting the Ang-2/VEGFR3 axis may be a viable option for the suppression of pathological lymphangiogenesis.

overall_design: LM tissue and cystic fluid were collected from patients (n=6) undergoing surgical resections. LM-ECs (n=9) were isolated from LM tissue and cystic fluid as previously described. HDLEC lines (n = 3, isolated from different patients) were purchased from PromoCell (PromoCell, Germany) and used as controls. All cells were cultured in EBM-2 medium (Lonza Group Ltd, Switzerland) supplemented with growth factors, 20% fetal bovine serum (R&D Systems, Inc. Minneapolis, MN), and 1% antibiotic-antimycotic (ThermoFisher Scientific, Waltham, MA) on fibronectin-coated plates and maintained at 37°C in a 5% CO2 humidified chamber. Cells were cultured to 80% confluence, trypsinized, and collected as pellets for RNA isolation.

middle: W

first: Haihong

last: Zhang

first: Syed

last: Mehdi

first: Gresham

middle: T

last: Richter

first: Charity

last: Washam

first: Stephanie

last: Byrum

first: June

last: Wu

first: Carrie

last: Shawber

first: Graham

last: Strub


title: Genes expression in the different passages of OECM-1 cell line received cetuximab

city: Taipei

first: Po-Hsien

last: Chiu

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Recent clinical studies showed those patients who underwent cetuximab treatment before IO therapy seem to be worse. However, the correlation between these therapies is unclear. We aimed to reveal that cetuximab resistance caused IO failure. Cetuximab resistant cells had lower STAT1 protein levels. In addition, STAT1 lost its transcriptional activity when we restored STAT1 in resistant cells. The above description suggested that STAT1 may obtain some modifications during cetuximab stimulation. We found IFN-related signaling had similar changes to STAT1 protein and inflammatory signature was increased. This study investigates the mechanisms of interplay between targeted therapy and IO treatment, providing proper therapeutic strategies to enhance the efficacy of IO in those cetuximab resistant HNSCC patients.

overall_design: We utilized RNA seq to figure out the changes in the different passages of cetuximab treatment(500μg/ml) in OECM-1.

first: Muh-Hwa

last: Yang


title: Rbfox2-dependent alternative splicing of Numb regulates Notch signaling during muscle stem cell activation

city: Hong Kong

first: Tom

last: Cheung

state: Please Select...

address: Clear Water Bay

country: Hong Kong

institute: HKUST

summary: Satellite cells (SCs), or muscle stem cells, are the resident somatic stem cells responsible for skeletal muscle regeneration. Most SCs remain quiescent in resting adult muscles but can activate rapidly upon receiving a stimulus. While Rbfox2 has been reported to play an essential role in regulating myoblast differentiation, its role in the activation process of SCs remains elusive. To investigate the role of Rbfox2 during satellite cell activation, we freshly isolated satellite cells from Rbfox2 conditional knockout mice and performed RNA-seq to profile the transcriptome changes upon Rbfox2 knockout.

overall_design: To investigate the role of Rbfox2 in SCs, we generated an Rbfox2 conditional knockout (cKO) mice by crossing Rbfox2 flox mice with Pax7CreERT2 mice, which enables the deletion of Rbfox2 specifically in SCs following tamoxifen injection. These mice were also crossed with Rosa26 EYFP mice to label Rbfox2-null SCs with yellow fluorescent protein (YFP). We then isolated satellite cells from Rbfox2 cKO and control mice, extracted the RNA and performed RNA-seq. Analysis is performed to identify differentially expressed genes and differentially spliced events.

first: Kangning

last: Lin

first: Jing

last: Liu


title: Effects of intrauterine hyperglycemia on offspring development in gestational diabetes mellitus based on placental transcriptomics

city: Linyi City

first: Peng

last: xi

state: Shandong Province

address: Jiefang Road, Linyi City

department: Neonatology

institute: Linyi People's Hospital

summary: Gestational diabetes (GDM) refers to diabetes diagnosed as diabetes in the second or third trimester of pregnancy, but not obvious before pregnancy. It is one of the most common complications of pregnancy, which can lead to perinatal asphyxia, neonatal hypoglycemia, macrosomia, cardiovascular abnormalities, obesity and other short-term and long-term adverse outcomes of the offspring. This study explores the differential expression of transcriptome between GDM and non GDM placenta, and explores the impact of subtle metabolic changes in the placenta on fetal growth and development during GDM in pregnant women.

overall_design: In this study, 16 samples of gestational diabetes (GDM, n=8) and non gestational diabetes (n=8) were analyzed by transcriptome sequencing (RNA seq). Using | log2Fold Change |>=2 and FDR<0.05 as the standard for screening differentially expressed genes (DEGs), GO functional annotation, KEGG pathway analysis, and protein-protein interaction network (PPI) analysis were performed on the selected differentially expressed genes (DEGs).

last: Xi

first: Zhou

last: Ting

first: Zheng

last: Fang

first: Liu

last: Qiang


title: Genes expression of OECM-1 and Cal-27 wild-type (WT) / cetuximab-resistant cell lines

summary: We performed RNA seq to compare the difference of genes between WT and resistant cells

overall_design: We established in vitro cetuximab-resistant cells by culturing HNSCC cells in the medium containing cetuximab (500μg/ml). Those cell lines were cultured for 30 passages (more than two months). After that, we collected RNA from parental cells and the resistant cells.


title: LXR agonism enhances T cell activation upon crosspresentation by LXR-DKO BMDCs.

