title: Genomics data for CCl4-induced mice liver fibrosis

city: Guiyang city

first: Tao

last: Huang

address: No.252 Shuangjiang Road

institute: the Affiliated Hospital of Guizhou Medical University

summary: Objective: To understand the transcriptome data of liver fibrosis induced by CCl4 in mice.Methods: C57BL/6 mice were used to duplicate the liver fibrosis model induced by CCl-4.After successful replication, mouse RNA was extracted for subsequent experiments.The basic principle of RNA extraction is to prevent RNA degradation during extraction, maximize RNA extraction efficiency, and ensure the extraction of high-quality RNA with good integrity and purity from target samples.According to the species (such as animal sample or plant sample) and sample status (such as animal tissue or animal cell) of the sample, select the appropriate extraction reagent and corresponding extraction method.The detection of high-quality RNA in samples is the basis for the success of the whole project. In order to ensure the accuracy of sequencing data, we performed quality inspection on samples, and the library construction can only be performed after the detection results meet the requirements for sequencing library construction.Sample test results are shown in the quality inspection report.After the library construction samples passed the test, the mRNA of eukaryotes was enriched with magnetic beads with Oligo (dT).Subsequently fragmentation buffer was added to randomly interrupt the mRNA.First-strand cDNA was synthesized using mRNA as a template with a six-base random primer (random hexamers), followed by buffer, dNTPs, and DNA polymerase I to synthesize the second-strand cDNA, which was subsequently purified using AMPure XP beads.Purified double-stranded cDNA was then end-repaired, A-tailed and ligated with sequencing adapters, followed by fragment size selection with AMPure XP beads, and finally PCR enrichment to obtain the final cDNA library.After library construction, insert size and effective concentration of the library were tested to ensure library quality.After passing the library test, different libraries were pooling according to the amount of data under the target and sequenced on the machine.RESULTS: RNA-seq data of CCL4-induced liver fibrosis model in mice were finally obtained in our experiment, which provided a molecular biological basis for our future study of liver fibrosis in mice.

overall_design: To invesitgate the effect of CCl4 on mice liver, C57BL/6 mice were used in this study. We then perform RNA-seq of 2 conditions. Sequencing contains adapter-bearing, low-quality reads. In order to ensure the quality of subsequent analysis, it is necessary to remove adaptor sequences, filter out reads with low quality (Low Quality, the number of bases with base quality value less than or equal to 25 accounts for more than 60% of the entire reads) and N (N indicates that the base information cannot be determined) ratio greater than 5%, obtain reads.HISAT2, which can be used for subsequent analysis, is a software for second-generation sequencing sequence alignment, which can align the whole genome, transcriptome and exome data with the reference genome. Using the improved BWT algorithm, it can efficiently align the sequencing reads to the reference genome. In this project, Clean Reads were aligned to the designated genome using HISAT2 software to obtain information on their location on the reference genome. The algorithm of HISAT2 is mainly divided into three parts: (1) aligning the whole sequencing sequence to a single exon of the genome; (2) aligning the sequencing sequence segment to two exons of the genome; and (3) aligning the sequencing sequence segment to more than three (including three) exons of the genome.


title: Phosphatase MAP4K4 regulates neutrophil development through the apoptosis pathway

status: Public on Feb 12 2025

city: Chengdu

first: chen

last: li

address: Renmin South Road

country: China

institute: Sichuan Univercity

type: Expression profiling by high throughput sequencing

summary: The role of MAP4K4 in the development of neutrophils remains largely unexplored. We utilized single cell sequencing (scRNA-seq) technology to elucidate the impact of Map4k4 deficiency on neutrophil maturation within mouse bone marrow. Through the application of scRNA-seq, we characterized the transcriptional changes across various stages of neutrophil development in both Map4k4-deficient (Map4k4-cKO) and control mice.

overall_design: Control or Map4k4-cKO mice c-Kit+ BM HSPCs mixed with BM cells at a 2:3 ratio to create a c-Kit/BM population artificially and analyzed using scRNAseq

first: Dan

last: Zhang

first: Guihua

last: Wang


title: Decoding SFRP2hi Fibroblast Progenitors in Sustaining Tooth Growth in Humans and Mice at Single-Cell Resolution

city: ChangChun

first: Zhengwen

last: An

state: JiLin

address: HeGuang Road 763

department: Department of Oral Biology

institute: Jilin University

summary: Single-cell transcriptomics has revolutionized tooth biology by uncovering previously unexplored areas. The mouse is a widely used model for studying human tissues and diseases, including dental pulp tissues. While human and mouse molars share many similarities, mouse incisors differ significantly from human teeth due to their continuous growth throughout their lifespan. The extent to which studies on mouse teeth can be applied to human disease translation remains underexplored. By leveraging multiple single-cell datasets, we constructed a comprehensive dental pulp cell landscape to clarify tissue similarities and species-specific differences between humans and mice. Notably, we identified a distinct cell population, Sfrp2hi fibroblast progenitors, found exclusively in mouse incisors and the developing tooth root of human molars. These cells are uniquely present to sustain continuous tissue growth. Mechanistically, we found that the transcription factor Twist1, regulated by MAPK phosphorylation, binds to the Sfrp2 promoter and modulates Wnt signaling activation to maintain stem cell identities. Our research reveals a previously unrecognized subset of dental mesenchymal stem cells instrumental in tooth growth. This distinct subset is evolutionarily conserved in both humans and mice, offering valuable translational insights.

