title: Developmental opioid exposure results in lasting transcriptome alterations in zebrafish (Danio rerio) embryos

city: Bozeman

first: Christa

last: Merzdorf

state: Montana

address: 109 Lewis Hall

department: MCB

institute: Montana State University

summary: The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well-documented, early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish (Danio rerio) embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant (Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL) and therapeutically relevant (Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL) from 2 to 24 hours post-fertilization (hpf), followed by another 24hrs of opioid-free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes (DEGs) than higher doses, potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total, 892 DEGs were identified across all conditions indicating continued differential gene expression well after cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix (ECM) organization, cell adhesion, and visual and nervous system formation. Key pathways include axon guidance, synapse formation, and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems, providing insights into the molecular mechanisms of opioid-induced alterations during development.

overall_design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent (FE; 0.629 pg/mL), fentanyl therapeutic (FT; 3.14 ng/mL), oxycodone effluent (OE; 10.6 pg/mL), and oxycodone therapeutic (OT; 35.14 ng/mL). Opioid exposure occurred from 0 to 24 hpf in zebrafish embryos, embryos were washed at 24hpf and allowed to develop in non-opioid solution until 48 hpf. At 48hpf, 50 embryos were sample were harvested for total RNA, cDNA library prep, and RNAseq.

first: North

last: Ryan

first: Mears

last: Lucas

first: Bothner

last: Brian

first: Dlakic

last: Mensur

first: Merzdorf

last: Christa


title: Overexpression of Mir-197 und Mir-769 in mouse iPSCs

status: Public on Jun 04 2025

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

type: Expression profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in many essential biological processes. Recently, targeted searches for human miRNA orthologs revealed that 15 miRNA families are lost in the Eumuroidea lineage, including the model organisms mouse and rat, but not in other mammals. We here characterize this loss in more detail and investigate potential consequences for the Eumuroidean regulatory network. We confirm that the miRNA loss was not compensated by other miRNAs in rat or mouse, and we identify a significant overlap in the function of their target genes. We heterologously express two human miRNAs, Mir-197 and Mir-769, in mouse inducible pluripotent stem cells (iPSCs) and compare effects on the transcriptome to those of induced miRNA levels in human iPSCs. This reveals overlapping sets of down-regulated mRNAs in the two species, likely representing remnants of an ancient miRNA-dependent regulatory network that predates the diversification of the human and mouse lineages.  The consequent elimination of established miRNA regulatory connections on the Eumuroidean lineage is accompanied by the lineage-specific loss of 37 transcription factors. Our results indicate that mouse and rat have modified their regulatory network of gene expression on transcriptional and post-transcriptional level compared to other vertebrate model organisms. This regulatory shift likely adds noise to studies of gene expression that, for example, use murine cells to study human diseases.

overall_design: Differential gene expression analysis upon overexpression for 48h of either miRNA Precursor hsa-miR-197-3p or miRNA Precursor hsa-miR-769-5p in murine iPSCs compared to miRNA Precursor Negative Control

first: Felix

last: Langschied

first: Matthias

middle: S

last: Leisegang

first: Fabian

last: Hahner

first: Ralf

middle: P

last: Brandes

first: Ingo

last: Ebersberger


title: Enhancement of memory and emotional functions by long-term ingestion of protease-treated porcine liver extract in mice

city: Saga city

first: Taiga

last: Kurihara

state: Saga (佐賀県)

address: 5-1-1 Nabeshima

country: Japan

institute: Saga University

summary: The relationship between diet and brain functions has garnered attention. Previous studies have shown that ingesting a protease-treated porcine liver decomposition product (PLDP) improves cognitive function in humans. In this study, we investigated the effects of PLDP ingestion on cognitive and emotional functions in mice. Mice were fed a PLDP-enhanced diet for 16 weeks and subjected to various behavioral assessments. PLDP ingestion enhanced long-term memory in Barnes maze test. Moreover, mice fed the PLDP diet exhibited reduced anxiety- and depression-like behaviors as evidenced by their performance in open-field, elevated plus maze, marble-burying, and forced swim tests. They also increased locomotor activity. RNA sequencing analysis of the brain tissue revealed substantial changes in gene expression, particularly in pathways associated with learning, memory, and anxiety regulation. Collectively, these results suggest that PLDP induces changes in gene expression associated with brain function, potentially contributing to the enhancement of cognitive function and psychological health. Furthermore, our findings not only enhance our understanding of the relationship between nutrition and brain function but also indicate the potential of interventions utilizing dietary components, such as PLDP, to support cognitive function and psychological health.

overall_design:
Mice were fed a PLDP-enhanced diet for 16 weeks
Total RNA was extracted from mouse brains following behavioral experiments using TRIZOL reagent (Thermo Fisher Scientific, Waltham, USA), according to the manufacturer's instructions. Samples were subjected to TruSeq Stranded mRNA library preparation (Illumina) and sequenced on a NovaSeq 6000 (2 ×150 bp; Illumina, San Diego, CA, USA) for a 6-Gb coverage. In total, 2303 differentially expressed genes (1,271 upregulated and 1,032 downregulated genes) with p-values < 0.05 were further analyzed using Qiagen Ingenuity Pathway Analysis (IPA) software (QIAGEN, Valencia, CA, USA).

first: Takeshi

last: Uemura


city: WuHan

first: Donghao

last: Gao

state: Hubei

address: College of Life Sciences, Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei Province, China.

department: College of Life Sciences

country: China

institute: WuHan University

summary:
Infection of Pseudomonas donghuensis HYS strain and its fur deletion mutant in Caenorhabditis elegans was conducted to assess changes in the expression profile of Caenorhabditis elegans, and potential core virulence factors were identified by measuring the gene expression levels of the HYS colonizing the nematode's intestine.
Preliminary studies indicate that P. donghuensis HYS exhibits significant toxicity towards Caenorhabditis elegans, yet the underlying mechanisms of this pronounced toxicity remain unclear. Previous work identified several virulence factors contributing to the toxicity of HYS through detection and functional validation; however, the molecular mechanisms responsible for its strong toxicity have not been elucidated. Therefore, we aim to analyze the mechanisms underlying HYS's pronounced toxicity by examining the responses of infected Caenorhabditis elegans. The Ferric uptake regulator (Fur) is responsible for maintaining iron homeostasis in Gram-negative bacteria, and given that HYS possesses a greater iron uptake capacity than other common species in the same genus, such as Pseudomonas aeruginosa, we hypothesize that Fur may play a critical role in the strong toxicity exhibited by HYS. Consequently, we infected Caenorhabditis elegans with both HYS and its fur deletion mutant and analyzed the changes in the expression profile of Caenorhabditis elegans. We observed a significant reduction in toxicity following the deletion of fur, indicating that Fur regulates core virulence factors. To identify these core virulence factors, we conducted transcriptomic sequencing of the pathogenic bacteria under various conditions and performed a screening for virulence factors.

sample_organism:
Caenorhabditis elegans
Pseudomonas donghuensis

overall_design: Preliminary research in the laboratory revealed that the HYS strain produces substantial colonization within 24 hours of infecting the host, and unlike other pathogenic bacteria that infect C. elegans, HYS infection results in significant mortality of the nematodes within this timeframe. Therefore, to ensure the quantity of Caenorhabditis elegans and the quality of RNA extraction, we selected the 24-hour time point for nematode collection, which were rapidly frozen in liquid nitrogen for total RNA extraction. We utilized Escherichia coli OP50, which is minimally toxic to the nematodes, as a negative control, while the infected nematodes with HYS and fur mutant served as the experimental groups, with three biological replicates for each condition, comprising 1000 nematodes per sample. Following RNA extraction, high-throughput sequencing was conducted at Majorbio. For the pathogenic bacterial samples, we established the HYS strain grown on NGM plates as the control, while the HYS strain colonizing the nematodes constituted the experimental group, which, along with the HYS-infected nematodes, was processed as the same sample for dual-RNA seq. Due to the inability of the fur deletion mutant to form colonies, we included the fur mutant strain grown on NGM plates as another experimental group. The colonized HYS samples were obtained by homogenizing 1000 nematodes fed with the HYS strain for RNA extraction, while a total of 10^10 bacteria from those grown on NGM plates were required for total RNA extraction. Subsequently, all samples were sent to Majorbio for high-throughput sequencing. After sequencing, the results of the interactions between the nematodes and bacteria were identified using the Caenorhabditis elegans and HYS genomes, while other sequences were identified using a separate genome.

first: ZhiXiong

last: Xie

first: Yelong

last: Lin


title: Higher-Order Olfactory Threat Associations in the Amygdala-Posterior Piriform Cortex Network

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Fear, while crucial for survival, is a component of a myriad of psychiatric illnesses in its extreme. Persistent fear memories can form through processes such as second-order conditioning (SOC), during which a second-order conditioned stimulus (CS2) acquires significance by associating with a first-order conditioned stimulus (CS1). The neural circuitry underlying SOC, particularly the roles of sensory cortices, remains poorly understood. We explored the mechanisms of olfactory SOC in rats, focusing on the basolateral amygdala (BLA) and posterior piriform cortex (pPC). Our results demonstrate that NMDAR-dependent plasticity in both regions is essential for SOC. The BLA mediates the CS2-CS1 association, while the pPC, receiving inputs from the locus coeruleus and BLA, is critical for memory encoding and retrieval. Transcriptomic analysis of Fos+ ensembles in the two structures shows distinct gene activation in excitatory neurons, highlighting key pathways involved in learning and memory. These findings highlight the pPC’s role in integrating sensory and affective information, essential for long-term threat memory consolidation.

overall_design: Employing a multi-omics approach, including single-nucleus RNA sequencing (sn-RNAseq) and assay for transposase-accessible chromatin sequencing (sn-ATACseq), we analyzed BLA and PC tissues from animals subjected to SOC. A total of 12 rats were used in this experiment, with three rats per group (paired or unpaired) at each time point (early consolidation or memory retrieval). Tissue samples were harvested from the BLA and pPC at two time points following SOC: 90 minutes post-conditioning and 90 minutes post-retrieval test. BLA tissue was extracted from frozen sections in the cryostat using a 1 mm diameter biopsy punch, while pPC tissue was collected using a 0.5 mm diameter punch at three lateral-to-medial locations. Single-nucleus suspensions were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics, User Guide Rev F, CG000338).

first: Tian

last: Qin

first: Tayebeh

last: Sepahvand

first: Zia

last: Hazan

first: Qi

last: Yuan


title: Changes in gene expression patterns in young and senescent fibroblasts in glycated three-dimensional collagen matrices