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

summary: Here, we analyze transcriptional profiles of OT-I CD8+ T cells co-cultured with LXR-/- bone marrow-derived dendritic cells pulsed with the SIINFEKL peptide in the absence or presence of the synthetic LXR agonist RGX-104.

overall_design: Differential gene expression analysis of flow cytometry-sorted OT-I CD8+ T cells after co-culture with LXR-/- bone marrow-derived dendritic cells in the presence or absence of the synthetic LXR agonist RGX-104.


title: RNA transcriptome analyses in shMETTL3 and shNUP93 in LNCaP, Hela and podocyte cells

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: To investigate the role of m6A in RNA export, we performed transcriptome profiling by high throughput sequencing.

overall_design: Nuclear and total RNA etraction followed by high throughput sequencing (RNA-seq) in shControl, shNUP93, shNUP93-resistant NUP93 wildtype and mutant (catalytically dead) expressing LNCaP, Hela and podocyte cell lines

first: Zhao

last: Zhang

first: Jihoon

last: Lee


title: N6-methyladenosine RNA methylome analyses in podocyte cell lines

summary: To identify N6-methyladenosine RNA methylome in podocyte.

overall_design: N6-methyladenosine RNA methylome profiling by high throughput sequencing (MeRIP-seq)


title: Genes expression between patients pre and post cetuximab treatment

summary: We performed RNA seq to investigate the difference between pre and post cetuximab treatments

overall_design: We recruited patients who underwent cetuximab treatment and collected samples before and after the treatments.


title: Expression Data from JAM-C or TAZ overexpressing ARPE-19 cells

city: Guangzhou

first: Chen

last: min

state: Guangdong

address: No.7 Jinsui Road, Tianhe District

institute: Zhongshan Ophthalmic Center, Sun Yat-sen  University, China

summary: Epithelial-mesenchymal transition (EMT) of retinal pigment epithelial (RPE) cells is a hallmark of PVR, which remains an unresolved clinical challenge leading to vision loss. Here, we identified disregulation of junctional adhesion molecule C (JAM-C) and transcriptional co-activator with PDZ-binding motif (TAZ) as key regulators of RPE EMT.

overall_design: To investigate the effect of JAM-C and TAZ in RPE cells, we overexpressed JAM-C or TAZ in ARPE19 cells using adevirus, with adGFP as control. We then used adGFP for comparison with adJAM-C or adTAZ by RNA-seq to construct the gene expression profile.

first: Weisi

last: Lu

first: Min

last: Chen

first: Xuri

last: Li


title: Effect of knockdown PHF8 on the transcriptional regulation of BCR-ABL1 fusion gene on CML cell line K562

city: jinan

first: Huimin

last: Feng

address: 107 Wenhua Xi Road

institute: Shandong University

summary: Epigenetic dysregulation plays a vital role in the pathogenesis of hematological malignancies. Histone demethylation is a key mechanism for epigenetic modification, of which dysregulation has an immeasurable effect on both TKI resistance and the transformation from CP CML to AP/BC CML. Here we report that PHF8 regulate the transcription of the driven fusion gene BCR-ABL1 in CML cells. The depletion of PHF8 promotes differentiation and inhibits proliferation. Furthermore, the proliferation-inhibited function of PHF8-knockdown have stronger effect on imatinib mesylate (IM)-resistant CML cells. We identified that PHF8 as a transcriptional modulator interacted with the promoter of the BCR::ABL1 fusion gene and alters the methylation levels of H3K9me1, H3K9me2 and H3K27me1, thereby promoting BCR::ABL1 transcription. Taken together, PHF8, as an oncogenic protein, was abnormally expressed in CML, altered the histone methylation levels of BCR::ABL1 promoter, and upregulated BCR::ABL1. Our study indicated that regulating histone demethylation is essential for BCR::ABL1 expression. Targeting PHF8 can be a promising therapeutic option for CML patients with TKI resistance.

overall_design: To investigate the mechanism and function of PHF8 in CML, we constructed the PHF8 knockdown CML cell lines with shRNA in K562. Than we performed gene expression profiling analysis using data obtained from RNA-seq of K562 with shNC and shPHF8.

first: Chunyan


title: RNA-seq for the soybean nodule

city: 广州

middle: Qian

last: Qian

state: 广东省

address: 天河区五山街道

institute: 华南农业大学

summary: To uncover the underlying molecular mechanisms of nodule by Bac.B and Bra.Q2 co-inoculation, a transcriptome analysis was performed. Compared to the individual inoculation of Bra.Q2, the co-inoculation of Bac.B and Bra.Q2 resulted in 3340 differentially expressed genes (DEGs). Among them, 1649 were up-regulated and 1691 were down-regulated. Furthermore, the KEGG pathway enrichment analysis indicated that these DEGs were significantly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, mitogen-activated protein kinase (MAPK) signaling pathway, and multiple N metabolism pathway.

overall_design: The experiment comprised two treatments:  low nitrogen application with Bra.Q2 inoculation (R), and low nitrogen application with Bac.B and Bra.Q2 inoculation  (BR)

first: Cuiyue

last: Liang

first: Jiang

last: Tian

first: Tianqi

last: Wang


title: Genomic correlates of LXR activation in dendritic cells and T cells

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

overall_design: Refer to individual Series


title: Podocyte


title: Fezf2 promotes differentiation of Aire-expressing and mimetic epithelial populations regulating thymic homeostasis

city: San Francisco

first: James

last: Gardner

address: 505 Parnassus Ave

institute: UCSF

summary: Fezf2 has been implicated in shaping tissue-restricted antigen (TRA) expression and as an “Aire-like” factor in the thymus. Here we demonstrate loss of Fezf2 results primarily in a developmental block in mTEC development with pronounced expansion of Ccl21a-expressing mTECs at the expense of thymic tuft cells and most Aire-high and recently described post-Aire “mimetic” populations. While loss of either Aire or Fezf2 leads to a loss of post-Aire mimetic subtypes, their transcriptional programs are distinct; whereas Aire positively regulates the expression of thousands of genome-wide targets, Fezf2 orchestrates a restricted transcriptional program balanced between induction and repression that largely impacts TEC development. Strikingly, most Fezf2-repressed genes map to Ccl21a-expressing mTECs, suggesting Fezf2 maintains a cellular state conducive to the development of Aire-expressing mTECs and downstream access to terminally differentiated mimetic programs. At least some mimetic cell programs appear to have functions beyond simply serving as antigen reservoirs; thymic microfold cells (M cells) organize the medullary B cell niche in a Ccr6-dependent manner and promote IgA class-switching, analogous to Peyer’s Patches. In Aire and Fezf2 KO mice, where development of thymic M cells is impaired, B cell class-switching is similarly disrupted. Therefore, our data reveal Fezf2 as a gatekeeper of mTEC terminal development which cooperates with Aire to allow the full program of medullary epithelial diversity, supporting unexpected layers of mimetic cell function that impact thymic homeostasis beyond antigen diversity.

overall_design: WT control (3 replicates), Fezf2 KO, and Aire KO CD45-, EpCAM+ TECs were sorted from C57BL/6 mice for scRNA-seq analysis of major TEC subpopulations

first: Xian

last: Liu

first: Joe

last: Germino

first: Yi

first: Jared

last: Balolong

first: Hong

last: Sun

first: Irina

last: Proekt

first: Vasilis

last: Ntranos

first: Mark

middle: S

last: Anderson

middle: M

first: Corey

last: Miller


title: Bacteria-derived indole-3-lactic acid affects epithelium-macrophage crosstalk during intestinal inflammation through regulating signaling and metabolic pathways [EC]

city: tianjin

first: Yu

last: kaiyuan

address: Meteorological Station Road 22

institute: Tianjin Medical University

summary: To investigate the the effect of EC-TMU supernatant on on intestinal epithelial cells, SW480 cells were stimulated with EC-TMU supernatant.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of SW480 cells stimulated with EC-TMU supernatant.

first: Kaiyuan

last: Yu

first: Qianqian

first: Xuan


title: Sex-(in)dependent Signatures of Estrogen Exposure: Transcriptomic, Morphological, and Histological responses in Embryonic Japanese Quail (Coturnix japonica)

city: Ste-Anne-de-Bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary: The present study aims to assess the importance of sex in designing toxicological experiments that are based on avian early-life stage tests and transcriptomics. The present study explores sex-dependent and -independent gene expression of embryonic Japanese quail after ethinylestradiol (EE2) exposure. EE2 was dissolved in dimethyl sulfoxide and injected into the air cell of eggs prior to incubation at nominal concentrations of 0 and 3.33 µg/g egg weight. At embryonic day 9, the left lobe of the liver was collected from 5 embryos per sex per treatment group for transcriptomic analysis.

overall_design: Liver mRNA profiles of male and female Japanese quail at embryonic day 9 following single exposure to either solvent or ethinylestradiol solution at embryonic day 0

first: Ejimedo

last: Madogwe

first: Emily

last: Boulanger

first: Raj

last: Duggavathi

first: Doug

last: Crump

first: Jessica

last: Head


title: Glucagon receptor agonism and treatment withdrawal effect on liver transcriptomes of diet-induced obese mice

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Glucagon is historically viewed as the main counter-regulatory hormone to insulin in glucose homeostasis. Although chronic glucagon receptor (GCGR) agonism induces hyperglycemia and glucose intolerance, acutely it also improves insulin secretion and action. Surprisingly, we found chronic treatment with the selective, long-acting GCGR agonist, IUB288, improved glycemia 4h after the last injection and hyperglycemia after 12h, compared to vehicle-treated controls, suggesting chronic GCGR agonism is not exclusively hyperglycemic. These periods of glycemic improvement were associated with enhanced AKT phosphorylation, despite control-like insulin levels, and could not be replicated by short acting GCGR agonists. Surprisingly, 4d IUB288 treatment in diet-induced obese (DIO) mice reduced ad libitum glycemia for a longer duration than observed in chow IUB288-treated mice. IUB288 treatment also increased glucose infusion rate, suppression of endogenous glucose production, and AKT phosphorylation during hyperinsulinemic-euglycemic clamps.

overall_design:
Livers were isolated from DIO mice treated for IUB288 for 4 days, at 4 hours or 22 hours after the last IUB288 injection. Vehicle-treated livers were isolated 22 hours after the last injection.
Transcriptomes were generated via RNA-seq in 8 biological replicate mice per treatment group (vehicle, 4 d-4 h IUB288, 4d=22 h IUB288).

first: Shelly

last: Nason

first: William

middle: C

last: Roell

first: Kirk

last: Habegger


title: Effect of nimodipine on gene expression during TGF-β induced fibrotic phenotype switching of human orbital fibroblasts

first: Qian

last: Chen

state: Guangdong Province

address: No. 54 Xianlie South Rd

department: Zhongshan Ophthalmic Center

institute: Zhongshan Ophthalmic Center

summary: To investigate the effects of nimodipine on TGF-β induced fibrotic phenotype switching of human orbital fibroblasts, we performed the RNA sequencing of human orbital fibroblasts (OFs) derived from Graves’ ophthalmopathy (GO) patients and co-cultured with TGF-β for 24 hours,with or without nimodipine pretreatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human orbital fibroblasts (OFs) co-cultured with TGF-β for 24 hours,with or without nimodipine pretreatment.

first: Quanyu

first: YunWei

last: Hu

first: Dan

last: Liang


title: Indolent primary cutaneous B cell lymphomas resemble persistent antigen reactions without signs of dedifferentiation

city: Vienna

first: Johannes

last: Griss

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary: Primary cutaneous B-cell lymphomas comprise a heterogeneous group of extranodal non-Hodgkin lymphomas. While primary cutaneous diffuse large B cell lymphoma - leg type (pcDLBCL-LT) is highly aggressive, the two other subtypes, primary cutaneous follicle centre lymphoma (pcFCL) and primary cutaneous marginal zone lymphoma (pcMZL), also termed primary cutaneous marginal zone lymphoproliferative disorder, usually follow an indolent disease course.  To better characterise these most common types of primary cutaneous B cell lymphomas, we performed a comprehensive, single-cell RNA-sequencing based analysis of biopsies from pcFCL, pcMZL, and pcDLBCL-LT skin lesions, in comparison to samples from benign reactive B-cell rich lymphoid proliferation (rB-LP)  lesions, as well as gastric MALT lymphoma, nodal FCL and nodal DLBCL. Our data show that all non-aggressive forms of primary cutaneous B cell lymphoma, as well as rB-LP, show a persistent germinal centre reaction, with all accessory germinal centre-support cells and continuous somatic hypermutation within the expanded B cell clone. By contrast, malignant clones of pcDLBCL-LT lesions and gastric MALT showed absence of all of these features. Our data further shows that pcMZL originates from naïve and not post-germinal centre B cells as currently believed and observed in gastric MALT. The modest clonal expansion in pcMZL may therefore be the result of a recognition of a distinct (unknown) antigen. Conversely, in pcFCL, B cells show an (antigen-driven) expansion of a single clone with a germinal centre phenotype, presumably through acquisition of a driving mutation. The lack of further differentiation of B cells in pcFCL, in contrast to nodal FCL, may explain its indolent clinical course. Our data indicates that in contrast to highly aggressive cutaneous B cell lymphoma (pcDLBCL-LT), pcMZL, and pcFCL, similar to rB-LP are characterised by a functional germinal centre reaction driven by antigen recognition and supports the classification of pcMZL as a lymphoproliferative disease.

overall_design:
Samples from primary cutaneous marginal zone (pcMZL), follicle center (pcFCL), and diffuse large B cell lymphoma leg type (pcDLBCL-LT) where compared to reactive B cell rich lymphoid hyperplasia (rB-LP) and gastric malt lymphoma (MALT).