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

summary: Glycation, or non-enzymatic glycosylation, has recently attracted increasing interest in the context of its impact on aging. Advanced glycation end products (AGEs) contribute to various age-related pathological conditions such as inflammation, fibrosis, stem cell aging, etc. However, the molecular mechanisms underlying the glycation-induced disruption of cell-matrix interactions during cellular senescence are not fully understood. The aim of this study was to investigate transcriptomic changes in young and senescent dermal fibroblasts (HdFbs) cultivated in post-glycated 3D collagen type I matrices after 10 and 17 days. Our findings indicate that the D-ribose-mediated glycation increases the accumulation of fluorescent AGEs and the stiffness of the matrices in a dose-dependent manner. The transcriptome alterations encompassed the modulation of age-related genes and signaling pathways, including the activation of genes related to senescence-associated secretory phenotype (SASP) in young cells. Notably, the alterations in the transcriptome profiles due to glycation were more pronounced (in terms of both the number of genes and their fold changes) on day 10 of cultivation compared to day 17 in both passages.

overall_design: We performed RNA-Seq to analyze the effect of D-ribose, as glycating agent, on gene expression profiles of normal fibroblasts on different stages of cell senescence. To assess the transcriptomic changes, we used human dermal fibroblasts (HdFb (d75)) at 12th (consider as “young”) and 20th (consider as “senescent”) passages cultured for 10 and 17 days inside 3D post-glycated collagen matrices.

first: Zulfiya

last: Guvatova

first: Evelina

last: Kudasheva

first: Yuri

last: Efremov

first: Peter

last: Timashev

first: Maria

last: Fedorova

first: Elena

last: Pudova

last: Snezhkina

first: Anna

last: Kudryavtseva

first: Alexey

last: Moskalev


title: Overexpression of Mir-197 und Mir-769 in human iPSCs

first: Stefan

last: Günther

overall_design: Differential gene expression analysis upon overexpression for 48h of either miRNA Precursor hsa-miR-197-3p or miRNA Precursor hsa-miR-769-5p in human iPSCs compared to miRNA Precursor Negative Control

first: Felix

last: Langschied

first: Matthias

last: Leisegang

first: Fabian

last: Hahner

first: Ralf

last: Brandes

first: Ingo

last: Ebersberger


title: Single-cell transcriptome conservation in a multispecies comparative analysis of fresh and cryopreserved insulinoma cell lines

city: Hatfield

first: Floryne

middle: Ottilie

last: Buishand

address: Hawkshead Lane

department: Clinical Science and Service

country: United Kingdom

institute: Royal Veterinary College

summary: Background Insulinoma is the most common pancreatic neuroendocrine tumour in dogs and humans. The understanding of driving factors and critical survival genes in insulinomas is limited and overall survival is poor for canine and human malignant insulinoma. This study aimed to use single-cell RNA-sequencing to conduct a multispecies analysis of insulinoma cell lines to understand their single-cell transcriptomic landscape. Secondly, the impact of freeze-thawing on the pancreatic beta single-cell transcriptome was investigated, to determine whether cryoarchiving of primary insulinoma samples may be feasible in future studies. Methods Single-cell transcriptomic analysis was performed using fresh and cryopreserved multispecies insulinoma cell lines (canINS, CM, INS-1 and MIN6). R and Seurat were used to perform cell clustering and specific cluster marker genes were identified by the FindMarkers function. Metascape was used to identify statistically enriched pathways for specific cell clusters. Differentially expressed genes between fresh and cryopreserved single-cell transcriptome profiles, were defined as genes with a log2 fold change >0.25 and a Bonferroni-adjusted P<0.05, based on the Wilcoxon rank sum test. Results Based on the specific cell line single-cell transcriptome profiles, five or six cell clusters were constructed per cell line. All cell lines expressed neuroendocrine markers and additionally INS-1 and MIN6 displayed a gene signature indicative of mature/functional pancreatic islet/beta-cells. DEPTOR, BICC1, GHR, CCNB2, CENPA, LMO4, VANGL1, and L1CAM were identified as cross-species conserved insulinoma cluster marker genes. Little effect was found of cryopreservation and thawing on overall gene expression at the single-cell level in insulinoma cell lines: only 6 and 29 genes had a log2 fold change > 1 in cryopreserved versus fresh canINS and CM, respectively. Conclusions canINS, CM, INS-1 and MIN6 are all principally relevant as insulinoma models and the demonstrated differences in their single-cell transcriptomic profiles could aid researchers in selecting the appropriate cell lines for specific study objectives. Cross-species conserved insulinoma cluster marker genes were identified that harbour oncogenes and their involvement in insulinoma tumourigenesis should be investigated in future studies. The good comparability between cryopreserved and fresh insulinoma cells allows for inclusion of cryopreserved insulinoma patient samples in future studies, which allows for reduced assay-based variability.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus
Rattus norvegicus

overall_design: Single-cell 3’ gene expression libraries were prepared for six insulinoma cell line samples (canINS-fresh, canINS-cryopreserved, CM-fresh, CM-cryopreserved, INS-1 and MIN6) using a Chromium NEXT Gem Single Cell 3 v3.1 Kit and dual index library construction kit (10x Genomics) targeting 10,000 cells per sample. Sequencing was performed on a NovaSeq 6000 sequencer (Illumina) using a 28 x 10 x 10 x 90 bp configuration. CellRanger (version 7.1.0, 10x Genomics) was used to process raw FASTQ files and to align reads to either the canine CanFam3.1, human GRCh38, murine GRMch38/mm10, or rat mRatBN7.2 genome.

middle: O

first: Dong

last: Xia

first: Lucy

middle: J

last: Davison


title: Overexpression of hsa-HLA-DRB1 may play a role in diabetic foot ulcers by regulating miRNA_12118 and FLT-1

city: Urumchi

first: Chao Bai

middle: Chao

last: Bai

state: Xinjiang

address: 393 Xinyi Road

department: Department of Vascular and Thyroid Surgery

institute: The First Affiliated Hospital of Xin-	Conflict of Interest Statement:	 jiang Medical University

summary: Introduction: We investigated the role and mechanism of hsa-HLA-DRB1 in the development and progression of diabetic foot ulcers. Methods: High-throughput sequencing was performed on three normal foot trauma tissues and diabetic foot ulcer tissues. The circRNAs with significant differences were identified. The downstream miRNAs were predicted by miRanda and RNAhybrid databases, and the mRNAs were predicted by the TargetScan database. Validation was performed with CCK8, flow cytometry, trabecular scratch assay, tubule generation assay, Western blot, dual luciferase assay, and RT-qPCR. Results: High-throughput sequencing identified 461 significantly different circRNAs, of which 260 were up-regulated and 201 down-regulated. Compared to normal tissue, hsa-HLA-DRB1 was highly expressed in diabetic foot ulcers. The hsa-HLA-DRB1/miRNA_12118/FLT-1 axis was constructed. In vitro, we found that HLA-DRB1 overexpression inhibited cell viability, wound healing, and tubule formation, promoted apoptosis, and enhanced FLT-1 expression in HUVECs. Conclusion: The upregulation of hsa-HLA-DRB1 may promote diabetic foot development by targeting miRNA_12118 and acting on FLT-1. Therefore, our study highlights the key role of the hsa-HLA-DRB1/miRNA_12118/FLT-1 axis in diabetic foot trauma.

first: Chao

first: Wenwen

last: Yang

first: Jianghao

last: Yan

first: Guangwei

last: Qi

first: Liuyu

first: Qingrui

last: Wu

first: Jieguang

last: Peng

first: Jun

last: Luo

first: Tao

last: Liu


title: Preterm birth increases susceptibility to hyperglycemia-induced glomerular alterations in the kidneys of male mice

city: Charlottesville

first: Jennifer

last: Charlton

address: 409 Lane Rd. Room 2035

country: USA

institute: University of Virginia

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

overall_design: Refer to individual Series


title: Preterm birth increases susceptibility to hyperglycemia-induced glomerular alterations in the kidneys of male mice [scRNA-seq]

summary: Diabetic kidney disease (DKD) is the leading cause of progressive chronic kidney disease in adults in the United States. However, the impact of preterm birth on the progression of DKD has not been studied. The goal of this project is to determine the effect of preterm birth on kidney health in a diabetic mouse model. CD-1 pups born preterm (19 days post conception (dpc)) and term (20 dpc) were studied, and outcomes of the male mice were reported, all compared to term mice. Preterm and term mice were treated with streptozotocin at six weeks to induce hyperglycemia. Body weight and blood sugar were monitored. Histologic, molecular, and imaging techniques were used to characterize the mice at 18 weeks. The preterm mice with diabetes had a lower podocyte density, lower proximal tubular fraction, and more atubular glomeruli compared to the term mice without diabetes. They also had a lower podocyte density and lower renin expression compared to term mice with diabetes. Based on single-cell RNA sequencing, preterm mice with diabetes had increased expression of genes related to the angiogenesis migration pathway-related in endothelial cells and increased expression of genes in the actin adhesion pathway in podocytes compared to term mice with diabetes. Furthermore, the preterm mice with diabetes exhibited a weaker endothelial cell-podocyte interaction compared to term mice with diabetes. These data suggest that preterm birth increases susceptibility to glomerular and tubular damage after a brief “second hit” of hyperglycemia. In conclusion, preterm birth disrupts endothelial-podocyte crosstalk and increases susceptibility to kidney injury induced by hyperglycemia.

overall_design: The whole kidneys from four animals (one animal from each group: T-ND, T-D, PT-ND, and PT-D) were disassociated to isolate the cells for single cell RNA-Sequencing (scRNA-Seq). Red blood cell lysis was performed and the cell suspension was FACS sorted to remove dead cells. cell sorter.

first: Aleksandra

last: Cwiek

first: Rachel

middle: K

last: Dailey

first: Ayyappa

last: Kameshwar

first: Masako

last: Suzuki

first: Jaya

last: Isaac

first: Kimberly

last: deRonde

first: Mark

last: Conaway

first: Kevin

middle: M

last: Bennett

first: Edwin

last: Baldelomar

first: Teng

last: Li

first: Teresa

first: Matthew

middle: R

last: Hoch

first: Nicholas

middle: W

last: Chavkin

first: Patrick

middle: D

last: Walker

first: Karen

last: Hirschi

last: Reidy


title: Mammary intra-epithelial lymphocytes promote lactogenesis and offspring fitness