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Submitter states that: due to restrictions from the ethics review board, we are not allowed to release the respective RAW data
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first: J

first: S

last: Gansberger

first: I

last: Oyarzun

first: M

last: Drach

first: V

last: Nguyen

first: L

middle: E

last: Shaw

first: U

last: Mann

last: Porkert

first: W

last: Weninger

last: Dolak

first: B

last: Aschenbrenner

last: Lichtenberger

first: C

last: Wagner

last: Simonitsch-Klupp

last: Farlik

last: Jonak

first: P

last: Brunner


title: Hnf1a mutation in insulin producing beta-cells affect cell function and identity in young and old mice

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

summary:
Purpose: Hnf1a is an important regulator of pancreas development. Mutation in this gene in humans lead to Maturity Onset Diabetes of the Young 3. Previous studies have shown that Hnf1a is important in function of insulin producing cells. However, they have not payed attention to islet cell identity, which we have focused on.
Methods: Male WT mice or mice carrying either a single (htz) or both (hmz) floxed alles of the Hnf1a gene specifically in insulin producing beta-cells controlled by RIP-cre were maintainted in normal housing condition and glyceamia were monitored twice a week. Islet cells were isolated from 6 or 40 weeks old mice of each group and mRNA were extracted before shipping to Qiagen for analysis.
Results: Mice carrying the floxed Hnf1a in beta-cells were mildly hyperglyceamic with alterations in expression of important cell identiy genes, potentially more sever with age.

overall_design: mRNA from pancreatic islets from male RIP-cre Hnf1a flox mice of 6 or 40 weeks.

first: Thomas

middle: A

last: Legøy

first: Andreas

middle: F

last: Mathisen

first: Luiza

last: Ghila


title: Microglial CLEC7A restrains amyloid beta plaque pathology in a mouse model of Alzheimer's disease

status: Public on Dec 29 2025

city: Charlottesville

first: Aman

last: Manglamurti

state: Virginia

address: 409 Lane Rd.

department: Neuroscience

institute: University of Virignia

summary: BACKGROUND: CLEC7A is a surface receptor that is highly upregulated on microglia in many Alzheimer’s disease (AD) models. Little is currently known about the role that microglial CLEC7A signaling plays in AD-related pathogenesis. METHODS: We utilized an inducible, central nervous system (CNS) macrophage-specific knockout of Clec7a to evaluate the role of CLEC7A in the 5xFAD mouse model of AD at 5 months of age. We used immunofluorescence microscopy, single nuclei RNA-sequencing, along with biochemical assays to evaluate plaque burden, microglial activity, and neuronal health. RESULTS: CNS macrophage-targeted deletion of CLEC7A in 5xFAD mice led to a two-fold increase in plaque burden, exacerbated neuritic dystrophy, and altered expression of neuronal health genes, but did not appreciably impact microglial activation, plaque engulfment, or disease-associated microglia (DAM) acquisition. DISCUSSION: These findings identify protective roles for CLEC7A in AD-related amyloidosis and suggest that CLEC7A-targeting therapeutics may offer promising strategies to treat AD.

overall_design: Comparison of CNS cell types using single-nuclei RNA sequencing of samples derived from brain tissue of 5xFAD (Alzheimer's disease pathology animals) and 5xFAD mice with inducible, conditional loss of Clec7a expression in CNS macrophages.

last: Mangalmurti

first: Kristine

last: Zengeler

first: Ava

last: Hollis

first: Emily

last: Golden

first: Gabrielle

last: Riddlemoser

first: John

last: Lukens


title: Effect of OMVs on gene expression of primary alveolar epithelial cell

city: Nanjing

first: Chen

last: Jing

state: Jiangsu

address: No.87, Dingjiaqiao, Gulou District

department: Department of Critical Care Medicine,

institute: Zhongda Hospital, School of Medicine, Southeast University

summary: The alveolar epithelial cell injury is essential for the initaitation and maintenance of inflammatory of lung in ARDS. Outer membrane vesicles (OMVs) are nanoparticles produced by the extrusion of the outer membrane of gram-negative bacteria deliver a range of bacterial molecules to host cells. Recent findings describe OMVs play vital roles in bacterial colonization, delivery of virulence factors, and disease pathogenesis.  We here report OMVs as a key regulator of  gene expression in primary alveolar epithelial cell.

overall_design: To investigate the effect of OMVs on alveolar epithelial cell, we isolated primary alveolar epithelial cell and sitimulated by OMVs or PBS for 24h. We then performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression profiling analysis of RNA-seq data for PBS and OMVs stimulated alveolar epithelial cell.

first: Jing

last: Chen


title: Gene expression changes in lymphocytes and monocytes from patients with traumatic brain injury: A prospective case-control study

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Background: Traumatic brain injury (TBI) can alter various immune functions, including immunosuppression, and constitutes a risk factor for nosocomial infections and organ dysfunction. Although TBI can induce a decline in immune cell function, the detailed mechanisms remains to be elucidated. This study aimed to characterize the mechanism of immunosuppression caused by TBI using a comprehensive transcriptome analysis of immune cells. Methods: Three patients with traumatic brain injury and acute subdural hematoma were admitted to our hospital. We focused on three major subsets of immune cells responsible for the immune response: CD4+ T cells, CD8+ T cells, and monocytes. We evaluated the changes in immune function after injury using comprehensive transcriptome analysis. Blood samples were collected immediately after admission and one week later, and the data were compared with those of healthy volunteers. Results: CD4+, CD8+ T cells, and monocytes, the expression of pathways involved in cellular metabolism—including oxidative phosphorylation, mTORC1 signaling, MYC targets V1 and V2, and the unfolded protein response—was downregulated on day 7 compared with day 1. These findings suggest a transition from marked immune activation and metabolic upregulation on day 1 to an attenuated immune response by day 7. In CD4⁺ T cells, pathways associated with tissue remodeling and repair, such as Hedgehog signaling and epithelial–mesenchymal transition (EMT), were upregulated from day 1 to day 7, indicating a shift from inflammatory responses toward inflammation resolution and tissue repair. Conclusions: Comprehensive transcriptome analysis might suggest impaired immune responses and pathway in CD4+ T cells, CD8+ T cells, and monocytes. This study contributes to the further elucidation of the mechanisms of immunosuppression due to traumatic brain injury.