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: Breastfeeding is an obligatory requirement of mammalian survival. This fundamental process is associated with the adaptation of maternal physiology including the transformation of the mammary gland into a milk-secreting organ. How maternal immunity contributes to mammary gland remodeling and function remains largely unknown. Here, we show that maternal adaptive immunity plays a critical role in shaping lactogenesis. Specifically, physiological adaptation during pregnancy is associated with thymic involution and a paradoxical enrichment in intraepithelial lymphocyte (IEL) precursors that no longer migrate to the gut, but instead preferentially accumulate within the mammary gland. Within this compartment, IEL precursors differentiate into T-bet-expressing unconventional CD8 lymphocytes with a cytotoxic signature which accumulate within the mammary epithelium in an IL-15-dependent manner. Mammary intra-epithelial lymphocytes control milk production by favoring differentiation and maturation of both contractile and milk-secreting cells, thereby promoting offspring fitness. Altogether, this work uncovers a previously unappreciated contribution of the maternal adaptive immune system in organismal remodeling during pregnancy that is associated with mammary gland development and function.

overall_design: Human breastmilk samples from three different donors 3, 10 and 11 months post-partum.


title: Alterations in Bile Acid Physiology in Wilson Disease

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

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

overall_design: We performed RNA-Sequencing in 6 month old wild-type and Atp7b KO mice. The fold change of gene change in WT vs. Atp7b KO was calculated.

first: Clavia' R

last: Wooton-Kee

first: Islam

last: Mohamed

first: Manal

last: Hassan

first: Kenneth

last: Setchell

first: Monica

middle: N

last: Rivas

first: Ayse

last: Coskun

first: Vasanta

last: Putluri

first: Nagireddy

first: Prasun

last: Jalal

first: Michael

middle: L

last: Schilsky

first: David

last: Moore


title: Epigenetic enhancer modifications determine the angiogenic to quiescent endothelial state transition

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

institute: DKFZ

summary: The transcriptomic changes in endothelial cells during the state transition from the angiogenic to the quiescent phenotype are controlled by extrinsic microenvironmental factors and intrinsic epigenetic determinants. While significant progress has been made in understanding the external factors and their molecular impacts on this transition, the internal, cell-intrinsic mechanisms driving endothelial state transition remain less explored. Here, we present a detailed multiomic analysis of the epigenetic-driven state transition in angiogenic versus homeostatic lung capillary endothelial cells by mapping the histone code, accessible chromatin, and DNA methylation. Comprehensive data integration revealed selective chromatin accessibility at enhancers but not at promoters close to state-determining genes. Notably, pathological reactivation of the vasculature during tumor progression required the reestablishment of angiogenic enhancer regions to hijack developmental transcriptional programs. Enhancer reestablishment was associated with the selective expression of chromatin-modifying enzymes and the preservation of DNA hypomethylation and chromatin accessibility at former angiogenic enhancers. The data establish an enhancer-driven model of the endothelial transcriptome during angiogenic to quiescent endothelial state transition, yielding deep mechanistic insight into the dynamic epigenetic landscape governing endothelial cell function and plasticity.

overall_design: Sequencing experiments were performed on FACS-sorted lung endothelial cells isolated from mice of different ages, including infant, young adult, and mature adult.

first: Hellmut

last: Augustin


title: Effect of corticosterone on the gene expression in the context of global hippocampal transcription

city: Magdalenka

first: Grzegorz

middle: Roman

last: juszczak

address: Jastrzebiec, ul Postepu 36A

country: Poland

institute: Institute of Genetics and Animal Biotechnology

summary: The composition of genomic mediators of glucocorticoids in brain remains elusive because of common problem of low statistical power of experiments and associated very low consistency of transcriptomic data. Other issues is underrepresentation of chronic experiments and interpretation of differentially expressed genes without understanding their contribution to the total transcriptomic activity. To fill existing gaps in knowledge we have performed a large transcriptomic experiment (48 mice in total) testing effects of prolonged treatment with corticosterone (5, 14 and 28 days) on hippocampal transcriptome (RNA sequencing) and, next, we have assessed the contribution of differentially expressed genes to total transcriptomic activity. The experiment showed that prolonged treatment with the corticosterone induced a set of transcriptomic effects that were replicable across treatment durations including genes relevant for human PTSD (Opalin, Pllp, Ttyh2, Lpar1) and prolonged stress in animals (Cnp, Fam163a, Fcrls, Tmem125). Part of affected genes is specific for oligodendrocytes, neurons, astrocytes, immune cells, vascular system and brain ventricles indicating that glucocorticoids may affect all components of the central nervous system. The data showed also that the largest changes in expression of corticosterone-responsive genes are restricted to genes that have relatively low expression level and small contribution to the overall pool of mRNAs in the hippocampus. As a result,  even large change in terms of the number of affected genes leads to small change in the number of mRNA copies. This means, in turn, that the transcriptomic changes induced by corticosterone are a low-cost effects for the brain.

overall_design: Adult male mice were assigned to three corticosterone-treated groups that received the glucocorticoid dissolved in drinking water (100 µg/mL) for 5, 14 or 28 nights and to three control groups that were euthanized at the same time as corticosterone treated animals. Bottles with drinking water were changed every evening at the end of the light phase. Euthanasia was performed during the first hour of the light phase following the last night of treatment to collect brain hippocampi for mRNA-seq.

last: Juszczak


title: Gene Expression Profiling of Nerve Biopsies from Pure Neural Leprosy Patients

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

summary: Leprosy may affect skin and nerves, leading to disability. Pure neural leprosy (PNL) lacks skin lesions, complicating diagnosis. Transcriptomic profiling reveals unique gene expression changes in PNL nerves, shedding light on immune response and pathogenesis. These findings may guide early diagnosis and improve patient outcomes. In the present study, gene profiling of nerve biopsies from patients with PNL revealed significant transcriptomic alterations compared to non-leprosy controls. Principal Component Analysis (PCA) of the 500 most differentially expressed genes separated the groups, with 1,199 genes showing differential expression (|log2FC| ≥ 1, FDR ≤ 0.1). Downregulated genes included GAS2L2, TRIM67, IL1RAPL1, MAP1LC3B2, and NTNG1, implicated in neuronal development and autophagy, while upregulated genes were linked to immune responses. Functional analyses highlighted inflammasome activation and autophagy impairment in PNL, correlating with nerve inflammation and architecture loss. We hope that our data will aid in identifying new markers, fostering strategies for early diagnosis, preventing disabilities, and improving the management of PNL patients.

overall_design: Nerve biopsies from pure neural leprosy (n = 7) and non-leprosy vasculitis (n = 9) patients were used. Samples come from convenience during routine diagnosis in an outpatient clinic in Rio de Janeiro, RJ, Brazil. Samples from patients with vasculitis were used as a control for non-infectious inflammatory peripheral neuropathy.

first: Mariana

last: M de Athaide

last: Leal-Calvo

first: Thabatta

last: Rosa

first: Roberta

last: Pinheiro


title: Comprehensive analysis of differences of RNA 5-methylcytosine in hepatic lipid metabolism

city: shanghai

first: Yueying

last: Yang

state: shanghai

address: No. 85/86, Wujin Road, Hongkou District, Shanghai

institute: Shanghai General Hospital

type: Methylation profiling by high throughput sequencing

summary: As living standards have risen, particularly with the widespread consumption of high-fat diets, non-alcoholic fatty liver disease (NAFLD) has emerged as the leading chronic liver condition globally, affecting nearly 30% of adults in China. Recent studies emphasize the role of 5-methylcytosine (m5C), an RNA modification, in key biological functions. Nevertheless, the connection between m5C methylation and NAFLD remains enigmatic. In this research, by leveraging RNA transcriptome sequencing (RNA-Seq) and methylated RNA bisulfite sequencing (Bis-Seq) in leptin receptor-deficient mice, we uncovered that genes associated with hypermethylation were primarily tied to lipid metabolism. Our analysis identified 156 overlapping and differentially expressed genes (DEGs) that showed significant alterations in both m5C modification and mRNA expression levels. Notably, 72 genes showed heightened expression and increased m5C modification, suggesting a positive correlation between m5C RNA modifications and NAFLD. These findings underscore the potential importance of m5C methylation in the progression of NAFLD.

overall_design: Male C57BL/6J and db/db mice aged 8 weeks were purchased from the GemPharmatech ( Shanghai, China). Mice were anesthetized with 10% chloral hydrate.

first: Xiaoying

last: Ding


title: Allantoin promotes MASLD progression

city: Qingdao

first: Xueqiang

last: Wang

state: China

address: 369 Dengyun Road, High-tech Zone

institute: University of Health and Rehabilitation Sciences

summary: Uric acid has garnered increasing attention for its association with metabolic dysfunction-associated steatotic liver disease (MASLD) in recent cross-sectional studies, although detailed understanding of its involvement remains limited. This study confirms a strong association between urate levels and elevated risk of both MASLD and type 2 diabetes (T2D) through a large-scale observational analysis of UK Biobank data. However, Mendelian randomization (MR) analysis involving over 2 million samples identified only causal effects of urate on serum triglyceride levels and the risk of T2D. Additionally, a targeted metabolomics study involving elderly Chinese participants revealed that, rather than UA, allantoin—a byproduct of UA oxidation—was significantly elevated in individuals with dyslipidemia or T2D. Notably, a significant negative correlation was found between serum allantoin level and fasting glucose, as well as serum triglyceride and cholesterol levels. Animal studies demonstrated that allantoin exacerbates hepatic lipid accumulation and glucose intolerance in mice fed a high-fat diet, which was accompanied by increased hepatic lipid biogenesis and reduced bile acid production. Interestingly, our findings indicate that allantoin exhibits a strong binding affinity for PPARα, suggesting that it may act as an inhibitor of PPARα, thereby promoting the progression of MASLD. These results underscore the critical role of allantoin, rather than UA, in the development of MASLD, offering valuable insights for the prediction and management of hepatic metabolic disorders.

overall_design: For allantoin intervention, mice were fed on  HFD for 4 weeks, the HFD-fed mice were then supplemented with allantoin in their drinking water at the concentrations of 0.06 mg/mL and 0.3mg/mL for additional 4 weeks. Liver were collected for RNA-seq.

first: Zhihui

last: Feng


title: Gut microbiota in pediatric patients with CNS tumors

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Brain and central nervous system (CNS) tumors are the leading cause of cancer-related deaths in both adults and children, particularly affecting those aged 0–14 years. Efforts to develop targeted therapies have largely been unsuccessful, with limited improvement in survival rates. This underscores the urgent need for more effective treatments. Recent research highlights the importance of the gut microbiota and its collective genomes, known as the microbiome, in maintaining overall health. The microbiome helps prevent infections and regulates immune responses both locally and throughout the body. There is a strong connection between the gastrointestinal (GI) system and the CNS, as the CNS plays a crucial role in controlling the GI tract’s function and balance. The relationship between the gut microbiota and the brain, referred to as the microbiota-gut-brain axis, is a complex interaction that may influence CNS cancer development and treatment outcomes. In this study, researchers examined the gut microbiota composition in a group of pediatric cancer patients, focusing on those with CNS tumors.

overall_design: The aim of this study was to investigate whether the gut microbiota (GM) composition in pediatric patients with CNS tumors exhibits distinct characteristics. A total of 33 pediatric patients were included, 11 of whom were diagnosed with CNS tumors, while the remaining 22 had other types of tumors. Microbial DNA was extracted from stool samples, and 16S rRNA gene libraries were generated and sequenced. The resulting Operational Taxonomic Unit (OTU) tables were used to analyze the gut microbiota composition.


title: Lefamulin: A Novel Pleuromutilin Effective Against Mycobacterium tuberculosis via Efflux Inhibition

city: wuhan

first: wenqi

last: dong

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Tuberculosis (TB) remains a major global health challenge, exacerbated by the increasing prevalence of drug-resistant strains. Drug repurposing is a crucial strategy for TB control, particularly in combating resistance. Through this approach, the anti-TB potential of lefamulin was identified as a candidate for systemic administration. Lefamulin demonstrates potent inhibitory activity against Mycobacterium tuberculosis (M.tb) in vitro , in vivo, and within intracellular environments. Notably, it exhibits synergistic effects when combined with the first-line anti-TB drugs rifampicin and isoniazid, as demonstrated in insect model.

overall_design: Logarithmic growth phase M.tb H37Rv cultures were incubated in 7H9 medium containing either 10× MIC of lefamulin (Lef group) or an equivalent volume of DMSO (control group). Following 7 hours of incubation, the cells were collected and lysed.

first: Wenqi

last: Dong

first: Gaoyan

first: Chen

last: Tan


title: miR-486-5p inhibits eNOS and angiogenesis in cultured endothelial cells by targeting MAML3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: Kidney ischemia-reperfusion injury (IR) is associated with endothelial injury. Administration of miR-486-5p protects against rat kidney IR injury, with localization to capillary endothelial cells, although it inhibits IR-induced endothelial nitric oxide synthase (eNOS) protein expression. We studied the effects of miR-486-5p on eNOS and endothelial cell function and determined its mRNA targets. Methods: Human umbilical vein endothelial cells (HUVECs) were transfected with miR-486-5p and assayed for proliferation, migrartion, and network formation. Biotinylated miR-486-5p was transfected for pull-down of bound mRNA, followed by RNA sequencing. Results: miR-486-5p markedly decreased eNOS mRNA and protein in HUVECs, although eNOS mRNA was not found to be a direct target of miR-486-5p. miR-486-5p inhibited angiogenesis, which was rescued with eNOS plasmid transfection. RNA sequencing of biotinylated miR-486-5p pull-down RNA revealed highly significant enrichmenet in predicted targets FOXO1, FOXP1, TNFSF4, MAML3, and CELSR3, and in the non-predicted target SPCS2. RT-qPCR validated these transcripts as inhibited miR-486-5p. While silencing of FOXO1 had no impact on eNOS protein, MAML3 silencing inhibited eNOS levels. Conclusion: miR-486-5p inhibits angiogenesis in endothelial cells via down-regulation of eNOS, which involves selective targeting of MAML3. These data support a novel pathway regulating endothelial cell function.

overall_design: To identify direct miR-486-5p targets in endothelial cells, HUVECs were transfected with either biotinylated miR-486-5p or biotinylated cel-miR-67 (negative control), followed by cell lysis after 24 hr and pull-down of bound RNA with streptavidin beads. The bound RNA was purified and analyzed by RNA-seq to screen for mRNA bound to biotinylated miR-486-5p (compared to the biotinylated cel-miR negative control).

first: Adrianna

last: Douvris

first: Ali

last: Maadelat

first: Christoper J.

last: Porter

first: Dylan

last: Burger

first: Kevin D.

last: Burns


title: Effect of depletion of PARP2 on gene expression in 3 month-old pancreas from Ela-myc mice

city: Barcelona

first: Neus

last: Martínez

address: Dr.Aiguader 88

department: Cancer

country: Spain

institute: Hospital del Mar Medical Research Institute

summary: Pancreatic cancer represents one of the most lethal tumours, characterised by an immunosuppressive microenvironment and a lack of cytotoxic immune cell infiltrates, which confers resistance to immunotherapy. Here, we demonstrate that the deletion of Poly(ADP-ribose)polymerase 2 (PARP2) delays tumour progression in c-Myc-driven and KRas-driven mouse models of pancreatic cancer. Transcriptomic analysis revealed that the absence of PARP2 induces an enrichment of pathways associated with anti-tumor immune responses and genomic instability.  Analysis of tumour-infiltrating immune cells within the tumor microenvironment showed that PARP2 deletion leads to an increase in effector CD4 and CD8 T cells as well as natural killer (NK) cells, accompanied by a significant reduction in pro-tumor regulatory T (Treg) cells and M2 macrophages. Collectively, our data support that selective PARP2 inhibition is a promising therapeutic strategy for pancreatic cancer by boosting anti-tumor immune response, thereby opening new avenues for combating this recalcitrant neoplasia.

overall_design: To investigate the role of PARP2 in pancreatic tumor development, we isolated pancreatic tissue from 3-month old Ela-myc wildy type and PARP2 knocked-out animals. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different animals of each genotype (WT or PARP2 KO).

last: Martínez-Bosch

first: Pilar

last: Navarro Medrano

first: José

last: Yélamos

first: Noemí

last: Manero-Rupérez


title: Transcription arrest induces formation of protective RNA granules in mitochondria

city: Boston

first: Katja

middle: G

last: Hansen

address: 77 Avenue Louis Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

summary: Mitochondrial gene expression regulation is required for the biogenesis of oxidative phosphorylation (OXPHOS) complexes, yet the spatial organization of mitochondrial RNAs (mt-RNAs) remains unknown. Here, we investigated the spatial distribution of mt-RNAs during various cellular stresses using single-molecule RNA-FISH. We discovered that transcription inhibition leads to the formation of distinct RNA granules within mitochondria, which we term inhibition granules. These structures differ from canonical mitochondrial RNA granules (MRGs) and form in response to multiple transcription arrest conditions, including ethidium bromide treatment, specific inhibition of the mitochondrial RNA polymerase, and depletion of the SUV3 helicase. Inhibition granules appear to serve a protective function, stabilizing certain mt-mRNAs during prolonged transcription inhibition. This phenomenon coincides with an imbalance in OXPHOS complex expression, where mitochondrial-encoded transcripts decrease while nuclear-encoded subunits remain stable. We found that cells recover from transcription inhibition via resolving the granules, restarting transcription and repopulating the mitochondrial network with mt-mRNAs within hours. We suggest that inhibition granules may act as a reservoir to help overcome OXPHOS imbalance during recovery from transcription arrest.

overall_design: HeLa S3 cells were treated either for 5 or 24 hours with 2 ug/ml Ethidium bromide or water in DMEM media and 10% FBS. RNAs were extracted and used for pair-end short-read sequencing on the Illumina NOVA seq platform for differential expression analysis of OXPHOS transcripts encoded in the mitochondrial and nuclear genome.

first: Autum

last: Baxter-Koenigs

first: Erik

last: McShane


title: Genome sequencing of hippocampus tissue after chronic treatment with DHEA in female mice

city: Shanghai

first: Shimin

last: Ren

address: Songtao Road 646

institute: Shanghai Institute of Materia Medica.Chinese Academy of Sciences

summary: To understand the molecular mechanism of how DHEA produces antidepressant-like behavior in female mice, we performed RNA sequencing (RNA-Seq), to compare genome-wide transcriptional changes in hippocampal tissue in female mice treated with DHEA or corn oil for 21 days.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different hippocampus tissues at one time points.

first: Xian

last: Wang

first: Xueying

last: Huang

first: Xin

first: Bing

last: Zhang


title: PROX1 is an Early Driver of AR Pathway Loss and Lineage Plasticity in Prostate Cancer

city: VANCOUVER

first: Yuzhuo

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: Lineage plasticity in prostate cancer is now recognized as a critical determinant of lethality. It represents a continuum, ranging from AR activity-low tumors to AR-null tumors that do not express a neuroendocrine prostate cancer (NEPC) program—referred to as double-negative prostate cancer (DNPC)—and fully AR-null NEPC tumors. Despite its importance, factors upregulated early in the process of lineage plasticity have yet to be identified. Identifying such factors is crucial for detecting tumors that are undergoing lineage plasticity or are at risk of developing it. Through integrative genomic analysis of metastatic castration-resistant prostate cancer patient tumors, patient-derived xenografts, and cell models, we found that PROX1 is upregulated early in the lineage plasticity continuum, particularly in AR activity-low tumors, and progressively increases in DNPC and NEPC tumors. Our functional studies demonstrated that PROX1 plays a pivotal role in NEPC, as its knockdown (KD) using lentiviral shRNA reduces the neuroendocrine phenotype, decreases cell proliferation, and increases apoptosis. In this dataset, we provide RNA-seq data from PROX1 KD in NEPC cells (NCI-H660), revealing key pathways altered by PROX1 suppression. These findings suggest that PROX1 is a promising target in NEPC treatment.

overall_design: Expression profiling by high throughput sequencing

first: Zhi

last: Duan

first: Mingchen

last: Shi

first: Joshi

last: Alumkal


title: Comparison of droplet- vs. microwell-based single-cell RNA sequencing methods for the analysis of human bronchoalveolar lavage cells after cryopreservation.