overall_design: We performed a retrospective, observational, case-control, single-center study.  Samples from the patients were collected at two timepoints: within 24 h of admission and on the 7th or 8th day of admission. PBMCs were isolated from fresh whole blood. Two panels were used to identify subsets of CD4+ T cells, CD8+ T cells, and monocytes from PBMCs. Total RNA was extracted from the sorted cells. Whole-transcriptome sequencing was performed on an Illumina NovaSeq 6000 platform using a pair-end sequencing strategy.

first: Hiroshi

last: Ito

first: Masakazu

last: Ishikawa

first: Hisatake

last: Matsumoto

last: Ogura

last: Okuzaki

first: Jun

last: Oda


title: Elevated exosomal Nm23-H1 subdues the pro-migratory potential of breast cancer cell-derived exosomes by altering downstream signaling cascades

first: Vasu

last: Saini

address: Clearwater Bay

institute: The Hong Kong University of Science and Technology

summary:
Purpose: Although Nm23-H1 lacks secretion signal peptide, its presence in the extracellular space and extracellular vesicles (EVs) is widely reported. Proteomics profiling revealed that EVs released by cancer cells may contain Nm23-H1 proteins but the role of vesicular Nm23-H1 remains unknown. Here, we investigated the function of vesicular Nm23-H1 by performing transcriptome analysis of the recipient post 24 h of PBS (control) or exosome treatment.
Methods: MCF-7 cells were treated with PBS or exosomes for 24 h. Cells were lysed in TRIzol. RNA quality was verified with Agilent 5400 fragment analyzer prior to library preparation. SMART-Seq2 library construction was performed, and sequencing was carried out in 2×100 cycle paired-end mode on a BGI DNBSEQ-G400 sequencer. FASTQ raw read files were trimmed using cutadapt to remove adapter sequences, primers, poly-A tails, and other types of unwanted sequences. The trimmed reads were then be mapped to the genome (UCSC hg38) using STAR with default parameters. Reads were quantified and differentially expressed genes (DEGs) were identified using DEBrowser (v1.19.1) as a graphical interface to DESeq2 with significance considered at q-value ≤ 0.05 and absolute fold change ≥ 1.2. qRT–PCR validation was performed using SuperScript® III First-Strand Kit and LightCycler 480 SYBR Green I assays.
Results: We examined the changes in the transcriptome of MCF-7 cells post exosome treatment. Polyadenylated RNA-sequencing was performed on RNA isolated from the recipient cells post 24 h of PBS (control) or exosome treatment. Upon 231 exo treatment, changes in the transcript levels of 122 differentially expressed genes (DEGs) were observed, whereas 231/H1 exo treatment induced a differential expression of 449 genes. A common set of 45 genes was found to be regulated by both 231 exo and 231/H1 exo treatments. More importantly, the comparison between 231/H1 exo and 231 exo treatments revealed 107 differentially expressed genes.
Conclusions: Our transcriptome analysis of the recipient cells post exosome treatment revealed multiple genes that are regulated upon exosome treatment. Exosomes with an elevated level of Nm23-H1 caused alterations in the transcript level of multiple cancer-related genes in the recipient cells. Moreover, it stimulated type I interferon signaling via STAT1 phosphorylation. These results indicate an atypical signaling pathway mediated by the uptake of exosomes with an elevated level of Nm23-H1, which may account for the anti-metastatic effect of Nm23-H1 in the tumor microenvironment.

overall_design: Deduce the differences in the downstream signaling orchestrated by the action of 231 exo and 231/H1 exo

first: Judy

last: Yam

first: Yung

middle: H

last: Wong


title: Wnt Regulates Cellular Differentiation and Retinoid Metabolism Genes in the Mouse Stomach

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

summary: Background & Aims: While recognized as a key regulator of gastrointestinal tissues, Wnt function in the stomach is poorly understood. This study aimed to define Wnt functions and identify Wnt-regulated genes in the stomach. Methods: Wnt signaling was localized using reporter mice. Proliferation was studied after canonical Wnt inhibition in vivo using Sox2-CreERT2; Ctnnb1fl/fl mice and in vitro using gastric organoid cultures. Wnt-regulated genes and potential effector pathways were identified by bulk RNAseq analysis of corpus and antral organoids 24 hours after Wnt inhibition. Retinoid metabolic components were localized in control and Wnt-inhibited mouse stomach by immunostaining. Results: Wnt signaling cells mapped to the base and proliferative region in both corpus and antrum. Wnt inhibition in vivo reduced proliferation and led to gastric stem cell loss. Cell signature analysis of RNAseq data revealed that gastric organoids adopt a surface cell transcriptional profile following Wnt inhibition instead of a basal cell profile. Furthermore, retinoid metabolism terms were differentially expressed after Wnt inhibition, with both corpus and antrum displaying decreased expression of retinoic acid target genes. Immunostaining mouse stomach showed differential localization of retinoid metabolic components in luminal pit cells (ALDH3A1), and basal chief/deep mucous cells (STRA6), with expression changes after b-catenin deletion consistent with the organoid analysis. Conclusion: Wnt signaling is required for gastric stem cell survival and promotes differentiation of cell types at the gland base. Retinoid metabolism is a candidate Wnt-regulated pathway, with cell-specific expression of key components. Localization of the retinol transporter STRA6 to high-Wnt cells at the gland base suggests that they are retinoic acid signaling cells.

overall_design: RNA-seq of gastric corpus and antral organoids derived from WT mouse gastric glands. On day 4 post-passage, 3 independent gastric organoid lines were treated with the Wnt inhibitor XAV939 with removal of exogenous Wnt/Rspondin and supplementation with Noggin-1 , or with vehicle (DMSO) in normal culture media.