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: Single-cell RNA sequencing (scRNA-seq) has emerged  as a powerful tool to investigate tissue biology and heterogeneity by providing gene expression data at the single cell level. Yet, the need to use fresh material has hampered investigations of human samples, due to obvious logistic reasons. In this project, we aimed to implement and compare cryopreservation methods on human bronchoalveolar lavage (BAL) cells in combination with two scRNA-seq methods, namely droplet-based (10x Chromium™), and microwell-based (Honeycomb™) entrapment.To this end, we aimed to analyze 4 BAL samples obtained from routine diagnostic procedures at the University Hospital (CHU, ULiège, Belgium). The BAL cells were divided into 2 fractions and processed using both techniques according to the manufacturers’ instructions and advices.Our results indicate that the droplet-based method showed a higher recovery rate of intact cells after sequencing and quality control filtering as compared to the microwell-based method. Both methods were able to capture ARN transcripts from fragile granulocytic cells. The proportion of the identified cells types, however, was different between the two methods. Of note, the average number of transcripts per cell was substantially higher with the droplet-based method, while the percentage of detected mitochondrial genes, indicative of stressed or dying cells, was much lower with the droplet-based method compared to the microwell-based method. So far, our results indicate that, in our hands and for the analysis of cryopreserved BAL cells, the droplet-based method display several advantages over the microwell-based method. Our data highlight the importance of determining the most appropriate methodology to obtain high-quality scRNA-seq data before embarking on expensive high-troughput analyses.

overall_design: 4 BAL samples obtained from routine diagnostic  procedures were processed in a pooled single-cell sequencing.

first: Pierre

last: Janssen

first: Joan

last: Abinet


title: Preterm birth increases susceptibility to hyperglycemia-induced glomerular alterations in the kidneys of male mice [bulk RNA-seq]

first: Jennifer

last: Charlton

overall_design: One whole kidney from the following animals group: T-ND n=5, T-D n=5, PT-ND n=5, and PT-D n=5, were disassociated and RNA was izolated for bulk RNA-Sequencing (RNA-Seq).

first: Aleksandra

last: Cwiek

first: Rachel

last: Dailey

first: Ayyappa

last: Kameshwar

first: Masako

last: Suzuki

first: Jaya

last: Isaac

first: Kimberly

last: deRonde

first: Mark

last: Conaway

first: Kevin

last: Bennett

first: Edwin

last: Baldelomar

first: Teng

last: Li

first: Teresa

last: Wu

first: Matthew

last: Hoch

first: Nicholas

last: Chavkin

first: Patrick

last: Walker

first: Karen

last: Hirschi

last: Reidy


title: Multi-omics analysis of the epigenetic effects of lipopolysaccharide-induced inflammation in Type II Pneumocytes

city: Minneapolis

first: Natalia

last: Tretyakova

state: Minnesota

address: 2231 6th St SE Room 2-147

department: Medicinal Chemistry

institute: University of Minnesota

summary: Chronic inflammation plays a central role in the pathogenesis of many lung diseases including asthma, SARS-COVID19, obstructive pulmonary disease (COPD), and lung cancer. Lipopolysaccharide (LPS) is an inflammatory agent produced by most Gram-negative bacteria and found in cigarette smoke. In a mouse model of inflammation, inhalation exposure to LPS induced COPD and increased the size and the multiplicity of lung tumors induced by tobacco-specific nitrosamines. In the present work, we employed a comprehensive multi-omics approach that monitored changes in DNA methylation/hydroxymethylation, gene expression, and global protein abundances in Type II pneumocytes of A/J mice following sub-chronic exposure to LPS.

overall_design: Male and female A/J mice were intranasally treated with lipopolysaccharide (LPS) or PBS for 3 weeks, and 3 weeks followed by 4 weeks recovery. There are three mice in each treatment group. The mice were sacrificed after treatment and Alveolar type II epithelial cells (Type II pneumocytes) were isolated from the harvested lung tissues. DNA and RNA were extracted from the isolated Alveolar type II epithelial cells. DNA were used for genome wide mapping of 5mC and 5hmC and RNA were used for RNA-seq.

first: Jenna

last: Fernandez

first: Qiyuan

last: Han

first: Andrew

middle: T

last: Rajczewski

first: Thomas

last: Kono


title: Food insecurity promotes adiposity in mice

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: The obesity epidemic continues to challenge global health, driven by multifaceted environmental and biological factors. Here, we investigate the impact of food insecurity, characterized by unpredictable food access, on body weight, food intake, and body composition in mice. Male and female C57BL/6J mice were subjected to a combination of intermittent fasting and 5% calorie restriction to resemble food insecurity situations. Our results reveal that this novel food insecurity model promotes fat accumulation and decreases lean mass in both sexes on a standard chow diet. While food insecurity did not exacerbate fat gain in male mice fed a high-fat diet, it further reduced lean mass. RNA sequencing of epididymal white adipose tissue from food-insecure male mice identified upregulated lipid metabolism genes and downregulated immune response genes, suggesting adipocyte expansion and potential immunity dysfunction. These results challenge the traditional view that obesity is solely driven by positive energy balance. Instead, our findings highlight the role of food insecurity in promoting metabolic adaptations favouring fat storage. Our data provide biological mechanisms that may explain the dramatic rise in obesity, underscoring the importance of socio-economic factors, beyond diet composition and energy balance, in understanding the complex etiology of obesity.

overall_design: PolyA RNA-seq of Mus musculus eWAT under two dietary regimes: control diet (Control) and a combination of intermittent fasting and 5% calorie restriction (Random Food Restriction)

first: Cláudia

last: Gil

first: Jens

last: Lund

first: Jan

last: Żylicz

first: Pablo

last: Ranea-Robles

first: Thorkild

middle: I

last: Sørensen

first: Christoffer

last: Clemmensen


title: A cascade of RNA binding proteins controls the switch from proliferation to differentiation in an adult stem cell lineage

city: Ithaca

first: Jongmin

last: Kim

state: NY

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

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

overall_design: Refer to individual Series


title: Mitochondrial Fatty Acid Synthesis and MECR Regulate CD4+ T Cell Function and Oxidative Metabolism

city: Nashville

first: Denis

last: Mogilenko

state: Tennessee

address: 1161 21st Ave S, MCN A3208B, Mogilenko Lab

department: Medicine

institute: Vanderbilt University Medical Cente

summary: Imbalanced effector and regulatory CD4+ T cell subsets drive many inflammatory diseases. These T cell subsets rely on distinct metabolic programs, modulation of which differentially affects T cell fate and function. Lipid metabolism is fundamental to CD4+ T cell metabolism yet remains poorly understood across these subsets. Therefore, we performed targeted in vivo CRISPR/Cas9 screens to identify lipid metabolism genes and pathways essential for T cell functions. These screens established mitochondrial fatty acid synthesis (mtFAS) genes Mecr, Mcat and Oxsm as key metabolic regulators. Of these, the inborn error of metabolism gene Mecr was most dynamically regulated. Mecrfl/fl; Cd4cre mice had normal naïve CD4+ and CD8+ T cell numbers, demonstrating MECR is not essential in homeostatic conditions. However, effector and memory T cells were reduced in Mecr-KO and the function of MECR promoted CD4+ T cell prolifferation, differentiate, and survive. Interestingly, T cells ultimately showed increased mTORC1 activity and signs of mitochondrial stress in the absence of MECR. Mecr-deficient T cells also had decreased mitochondrial respiration, reduced TCA intermediates, and accumulated intracellular iron, which contributed to increased cell death and sensitivity to ferroptosis. Importantly, MECR-deficient T cells exhibited fitness disadvantages in in vivo inflammatory, tumor, and infection models and were less effective at driving disease in a model of IBD. Thus, mtFAS and MECR play an important role in activated T cells and may be a target to modulate immunological function in inflammatory diseases. These findings may also provide insight to the immunological state of MECR- and other mtFAS-deficient patients.

overall_design: Mecr fl/fl/ Cd4 cre - or Mecr fl/fl/ Cd4 cre + naïve T cells were transferred into Rag1-/- mice to develop Inflammatory Bowel Disease. After disease development, CD4+ T cells were isolated from the spleens of Rag1-/- mice and subjected to RNA isolation.

first: KayLee

last: Steiner

first: Anton

last: Zhelonkin

middle: A

first: Jeffrey

middle: C

last: Rathmell


title: Methyl-Micro-C

city: Los Angeles

first: Suhn

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Simultaneous measurement of epigenetic signatures from the same cell and tissue provides significant benefits for research, especially when resources are limited, and precise analysis is essential. Here, we report a technique called Methyl-Micro-C to simultaneously map chromatin accessibility, interaction, and DNA methylation in the same sample. Methyl-Micro-C enhances the resolution of chromatin interaction and the coverage of CpGs by combining MNase-mediated fragmentation with enzymatic conversion. This technique is relatively straightforward, making it easy for researchers to apply. It also allows for the profiling of three-dimensional epigenomes with consistent chromatin accessibility, interaction, and DNA methylation signals in a cost-efficient manner.

overall_design: We developed the Methyl-Micro-C method and compared chromatin accessibility, interaction, and DNA methylation using Micro-C, EM-seq, NOMe-seq, and NOMe-Hi-C data.

first: Leonardo

last: Gonzalez-Smith

first: Claire

last: Stevens

first: Huan

last: Cao

first: Zexun

last: Wu


title: The effects of TM on the transcriptome of C. elegans

city: Changsha

first: Guolin

last: Li

state: Hunan

address: 177 Lushan Road

institute: Hunan Normal University

summary: To screen potential molecular regulators mediating tetrathiomolybdate(TM)-induced longevity in C. elegans, we analyzed the transcriptome of worms in control and tetrathiomolybdate treatment groups.

overall_design: Gene expression profiling analysis of RNA-seq data for control and 4 days administration of tetrathiomolybdate (TM) in C. elegans

first: Yiming

last: Zhou

first: Fang

last: Wei


title: The embryonic DPPA3 gene stimulates the expression of pregnancy-related genes in bovine endometrial cells

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin, Madison

summary: Extracellular vesicles (EVs) released by cells contain mRNAs, miRNAs, lncRNAs, lipids, and proteins, playing crucial roles in cell-cell communication. While full-length mRNA transcripts have been documented in EVs secreted by cancer cells, there are no reports on full transcripts secreted by embryos. Our study aimed to identify extracellular vesicle mRNAs in the culture media of bovine embryos and investigate their roles in embryo-mother communication. Following the isolation of EVs from in-vitro fertilization media samples and RNA sequencing, we identified full mRNA transcripts of three genes: SLBP2, ACCSL, and DPPA3. We selected DPPA3 for further investigation. To examine the role of DPPA3 in embryo-mother communication, an in vitro transcribed mRNA of DPPA3 was transfected into bovine endometrial epithelial cells. Transfected and control cells were subsequently analyzed for RNA sequencing to assess the effects of DPPA3 on gene expression. A total of 24 genes were found to be upregulated, and one gene was downregulated (FDR < 0.01) following DPPA3 transfection. Among the 18 annotated genes, 17 have known functions in pregnancy recognition in ruminants or have been previously identified as upregulated in pregnant animals. In addition to RNA sequencing, transfected and control cells underwent proteomic analysis. A total of 34 proteins were differentially expressed (FDR < 0.01, p < 0.05, fold change > 1.5), with 19 upregulated and 15 downregulated. Two proteins, ISG15 and MX1, overlapped with the differentially expressed mRNAs. To mimic the natural transfer of EVs from embryos to endometrial cells, we performed co-culture of day 8 blastocysts or supplemented the cells with embryo-conditioned culture media. DPPA3 expression was detected in endometrial cells exposed to embryo-conditioned media after just 30 minutes, with slight upregulation of ISG15 and MX1 also observed. The expression of these classic interferon-stimulated genes in endometrial cells increased from 0.5 to 10 hours when exposed to blastocysts or embryo-conditioned media. Overall, these results demonstrate that DPPA3 mRNA secreted from embryos may play a role in early embryo-mother communication and maternal recognition of pregnancy prior to major interferon tau secretion. Importantly, our study highlights the significant role of EVs in cell-cell communication through mRNA signaling from the embryo to the mother.