first: Elizabeth

last: Delgado

first: Elise

last: Hibdon

first: Theresa

last: Keeley

first: Christopher

middle: Q

last: Huynh

first: Linda

last: Samuelson


title: Acute Myeloid Leukemia Promotes the Development and Function of Type 3 Innate Lymphoid Cells

city: Columbus

first: Bethany

middle: L

last: Mundy-Bosse

state: OH

address: 460 W 12th Ave

department: Department of Internal Medicine

institute: The Ohio State University

summary: Acute myeloid leukemia (AML) is an aggressive hematologic malignancy with poor overall survival. Understanding how dysregulated immunity contributes to the development and progression of AML is an active area of investigation. Prior work has demonstrated functional defects in natural killer (NK) cells; however, the role of non-NK innate lymphoid cells (ILCs) in AML is not completely understood. Conventional ILC3s are non-cytotoxic and regulate mucosal immunity by secreting cytokines. Prior studies showed that AML blasts secrete aryl hydrocarbon receptor (AHR) ligands, and AHR is required for ILC3 development and function. In this study, we discovered an expansion of ILC3s in both a murine model of AML and in AML patients. Modeling studies demonstrated ILC3 expansion was mediated by AHR activation. ILC3s in the setting of AML had increased cytokine production, and co-culture of ILC3s significantly increased AML colony formation, which was mediated by TNFα. Furthermore, co-transfer of ILC3s with AML led to more rapid disease progression in vivo. These data support a model in which AML promotes ILC3 expansion and function to aid AML growth and survival.

overall_design: BM from leukemic or WT transplanted mice were enriched for ILCs and progenitors by negative selection and sorted as Lin negative (CD3, CD14, CD19, Ter119, TCRβ, Gr1, Fcεr1α) CD45.1+ live cells. These cells were subjected to paired-end single cell RNA-sequencing using 10X Genomics Single Cell 3’ v3.1 and libraries were sequenced using NovaSeq SP instrument.

first: Thanh Thanh

last: Dinh

first: Matthew

last: Lordo

first: Chinmayee

last: Goda

first: Patrick

last: Collins

first: Adrienne

last: Dorrance

last: Mundy- Bosse


title: DOT1L-mediated CDK9 methylation is essential for DNA double-strand break repair

city: Seoul

first: Yugyeong

last: KIM

address: 84, Heukseok-ro

department: Life science

country: South Korea

institute: Chung-Ang University

summary: P-TEFb is a key regulator of transcription elongation and is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. DOT1L is a histone H3K79 methyltransferase. Here, we show that treatment with the DOT1L inhibitor EPZ-5676 induces transcriptome changes in HCT116 cells. We further demonstrate that DOT1L methylates CDK9 at lysine 56 and that CDK9 methylation-deficient mutant  K56A reshapes genome-wide CDK9 occupancy. Notably, changes in CDK9 occupancy are particularly pronounced at double-strand break (DSB)-related genes and are associated with the regulation of their transcription. This idataset includes RNA-seq and ChIP-seq data generated from HCT116 cells.

overall_design: ChIP-seq were pereformed in CDK9-knockdown HCT116 cells reconstituted with either CDK9 WT or K56A mutant.

last: Kim

first: Hyebin

last: Park

first: Sang Beom

last: Seo


title: Epigenetic Signatures of Brain Aging by Single Nucleus Methylation Sequencing [FC-9mo-m-020]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating aging effects on the epigenomic features of brain is critical to understand brain functional decline and neurodegeneration. Single nucleus methylation sequencing was applied to brain regions of both male and female mouse at the age of 2, 9 and 18 months. We use these data to identify the epigenomic changes with aging in mouse brains.

overall_design: Apply snmC-seq3 to mouse brain regions to identify aging effects on epigenomics

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Jacinta

middle: D

last: Lucero

first: Julia

middle: K

last: Osteen

first: Huaming

last: Chen

first: M

last: Behrens


title: CRATER tumor niches facilitate CD8+ T cell engagement and correspond with immunotherapy success [Spatial transcriptomics]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: T cell-mediated tumor killing underlies immunotherapy success. Here, we used long-term in vivo imaging and high-resolution spatial transcriptomics of zebrafish endogenous melanoma, as well as multiplex imaging of human melanoma, to identify domains facilitating the immune response during immunotherapy. We identified cancer regions of antigen presentation and T cell engagement and retention (CRATERs) as pockets at the stroma-melanocyte boundaries of zebrafish and human melanoma. CRATERs are rich in antigen-recognition molecules, harboring the highest density of CD8+ T cells in tumors. In zebrafish, CD8+ T cells formed prolonged interactions with melanoma cells within CRATERs, characteristic of antigen recognition. Following immunostimulatory treatment, CRATERs expanded, becoming the major sites of activated CD8+ T cell accumulation and tumor killing. In humans, elevation in CRATER density in biopsies following immune checkpoint blockade (ICB) therapy correlated with a clinical response to therapy. CRATERs are structures that show active tumor killing and may be useful as a diagnostic indicator for immunotherapy success.

overall_design: A 10um slice of BRAF(V600E)/p53mitfa specific null/Tyrosinse mitfa specific null zebrafish melanoma tumor was analyzed using Slide-SeqV2 spatial transcriptomics.

first: Georgia

last: Stirts

first: Sophia

last: Liu

first: Qiyu

last: Gong

first: Irving

last: Barrera

first: Aya

last: Ludin

first: Fei


title: Comparative analysis of DEE model brain transcriptomes

city: Dunedin

first: Caroline

last: Beck

state: Otago

address: 340 Great King Street, North Dunedin

department: Zoology

country: New Zealand

institute: University of Otago

summary: Developmental and epileptic encephalopathy (DEE) caused by rare mutations in 118 different genes leads to profound disability and seizures starting in infancy. To generate models of developmental and epileptic encephalopathy, we used CRISPR/Cas9 to knock down 2 causative genes, ap3b2 (DEE48) and eef1a2(DEE33) in Xenopus laevis tadpoles and confirmed editing and seizure-like behaviours. We then analysed the brains of these tadpoles using transcriptomics, to see how development is changed by loss of function of these genes. We found that many genes associated with GABA signalling, Na and Ca2+ ion transport, axon guidance, dendrite development and transport across the blood brain barrier and are down regulated in both models compared to controls. This shows how DEE caused by loss of fuction of different genes that do not code for known functionally linked proteins can lead to similar brain developmental phenotypes and seizure suceptibility.

overall_design: Fertilised embryos from two female X. laevis frogs were injected with Spy-Cas9-NLS bound to one of three sgRNAs targeting ap3b2, eef1a2 (both generating truncated LOF edits) or a scrambled guide with no targets (control). This generates mosiac CRISPants, in the same wildtype background, with around 80-90% of the target gene edited. We compared the tadpole brain transcriptomes these loss of function models of DEE48 and DEE33 with controls that had been injected with the scrambled sgRNA (no editing). Due to the small size of stage 47 tadpole brains, we pooled 6 animals for each sample. Five biological replicates were analysed for each condition. We sought differentailly expressed genes between controls and either eef1a2 or ap3b2 CRISPant brains, and found many genes and pathways in common between the two DEE models.

first: Beck

last: Caroline

first: Robson

last: Sam

first: Banerjee

last: Sulagna


title: Reduction of the HIV-1 reservoir in T cells from people with HIV-1 on suppressive antiretroviral therapy using expanded natural killer cells

city: Cleveland

first: Konstantin

last: Leskov

state: OHIO

address: 2109 Adelbert Rd, Wood W200

department: Molecular Biology and Microbiology

institute: Case Western Reserve University School of Medicine

summary: Treatment with latency-reversing agents (LRAs) alone has been ineffective in reducing HIV-1 reservoirs in people living with HIV-1 (PLWH) who are on antiretroviral therapy (ART), due to inefficiencies in reservoir reactivation and adaptive immune responses. However, NK cells activated with cytokines may be able to target HIV-1 reservoirs more effectively. To explore the therapeutic potential of NK cells, we expanded blood NK cells from multiple donors ex vivo into CD56brightCD16+ “eNK” cells using artificial antigen-presenting cells (aAPCs) expressing membrane-bound IL21. eNK cells express multiple activating receptors and are highly cytotoxic against specific target cells. They can also kill HIV-infected CD4+ T cells via antibody-dependent cell-mediated cytotoxicity (ADCC) using broadly neutralizing antibodies (bNAbs) against HIV-1 Env gp120/gp41. Notably, eNK cells from PLWH on ART efficiently killed autologous HIV-1+ T cells reactivated by a combination of vorinostat (SAHA) and IL-15 or an IL-15 superagonist (N-803), as evidenced by declines in proviral load, inducible HIV-1 mRNA, and virus release. Adoptive immunotherapy with eNK cells combined with LRA treatment thus presents a promising strategy to reduce the latent HIV-1 reservoir in PLWH.

overall_design: NK cells were isolated from cryopreserved PBMCs of PLWH. Non-expanded NK cells are referred to as primary NK cells while NK cells expanded with C9.K562-mbIL21 aAPCs for 2 weeks are referred to as "eNK". In this experiment we are comparing the transcriptional profiles of primary NK cells vs eNK cells.

first: Mary Ann

last: Checkley

first: Cheryl

last: Cameron


title: Bacteria-derived indole-3-lactic acid affects epithelium-macrophage crosstalk during intestinal inflammation through regulating signaling and metabolic pathways

first: Yu

last: kaiyuan

address: Meteorological Station Road 22

institute: Tianjin Medical University

summary: To investigate the underlying molecular mechanism of ILA effect on CCL2/7 expression, we examined the gene expression profiles of SW480 cells treated by LPS and ILA using RNA sequencing

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of SW480 cells.

last: Kaiyuan


title: Remodeling of Suppressive Melanoma Microenvironments by Particle-Mediated Modulation of the STING/IL-6/PD-L1 Axis Improves Tumor Immunity and Survival

city: New York

first: Genomics-core-facility

last: WCM

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: Despite the considerable success of clinically approved immune-based therapies for treating advanced melanoma, a significant fraction of these patients are not responsive due to mechanisms engaged by the tumor to evade the immune system. Here we report the surprising finding that a clinically validated and tunable self-therapeutic ultrasmall silica nanoparticle prolongs survival in a highly resistant melanoma model in combination with IL-6 and PD-L1 inhibition through its activation of the STING/IL-6/PD-L1 axis and reprogramming of the tumor microenvironment (TME) towards a proinflammatory phenotype. Induction of significant cytotoxic and anti-tumor inflammatory responses lead to differential activation of immune cell populations in a model- and CD8-dependent manner via Type I/II interferon pathways after systemic particle injection. Importantly, these immunostimulatory responses accompany significant reductions in cell populations and receptors driving suppressive activities. Mechanistic insights highlight the potential clinical utility of this platform to maximize anti-tumor immunity and efficacy by subverting suppressive components in the TME.

overall_design: Experimental samples were treated with or without C' dots. Total RNA was extracted from FFPE sections using the Quick RNA FFPE kit (Zymo Research) and its integrity checked using a 2100 Bioanalyzer with a DV200 reading as 47-61% for all samples before downstream processes such as library preparation and sequencing.

first: Michelle

last: Bradbury


title: Dominant-negative TP53 mutations potentiated by the HSF1-regulated proteostasis network

city: Cambridge

first: Vincent

last: Butty

address: 77 Massachusetts Avenue 68-317A

department: Biology

institute: MIT

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

overall_design: Refer to individual Series


title: LXR agonism elicits a pre-effector state in naïve CD8+ T cells [ATAC-seq]

city: Berlin

first: Benjamin

last: Ostendorf

address: Augustenburger Platz 1

institute: Charité University Medicine

summary: Here, we assess chromatin accessibility profiles of naïve CD8+ T cells after 24 hours of exposure to either the LXR agonist RGX-104 or DMSO in the absence of TCR stimulation.

overall_design: ATAC-seq of naïve CD8+ T cells in absence or presence of a synthetic LXR agonist.


title: Hnf1a mutation in insulin producing beta-cells affect cell function and identity in adult mice

first: Simona

last: Chera

summary:
Purpose: Hnf1a is an important regulator of pancreas development. Mutation in this gene in humans lead to Maturity Onset Diabetes of the Young 3. Previous studies have shown that Hnf1a is important in function of insulin producing cells. However, they have not payed attention to islet cell identity, which we have focused on.
Methods: Male WT mice or mice carrying either a single (htz) or both (hmz) floxed alles of the Hnf1a gene specifically in insulin producing beta-cells controlled by RIP-cre were maintainted in normal housing condition and glyceamia were monitored twice a week. Islet cells were isolated from 12 or 24 weeks old mice of each group and mRNA were extracted before shipping to Qiagen for analysis.
Results: Mice carrying the floxed Hnf1a in beta-cells were mildly hyperglyceamic with alterations in expression of important cell identiy genes, potentially more sever with age.

overall_design: mRNA from pancreatic islets from male RIP-cre Hnf1a flox mice of 12 or 24 weeks.