overall_design:
To elucidate mRNAs contained within bovine embryo conditioned IVF media, we performed RNA seq from EVS and discovered DPPA3 as a secreted transcript
DPPA3 mRNA was made via in vitro transcription and then transfected into bovine endometrial epithelial cells
To evaliuate DPPA3's effect in endometrial cells,  RNA sequencing was performed from control and transfected cells as well as cells exposed only to the transfection reagent (JETmessenger)

first: Jessica

last: Townsend

first: Nicole

last: Gross

first: Zongkai

last: Peng

first: Francisco

last: Peñagaricano

first: Zhibo

last: Yang

first: Nagib

last: Ahsan


title: phe-gradient-ANR EndOMiX project

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

summary: ngs2021_12_endomix-phe-gradient-Identify the physiological response of poplar to the presence of 8 Phenanthrene gradient concentration.-As part of the ANR EndOMiX project, we carried out an experiment with poplars (Populus canadensis: hybrid Populus deltoides x nigra) grown in soil with a gradient of contamination in Phenanthrene (PHE), we have 8 different concentrations of PHE, and 4 biological replicates (pots with independent plants). We harvested after 4 weeks of growth, the roots and leaves of the poplars from which the RNAs were extracted for sequencing.

overall_design: 64 samples with 4 biological replicats. dose response

first: Aurélie

last: Cebron

first: Lilian

last: Greau

first: Alexandra

last: Launay-Avon


title: Astrocytes RNA-seq of 3 and 9 month-old mice THY-Tau22 basal.

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

institute: CNRS

summary: This project aims to identify transcriptomic changes of astrocytes associated with Tau pathology.

overall_design: 3 and 9 month-old mice astrocytes were isolated by magnetic sorting (ACSA-2 beads) in basal conditions (home cage). In total we have 4 groups :  WT HC (3mo), Tau HC (3mo), WT HC (9mo), Tau HC (9mo).

first: Anne-Laurence

last: Boutillier

first: Isabel

last: Paiva

first: David

last: Blum

first: Johanne

last: Gambi


title: Ablation of LRP6 in alpha-smooth muscle actin-expressing cells abrogates lung inflammation and fibrosis upon bleomycin-induced lung injury

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Low-density lipoprotein receptor-related protein 6 (LRP6) is a receptor for Wnt ligands. Tissue fibrosis is a progressive pathological process with excessive extracellular matrix proteins (ECM) deposition. Myofibroblasts, identified by alpha-smooth muscle actin (αSMA) expression, play an important role in tissue fibrosis by producing ECM production and interacting with immune cells. Here we found that Dickkopf1 (DKK1) induced gene expressions is associated with inflammation and tissue repair in lung fibroblasts. We demonstrated that genetic deletion of LRP6 in αSMA-expressing cells using Acta2-cre Lrp6fl/fl (Lrp6AKO) mice abrogated bleomycin (BLM)-induced lung inflammation and fibrosis phenotype, suggesting a potential role for DKK1-LRP6 axis in modulating fibrotic processes. Our results highlight LRP6’s crucial role in fibroblasts in regulating inflammation and fibrosis upon BLM-induced lung injury.

overall_design: To investigate DKK-1 mediated gene expression in vitro, in wildtype mouse lung fibroblasts.

first: SuJeong

last: Song

first: Eun-Ah

last: Sung

first: Theingi

last: Aung

first: Min

middle: H

last: Park

first: Patricia

middle: J

last: Sime

first: Wook-Jin

last: Chae


title: A cascade of RNA binding proteins controls the switch from proliferation to differentiation in an adult stem cell lineage [array]

first: Jongmin

last: Kim

summary:
ABSTRACT: The mechanisms that regulate the switch from precursor cell proliferation to onset of differentiation in the adult stem cell lineages that maintain or repair many tissues in the body must be carefully regulated to assure production of sufficient progeny to maintain tissues yet prevent overproliferation that may lead to oncogenic progression. We are investigating the mechanisms regulating the switch from transit amplifying divisions to onset of differentiation in the Drosophila male germ line adult stem cell lineage, where spermatogonia undergo a limited number of mitotic divisions before switching to the spermatocyte program that sets up differentiation and meiosis. The number of transit amplifying spermatogonia divisions is set by accumulation of the Bag of marbles (Bam) protein to a critical threshold. Here we identify repression of Held Out Wings (how), homolog of mammalian Quaking, as the key target of Bam enabling the mitosis to differentiation switch. Knock down of how in germ cells was sufficient to allow spermatogonia mutant for bam or its partner bgcn to differentiate, while forced expression of nuclear-targeted How protein in otherwise wild-type spermatogonia resulted in continued proliferation of spermatogonia at the expense of differentiation. Our findings suggest that Bam targets how RNA for degradation by acting as an adapter to recruit the CCR4-NOT deadenylation complex via binding its subunit, Caf40. Our data support the model that the switch from proliferation to differentiation in this model adult stem cell lineage is regulated by a cascade of RNA-binding proteins.
We used microarray to profile a time-course gene expression change from spermatogonia to spermatocytes for 48 hours in 8-hour intervals. We used the Bam-induced synchronous differentiation strategy we developed (PMID: 28522526). bam mutant testes are filled with developmentally arrested, overproliferating spermatogonia. By a pulse of Bam expression using 30 minutes of heat shock for the bam mutant flies bearing heat shock promoter driven Bam transgene, we induced synchronous differentiation of spermatogonia to spermatocytes. These cells stopped dividing and initiated the expression of early spermatocyte genes by 24 hours post-heat shock (PHS). By 48 PHS, they became young spermatocytes expressing hundreds of testis-specific genes. As a control, we used bam mutant flies without hs-Bam transgene but received the same 30 minutes of heat shock treatment.

overall_design: Experimental (hs-Bam; bam-/-): 1) no HS, 2) 8hr PHS, 3) 16hr PHS, 4) 24hr PHS, 5) 32hr PHS, 6) 40hr PHS, 7) 48hr PHS; Control (bam-/-) 1) no HS, 2) 8hr PHS, 3) 16hr PHS, 4) 24hr PHS, 5) 32hr PHS

first: Margaret

last: Fuller


title: ACE2 shedding exacerbates sepsis induced gut leak via loss of microbial metabolite 5-MTP

city: Guangzhou

first: Gong

last: Jiacheng

address: Shatai South Road, Baiyun District

institute: Southern Medical University

summary:
Sepsis, a critical organ dysfunction resulting from an aberrant host response to infection, remains a leading cause of mortality in ICU patients. Recent evidence suggests that angiotensin converting enzyme 2 (ACE2) contributes to intestinal barrier function, the mechanism of which is yet to be explored. The findings of this study indicate that ACE2 shedding significantly weakens the integrity of the intestinal barrier in septic conditions. Mice lacking ACE2 exhibited increased intestinal permeability and higher mortality rates post-sepsis compared to their wild-type counterparts. Notably, ACE2 deficiency was associated with distinct alterations in gut microbiota composition and reductions in protective metabolites, such as 5-methoxytryptophan (5-MTP). 5-MTP was barely detected in ABX mice, while its level was reversed by FMT of WT mice. Supplementing septic mice with 5-MTP ameliorated gut leak through enhanced epithelial cell proliferation and repairment.
The relationship between intestinal barrier integrity and the expression of ACE2 in septic mice was explored in both ACE2 knockout and overexpressing mice. Intestinal barrier function was assessed through measurements of intestinal tight junction proteins and permeability tests. The resulting bacteria translocation and multi-organ dysfunction were also evaluated.

overall_design: To investigate the mechanism by which 5-MTP counteract the sepsis induced barrier damage, RNA-seq was performed on WT CLP mice treated with either 5-MTP or PBS.

first: Jiacheng

last: Gong


title: Impact of GNA13 overexpression on gene expression changes in LNCaP cells

city: Singapore

first: Patrick

last: Casey

address: 8 College Road

department: Cancer and Stem Cell Biology

country: Singapore

institute: Duke NUS Medical School

summary: GNA13 has been shown to have multiple oncogenic roles in many different solid tumors including prostate cancers. However, the molecular mechanisms that drive GNA13-induced oncogenesis and metastasis is not understood completely. To elucidate the mechanisms driven by GNA13 in prostate cancer cells, we performed total RNA sequencing in LNCaP cells after overexpressing the wild-type GNA13 cDNA in a pBabe-puromycin vector.

overall_design: RNA sequencing of LNCaP cells stably expressing pBabe-GNA13 or pBabe-vector, each in three biological replicates

first: Suhail

last: Rasheed

first: Sujoy

last: Ghosh

first: Veerabrahma

middle: P

last: Seshachalam


title: Activated NK cells with a predominance of inhibitory receptors and a decidual-like phenotype expand after autologous HSCT in children with tumors

city: Adelaide

first: Naiara

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

summary: In this study, we wanted to study the changes in the NK cell transcriptome after culturing in the presence of IL-15 and TGF-beta by using single cell RNA sequencing (sc-RNAseq)

overall_design: Peripheral blood mononuclear cells were collected from a healthy donor and cultured in the presence of IL-15+TGF-beta or non-stimulus. Cells were cultured for 1 and 4 days. Next, sc-RNAseq was performed using Illumina Novaseq 6000.