first: Thomas

last: Legøy

first: Andreas

last: Mathisen

first: Luiza

last: Ghila


title: Piezo1 Knockdown Activates PI3K/AKT and Enhances SPP1 to Drive M2 Macrophage Polarization and Reduce Cardiac Inflammation

city: kunming

first: yunnhan

last: zhang

address: 528 Shahe Road

institute: Fuwai Yunnan Cardiovascular  Hospital

summary: We have successfully established a mouse model with myeloid cell-specific knockdown of Piezo1.   The intraperitoneal injection of lipopolysaccharide (LPS) resulted in a significant increase in cardiac macrophage infiltration, as well as an increase in the expression of inflammatory factors and the inflammatory response.   However, myeloid cell-specific knockdown of Piezo1 impaired this response, leading to an increase in macrophage polarization towards the M2 type and the decreased inflammatory response.   As a result, myocardial injury caused by sepsis was attenuated.   We have also demonstrated that the PI3K/AKT pathway is significantly activated after Piezo1 knockdown, resulting in reduced myocardial dysfunction.

overall_design: RNA-sequencing profiling of macrophages from Piezo1^flox/flox and Piezo1^flox/flox Lyz2-Cre C57BL/6J mice following lipopolysaccharide (LPS) treatment.

first: Yunhan

last: Zhang

first: Ying

first: Jiaoyan

last: Song

first: Ziwen

last: Zhao

first: Wenhao

last: Ju

first: Hao

first: Shuang

last: Li


title: Gene expression profiles of ovarian endometriotic cyst stromal cells treated with tucidinostat

city: Yufu-shi

first: Saki

last: Aso

address: 1-1 Hasamamachi Idaigaoka

institute: Oita University

summary: We previously demonstrated that the expression of histone deacetylase (HDAC) 10 is elevated in ovarian endometriotic cyst stromal cells (ECSCs) compared to normal endometrial stromal cells (NESCs). HDAC10 inhibitor, tucidinostat (10 μM) inhibited the cell proliferation of ECSCs and induced the apoptosis and G0/G1 cell cycle arrest of these cells. GThe objective of this study to unveil the role of HDAC10 in the pathogenesis of endometriosis. We  cultured ECSCs with an HDAC10 inhibitor, tucidinostat (10 μM), isolated the total RNAs, and subjected to next-generation RNA sequencing to identify the target genes of HDAC10. Gene Ontology analysis identified upregulated genes. We will introduce these genes into endometriosis stromal cells and examine whether they induce cell proliferation inhibition and apoptosis promotion similar to HDAC10 inhibitors. This will help us evaluate whether HDAC10 inhibitors are promising candidates for endometriosis treatment. We found that somatostatin receptor 2 (SSTR2), dachshund homolog 11 (DACH1), and interferon regulatory factor 6 (IRF6) are the possible target genes of HDAC10.

overall_design: ECSCs isolated from 4 patients were placed on 10-cm culture plates (Corning, New York, NY, USA) and incubated with or without tucidinostat (10 M, Cat. No. S8567, Selleckchem, Houston, TX, USA) for 48 h. Then, total RNA was extracted with an RNeasy Mini kit (Qiagen, Valencia, CA, USA). The quality of the extracted RNA was confirmed by measuring the absorbance at 230 nm, 260 nm, and 280 nm using a spectrophotometer (NanoDrop 2000, Thermo Scientific, Wilmington, DE, USA) and by an Experion System (Bio-Rad Laboratories, Hercules, CA, USA). The samples were then subjected to RNA-sequence analyses .

first: Kaei

last: Nasu

first: Yoko

last: Aoyagi

first: Kentaro

last: Kai


title: Abrogation of Oncogenic RAS Signaling by a RAS(ON) Inhibitor Doublet Primes Immune-refractory KRASG12C-mutant NSCLC for Immune Checkpoint Blockade

city: Redwood City

first: Ximo

last: Pechuan-Jorge

address: 700 Saginaw Drive

institute: Revolution Medicines

summary: To address RAS pathway hyperactivation and targeted therapy resistance in KRASG12C-mutant NSCLC, we evaluated the potential of the RAS(ON) G12C-selective covalent inhibitor elironrasib and the RAS(ON) multi-selective inhibitor daraxonrasib combination to maximize RAS pathway suppression and forestall pathway reactivation in a series of preclinical models. We demonstrate that the RAS(ON) inhibitor doublet induces profound and sustained tumor regressions and overcomes the increased RAS pathway oncogenic flux that underlies resistance to inactive state–selective KRASG12C inhibitors in NSCLC. Additionally, in immune-competent preclinical models, the RAS(ON) inhibitor doublet enhances tumor immune recognition by boosting antigen presentation and remodeling the suppressive tumor microenvironment, thus promoting immune-dependent complete regressions and sensitization of an immuno-refractory model to checkpoint blockade. Collectively these findings provide a preclinical rationale for the evaluation of a targeted RAS(ON) inhibitor doublet therapy regimen in combination with immune checkpoint blockade in patients with KRASG12C-mutant NSCLC.

overall_design: Mice bearing NCI-H2122 subcutaneous xenograft tumors were treated with 7 consecutive daily doses of elironrasib at 100 mg/kg and daraxonrasib at 25 mg/kg as single agents or in combination. Tumors were harvested at 8 and 24 hours post the last dose (n = 3 per time point) for bulk RNA sequencing analysis.  Mice bearing 3LL-ΔNRAS subcutaneous syngeneic tumors were treated for 8 consecutive daily doses of elironrasib at 30 mg/kg and daraxonrasib at 25 mg/kg as single agents or in combination. Tumors were harvested at 24 hours post the last dose (n = 5 per time point) for bulk RNA sequencing analysis


title: Effect of Dox-induced Cas13 expression in stable cell lines on the mouse transcriptome and co-cultured human PSCs

city: Dallas

first: Leijie

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

summary: In the mouse EpiSCs-iCas13 stable cell line, addition of doxycycline induces Cas13 expression, which further triggers collateral effects and slows down cell proliferation. In co-culture of mouse and human cells, under normal conditions, mouse EpiSCs hold a proliferative advantage, whereas human PSCs are at a disadvantage and show almost no growth. Upon doxycycline treatment in the co-culture, Cas13 expression in mouse cells triggers collateral effects that reduce their proliferation, thereby providing a relative advantage for human PSCs. As a result, the proliferation of human PSCs is markedly enhanced, showing a growth pattern more comparable to that observed in separate cultures of human PSCs.

overall_design: Cells from separate cultures and co-cultures, with or without doxycycline treatment, were collected on day 4. Total RNA was extracted, followed by RNA-seq and subsequent transcriptome analysis.

first: Bingbing

last: He

first: Jun

last: Wu