first: Francisco

last: Borrego

first: Gabirel

last: Astarloa-Pando

first: Laura

last: Amo

first: Victor

last: Sanda Mera


title: A cascade of RNA binding proteins controls the switch from proliferation to differentiation in an adult stem cell lineage [RNA-Seq]

summary: ABSTRACT: The mechanisms that regulate the switch from precursor cell proliferation to onset of differentiation in the adult stem cell lineages that maintain or repair many tissues in the body must be carefully regulated to assure production of sufficient progeny to maintain tissues yet prevent overproliferation that may lead to oncogenic progression. We are investigating the mechanisms regulating the switch from transit amplifying divisions to onset of differentiation in the Drosophila male germ line adult stem cell lineage, where spermatogonia undergo a limited number of mitotic divisions before switching to the spermatocyte program that sets up differentiation and meiosis. The number of transit amplifying spermatogonia divisions is set by accumulation of the Bag of marbles (Bam) protein to a critical threshold. Here we identify repression of Held Out Wings (how), homolog of mammalian Quaking, as the key target of Bam enabling the mitosis to differentiation switch. Knock down of how in germ cells was sufficient to allow spermatogonia mutant for bam or its partner bgcn to differentiate, while forced expression of nuclear-targeted How protein in otherwise wild-type spermatogonia resulted in continued proliferation of spermatogonia at the expense of differentiation. Our findings suggest that Bam targets how RNA for degradation by acting as an adapter to recruit the CCR4-NOT deadenylation complex via binding its subunit, Caf40. Our data support the model that the switch from proliferation to differentiation in this model adult stem cell lineage is regulated by a cascade of RNA-binding proteins.

overall_design: We used RNA-Seq to profile a time-course gene expression change from spermatogonia to spermatocytes for 32 hours in 8-hour intervals. We used the Bam-induced synchronous differentiation strategy we developed (PMID: 28522526). bam mutant testes are filled with developmentally arrested, overproliferating spermatogonia. By a pulse of Bam expression using 30 minutes of heat shock for the bam mutant flies bearing heat shock promoter driven Bam transgene, we induced synchronous differentiation of spermatogonia to spermatocytes. These cells stopped dividing and initiated the expression of early spermatocyte genes by 24 hours post-heat shock (PHS). We analyzed this dataset together with accompanying microarray measurement to map transcriptional changes during proliferation to differentiation transition of germ cells in spermatogenesis. SAMPLE DESIGN: Experimental (hs-Bam; bam-/-): 1) no HS, 2) 8hr PHS, 3) 16hr PHS, 4) 24hr PHS, 5) 32hr PHS


title: RGG motif-containing Scd6/LSM14A proteins regulate the translation of specific mRNAs in response to hydroxyurea-induced genotoxic stress

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

summary: RGG motif-containing proteins are the second largest group of RNA-binding proteins. Here, we identify a unique and conserved role of yeast Scd6 and its human ortholog LSM14A in hydroxyurea (HU)-mediated genotoxic stress response. Scd6/LSM14A, but not all tested RGG-containing proteins, localize to cytoplasmic puncta in an RGG-dependent manner upon HU treatment. The absence of Scd6 increases cellular HU tolerance under normal conditions but sensitizes the cells to HU upon overexpression of SRS2, which is known to dampen the response to DNA damage. Scd6 binds the SRS2 mRNA to repress its translation upon HU stress. This interaction occurs in cytoplasmic granules and is modulated by the arginine methylation status of Scd6 and the Scd6 LSm domain, which acts as a cis-regulator of Scd6 arginine methylation. Polysome profiling experiments indicate that LSM14A regulate the translation of mRNAs encoding non-homologous end joining (NHEJ) DNA damage repair factors such as DNL4 (DNA ligase 4) and RTEL1 (the Srs2 ortholog), as well as the NHEJ activity in response to HU. Overall, the work shows the contribution of arginine methylation and the RGG-containing proteins Scd6/LSM14A in the genotoxic stress response by determining the translation status of a subset of mRNAs.

overall_design: We performed transcriptome and translatome analysis (RNA-Seq) on A2058 melanoma cells transfected with scrambled siRNA or siRNA specific to LSM14A cells and treated with hydroxyurea (HU) or not (NT).

first: Gayatri

last: Mohanan

first: Raju

last: Roy

first: Hélène

last: Malka-Mahieu

first: Swati

last: Lamba

first: Lucilla

last: Fabbri

first: Anusmita

last: Biswas

first: Sylvain

last: Martineau

middle: M

first: Stéphan

last: Vagner

first: Purusharth

last: Rajyaguru


title: Unveiling the Anti-Aging Potential of 3HB: Lifespan Extension, Healthy Life Improvement, and Cellular Senescence Delay

city: Beijing

first: yongpan

last: an

address: xueyuanlu

institute: Peking University

summary: Aging is a significant risk factor for chronic diseases and disability, yet effective anti-aging interventions remain elusive. We explored the potential of 3-hydroxybutyrate (3HB), an endogenous metabolite with established safety, to modulate longevity in mice. Our findings demonstrate that 3HB supplementation effectively delays cellular senescence, extending yeast lifespan by 51.3% and the median lifespan of naturally senescent mice by 21.0%. Notably, 3HB prolonged healthy lifespan in mice while mitigating age-related tissue morphology changes and organ senescence. Mechanistically, we identified that 3HB's anti-aging properties are mediated through its ability to delay cellular senescence and metabolic reprogramming, while promoting the production of beneficial metabolites like trigoneline and isoguvacine. These findings highlight the promising therapeutic potential of 3HB as an anti-aging intervention and provide novel insights into its underlying mechanisms.

overall_design: We performed RNA sequencing using kidney tissue from 2-month-old, 20-month-old, and 3HB-intervened 20-month-old ICR mice

first: Yongpan

last: An

first: Zhengwei

last: Xie


title: JMJD1C facilitates long distance genomic interactions by promoting condensates formation of key leukemic transcription factors in multiple AML cells [ChIP-seq]

first: Qian

last: Chen

address: Qinghuayuan Stress

institute: Tsinghua University

summary: Dysregulation of transcriptional programs that establish and maintain specific cell identities can lead to various diseases, especially cancer. Acute myeloid leukemia (AML) is an extremely heterogeneous malignancy with frequent genetic mutations such as transcription factors (TFs) and epigenetic factors, resulting in gene dysregulation, differentiation blockade and aberrant proliferation of immature clonal myeloid cells. Various AML subtypes usually involve in distinct genetic alterations, and most studies and therapeutic drugs are focused on specific AML genetic abnormalities. However, whether these seemingly different AML subtypes share a universal transcriptional programs and regulation mechanism is not clear. Identification of such program could help finding of common vulnerabilities and thus future therapeutics against multiple AML subtypes. In this study, we set out to elucidate the underlying mechanism that explains the general dependency towards JMJD1C by AML with different genetic backgrounds. Towards this goal, we first identify RUNX1 as a transcription factor that recruits JMJD1C to chromatin in multiple types of leukemia. Second, we show that JMJD1C directly interacts with RUNX1 at the N-terminus and they co-regulate a set of genes required by leukemic cells. Finally, we found that the N-terminus of JMJD1C could form liquid-like biomolecular RUNX1-containing condensates that are independent of its enzymatic activity, to mediate promoter-enhancer interactions to activate downstream gene expression.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for JMJD1C and RUNX1 in multiple AML cell lines.

first: Mo


title: Mouse proteome pofiler array from AP and NP group.

city: Keelung City

first: Yu-Chiau

last: Shyu

address: No. 200, Ln. 208, Jijin 1st Rd., Anle Dist.

country: Taiwan

institute: Chang Gung Memorial Hosipital

summary: Cytokine array analysis was performed on serum samples from mice undergoing either AP or NP wound therapy in the early stages of wound healing, specifically at 0, 0.5, 2, and 16 hrs post-injury.

overall_design:
To assess the impact of NPWT on wound recovery in mice, we conducted a randomized division of mice into two groups: one subjected to traditional wet dressing under atmospheric pressure (AP: 0, 0.5, 2, 16 hrs) and the other to negative pressure (NP: 0.5, 2, 16 hrs) wound therapy. After wound therapy, we collected the blood sample and detected 111 cytokines levels through cytokines array kit, each cytokines two repeated, and each experiment two repeated (exclude AP 0hrs).
Please note that each .xlsx data file contains the raw, normalized, and fold-change data for both replicates and is linked to the corresponding rep1 sample records.

first: Hua-Sheng

last: Chiu

first: Pavel

last: Sumazin

first: Po-Cheng

last: Liao

first: Chien-Tzung


title: Targeting METTL3 protein by PROTAC: A Novel Therapeutic Approach for Acute Myeloid Leukemia

city: Gainesville

first: Yutao

last: Zhang

state: FL

address: 2033 Mowry Road, CGRC 285

institute: University of Florida

summary: Despite numerous studies suggesting that RNA m6A transferase core complex including METTL3 and METTL14 play essential roles in both the initiation and maintenance of Acute myeloid leukemia (AML), effective pharmacological targeting of these two proteins remains elusive. Here, we report the development and evaluation of a novel METTL3 degrader, ZW27941, designed to induce METTL3 degradation via the VHL-mediated proteasomal degradation pathway. ZW27941 exhibited potent and selective degradation of METTL3 and its binding partner METTL14, leading to significant anti-leukemic activity in AML cell lines. Furthermore, ZW27941 demonstrated synergistic or additive effects when combined with standard AML therapeutics, such as Cytarabine and Venetoclax. Our findings suggest that selective METTL3 degraders, exemplified by ZW27941, hold promise as a novel therapeutic approach for AML, particularly when used in combination with existing treatments to enhance efficacy and overcome resistance mechanisms.

overall_design: To explore the regulatory role of the METTL3 degrader ZW27941 in  AML cells, we treated MOLM13 cells with DMSO or ZW27941 (1 μM) for 24 h, and then performed gene expression profiling analysis using data from RNA-seq of those cells. Comparative gene expression profiling analysis of RNA-seq data for DMSO treated MOLM13 cells and ZW27941 (1 μM) treated MOLM13 cells.

first: Rukiye

last: Nar

first: Zhixing

last: Wu

first: Yafang

last: Li

first: Alexis

last: Smith

first: Jue

last: Wang

first: Fang

last: Yu

first: Sanhui

last: Gao

first: Chunjie

first: Zhiguang

last: Huo

first: Guangrong

last: Zheng

first: Zhijian

last: Qian


title: RNA sequencing of lung tissues from Mycobacterium orygis infected and healthy cattle.

city: Hyderabad

first: Bappaditya

last: Dey

state: Telangana

address: Survey No. 37, Extended Q City Road, Gachibowli

country: India

institute: National Institute of Animal Biotechnology

summary: Whole RNA transcriptome was performed on bovine lung granulomatous tissues from Mycobacterium orygis infected cattle and compared with healthy cattle lung tissues.

overall_design: Bovine lung tissues displaying granulomatous lesions and healthy lung tissue from crossbred Sahiwal X Holstein Friesian cattle were collected. Whole transcriptome sequencing was performed using paired-end sequencing in a  Illumina NovaSeq 6000 platform.

first: Rishi

last: Kumar

first: Sripratyusha

last: Gandham

first: Vinay

last: Bhaskar

first: Manas

middle: R

last: Praharaj

first: Hemanta

middle: K

last: Maity

first: Uttam

last: Sarkar


title: JMJD1C facilitates long distance genomic interactions by promoting condensates formation of key leukemic transcription factors in multiple AML cells

first: Qian

last: Chen

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

overall_design: Refer to individual Series


title: Application of RNA-seq for single nucleotide variation identification  patients with hereditary diseases: analysis of trasncriptomic data and perspective use

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

institute: National Research Center «Kurchatov Institute»

summary: Background: Various DNA sequencing methods, including particular genes sequencing, whole genome sequencing or exome sequencing, are presently used to identify single nucleotide variations (SNVs) associated with inherited diseases. Most of the known mutations and polymorphisms associated with hereditary diseases are localized in the coding regions and cause an amino-acid substitution, appearance of new stop codon or open reading frame shifts. These types of mutations can be identified using transcriptome sequencing.  Full transcriptome sequencing is widely used to study diseases. The results of such investigations are usually available in public databases. This data could be tapped for identification of novel mutations and disease-associated variants. In this study, we are analyzing the potential use of full transcriptome sequencing for SNV identification, using RNA-seq of myocardium of patients with HCMP as an example.  The goal of the current study is development of pipeline for SNV identification from RNA-seq data and application of this pipeline to identification of putative pathogenically significant SNV. Results:  The algorithm of identification of SNV based on transcriptomic sequencing data has been developed. The algorithm was evaluated and the optimal quality threshold was determined based on allelic discrimination for the rs397516037 mutation (MYBPC3 c.3697C>T) among patients. A quality threshold of 75 was selected, at which false-positive and false-negative results for the rs397516037 variant were excluded. 43587 total SNVs with 75 and higher quality was identified in 48 transcriptomes of HCMP patients. In order to further verify the results obtained using the algorithm, 8 SNVs were selected in the MYBPC3 and MYH7 genes. Each of these 8 SNVs was confirmed by Sanger sequencing.  Conclusions:  The developed method has proven its effectiveness in identifying putative pathogenic variants in RNA-seq data. Its use will be especially useful in the context of large volumes of accumulated transcriptomic data that have not been analyzed in this way before. However, it is necessary to consider the limitations and scope of this method. The study was conducted on the basis of a disease and mode of inheritance are well suited for this method, but in other cases its applicability should be assessed individually.

overall_design: Examination of transcriptiomic profiles of the myicardium, derived from HCMP and IHD patients

first: Chumakova

last: Anastasia

first: Vlasov

last: Ivan

first: Filatova

last: Elena

first: Klass

last: Anna

first: Lysenko

last: Andrey

first: Salagaev

last: Gennady

first: Shadrina

last: Maria

first: Slominsky

last: Petr


title: An integrative approach zinc induced integrated stress response as a key driver for β cell failure in human type 2 diabetes

city: Shanghai

first: Xiangyi

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

summary: Dysfunctional pancreatic islet β cells are a hallmark of type 2 diabetes (T2D), yet effective therapies to protect these cells from dysfunction are lacking. In this study, through a combination of islet single-cell data from independent cohorts and machine learning, we reveal zinc-induced integrated stress response (ISR) as a potential target for β cell protection. Validating our findings with human embryonic stem cell-derived β cells (SC-β cells) and human primary islets, we confirm that inhibiting zinc transportation shields β cells from exacerbated endoplasmic reticulum stress (ER stress) and concurrent integrated stress response (ISR). Mechanistically, our results discover that elevated zinc transportation exacerbates ER stress, promoting phosphorylation of the eukaryotic translation initiation factor 2 (eIF2α) subunit, thereby initiating ISR, enhancing stress granule formation, and ultimately leading to β cell death as a pivotal pathomechanism for β cell loss. Furthermore, through compound screening targeting zinc transportation with SC-β cells, we discover that low-dose (nanomolar) anisomycin significantly inhibits zinc transportation, preventing β cell loss from various stress-induced cell deaths. Significantly, in vivo administration of anisomycin in mice protects β cells and prevents diabetes induced by streptozotocin (STZ) and type 2 diabetes (high-fat diet, HFD). Collectively, our findings highlight the potency of combining large-scale single-cell data, machine learning, human embryonic stem cell-derived cells, and compound screening to identify potential therapeutic molecules against complex diseases.

overall_design: We generated hESCs reporter cell line (MEL1 Nkx6.1:linker2a:mCherry; INSGFP/w) that enable to precisely and dynamically trace SC-β cells during differentiated stages. Meanwhile, WFS1 knockout hESCs reporter cell line (WFS1-/-) was established by using a CRISPR/Cas9 knock-out strategy to mimic severe mutations identified from WS patients. We performed single-cell RNA sequencing (scRNA-Seq) for WFS1-/- and WFS1-/- + Inh19 SC-islets by sorting out GFP and mCherry double-positive SC-β cells with high INS and NKX6.1 expression

first: Rui

last: Hu

first: Weida

last: Li


title: Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming

city: nanjing

first: Shizhen

last: Zhou

state: jiangsu

address: 鼓楼区汉口路58号

institute: Department of General Surgery, Nanjing Drum Tower Hospital

summary: Colorectal cancer (CRC) is a common malignant neoplasm influenced by both genetic and environmental factors, and its incidence correlates with the composition of the gut microbiota. Relevant studies have demonstrated that gut microbiota dysbiosis is associated with CRC progression. However, the relationship between CRC tumor proliferation and dysregulation of tryptophan metabolism remains unclear. Our investigation addresses the role and mechanisms of amino acid metabolites in tumor progression based on the dysregulation of tryptophan metabolism in clinical CRC patients. Using metagenomic sequencing and targeted tryptophan metabolomics, our research delineates the aberrant levels of indole-3-lactic acid (ILA) in CRC patients. ILA inhibits glycolysis via the STAT3-HK2 axis and exerts a suppressive effect on CRC independent of the aryl hydrocarbon receptor (AHR). By elucidating the inhibitory role of ILA in CRC and uncovering its underlying mechanisms, our study provides a prospective therapeutic avenue for CRC treatment.

overall_design: Co culture ILA (1mM) with HCT116 cells for 24 hours, with the same concentration of DMSO as the control. Observe the effect of ILA on mRNA expression in HCT116 cells.

first: Kai

last: Wang


title: Effect of CSPTTK21 on 12 month-old Thy-Tau22 mice, hippocampal samples (ChIP H3K27ac)

first: Charles

last: DECRAENE

summary: This project aims to identify epigenetic signatures (histone acetylation-related) associated with Tau pathology in hippocampal region of Thy-Tau22 mice in basal conditions and after treatment with CSP-TTK21. For this we performed ChIP for H3K27ac in whole hippocampus of 12 month-old Tau reated with the vehicle CSP or CSP-TTK21, as well as of CSP-treated 12 month-old WT mice.In total we have 6 IPed samples (Biological duplicates were analyzed) and 3 Inputs. Spike-in from drosophila chromatin was added to the samples.

overall_design: ChIP-Seq

first: Anne-Laurence

last: Boutillier

first: Isabel

last: Paiva


title: JMJD1C facilitates long distance genomic interactions by promoting condensates formation of key leukemic transcription factors in multiple AML cells [RNA-seq]

first: Qian

last: Chen

overall_design: RNA-seq when RUNX1 was knocked-down in Kasumi-1 and MOLM13 cells and RNA-seq when JMJD1C was knocked-down in MOLM13 cells.

first: Mo


title: Extracellular vesicles derived from ASCs Deliver Mitochondria Reprogramming DCs Metabolism to Alleviate Rat TMJOA

city: Chongqing

first: Jie

state: Chongqing

address: 426# Songshibei Road, Yubei District

department: College of Stomatology

institute: Chongqing Medical University

summary: EVs contain mitochondria that are transferred to condylar DCs. This action triggers ERK1/2/FoxO1/ autophagy pathway internalization of phagocytosed mitochondria by mitochondrial recipient cells, which subsequently affect fatty acid metabolism in DCs to metabolically reprogram them. Thus, DCs changed from an activation state to a tolerance state. Taken together, our findings suggested that EVs reprogram the states of condylar DCs by transferring functional mitochondria into them and affecting their fatty acid metabolism, which highlights the therapeutic value of EVs for TMJOA.

overall_design: To explore the mechanism by which EVs exert their effects, we subjected DCs with different treatments to RNA sequencing

first: Ziyi

last: Mei


title: Transcriptomic characterization of human primary prostate stromal cells upon exposure to chemotherapy and treatment by a natural flavonoid apigenin

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Senescent cells accumulate in a wide variety of solid tissues of mammalian species with advancing age, functionally promoting chronic inflammation and causing age-related diseases. Apigenin is one of the most abundant flavonoids in fruits and vegetables of human diet with several demonstrated health benefits. The aim of the present study is to investigate the influence of apigenin, the natural phytochemical agent with antioxidant, anti-inflammatory and anticancer properties reported by former studies, on human primary stromal cells induced senescent in vitro by a genotoxic agent frequently used in clinical oncology. We mainly focused on the capacity of apigenin in controlling the expression of a full spectrum senescence-associated secretory phenotype (SASP), one of the major hallmarks of senescent cells.

overall_design: High-throughput RNA-seq examination of genome-wide transcriptional alterations of primary normal human prostate stromal cells (PSC27) that underwent senescence-inducing treatment by the chemotherapeutic agent bleomycin. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

first: Hongwei

last: Zhang


title: Sorting of neuronal hiippocampal signatures (ChIP-Seq H3K27ac H3k27me8)

summary: This project aims to identify neuronal signatures in the hippocampus of Home Cage WT mice. For this, we sorted neuronal and  non neuronal nuclei (NeuN+ and NeuN- ) of total hippocampus from 5-month-old WT mice. ChIP experiments were performed for 2 different histone marks (H3K27me3 and H3K27ac) in about 4-500000 sorted NeuN+ and NeuN- nuclei.  H3K27ac signatures were also assessed in 12 month-old WT mice. We have INPUT DNA For each condition (NeuN+ and NeuN-).


title: Transcritptomic on Ageing and learning processes (RNA-Seq)

summary: This project aims to assess the transcriptomic signature in the dorsal hippocampus associated with physiological ageing. For this we extracted total RNA from dorsal hippocampal tissues from 3- and 18-month-old mice (n=4) and analzed  the differential expressed genes.

overall_design: RNA-Seq