overall_design: Mouse incisors from mandibles were carefully dissected from 15 C57BL/6 mice aged 7 weeks. The incisor pulp, with minimal inclusion of dental epithelium, was isolated and analysed using scRNAseq.

first: Tianyuan

last: Zhao

first: Zewen

last: Sun

first: Qing

last: Zhong

first: Xiaoyi

last: Yu

first: Tianmeng


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [sorted_alpha_nkx2.2_KO_RNAseq]

city: Aurora

first: Lori

last: Sussel

state: Colorado

address: 1775 Aurora ct.

country: USA

institute: CU Anschutz

summary: Transcription factors (TF) are indispensable for maintaining cell identity through regulating cell specific gene expression. Distinct cell identities derived from a common progenitor are frequently perpetuated by shared TFs; yet the mechanisms that facilitate their cell specific regulatory targets are poorly characterized. We report that the TF NKX2.2 is critical for the identity of pancreatic islet α cells by directly activating α cell genes and repressing alternate islet cell fate genes. When compared to the known role of NKX2.2 in islet β cells, we demonstrate that NKX2.2 regulates novel α cell target genes, facilitated in part by α cell specific DNA binding at gene promoters. Furthermore, we have identified the reprogramming factor KLF4 as having enriched expression in α cells, where it co-occupies NKX2.2-bound α cell promoters and is necessary for NKX2.2 binding in α cells to co-regulate many NKX2.2 α cell transcriptional targets.  Misexpression of Klf4 in β cells is sufficient to manipulate chromatin accessibility, increase binding of NKX2.2 at α cell specific promoters sites, and alter expression of NKX2.2-regulated cell specific targets.  This study identifies KLF4 is a novel α cell identity factor that cooperates with NKX2.2 to regulate α cell identity.

overall_design:
To investigate the gene expression regulation by NKX2.2 in in vivo pancreatic alpha cells.
Pancreatic alpha cells were FACS purified from C57B1/6J mouse pancreatic iselts using the genotypes Nkx2.2fl/fl;Gcg-iCre;Rosa25:tdTomato or Nkx2.2+/+;Gcg-iCre;Rosa25:tdTomato
Using 3 mutant samples and 4 control samples differential gene expression analysis on this RNAseq were conducted using DESEQ2 with no batch correction.

first: Elliott

middle: P

last: Brooks

first: Kristen

middle: L

last: Wells

first: McKenna

middle: R

last: Casey


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [aTC_klf4_KD_nkx2.2_ChIPseq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
To charcterize the changes in genomic occupancy of NKX2.2 when Klf4 expression is knocked down  in alphaTC alpha cells
Chromatin immunoprecipication was performed on alphaTC6 alpha cell culture using an anti-NKX2.2 antibody that was transfected with either a Klf4 siRNA knockdown  or siScramble control
ChIP-seq was done on 3-4 biological replicates in both the klf4 knockdown and scramble control of the NKX2.2 ChIP and input samples. Csaw was used to perform the differential binding analysis.


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [aTC_nkx2.2_ChIPseq]

overall_design:
To charcterize the genomic occupancy of NKX2.2 in alphaTC alpha cells
Chromatin immunoprecipication was performed on alphaTC6 alpha cell culture cells using an anti-NKX2.2 antibody
ChIP-seq was done on 2 biological replicates of the NKX2.2 ChIP and input samples and Macs2 peak calling was used to find binding peaks


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [MIN6_klf4_OE_RNAseq]

overall_design:
To investigate the effect of Klf4 misexpression on the Min6 beta cell transcriptome.
Pancreatic beta cell culture MIN6  were transfected with either Klf4-OE expression plasmid to overexpress Klf4 or a empty vector control
RNAseq on 4 biological replicates were used per treatment group to perform  differential gene expression analysis on this RNAseq were conducted using edgeR with batch correction.


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [aTC_klf4_KD_RNAseq]

overall_design:
To investigate the gene expression regulation by Klf4 in in vitro pancreatic alpha cells.
Pancreatic alpha cell culture alphaTC6 we transfected with either Klf4 siRNA pool to KD Klf4 or a siScramble control
RNAseq on 4 biological replicates were used per treatment group to perform  differential gene expression analysis on this RNAseq were conducted using EdgeR with batch correction.


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [islet_alpha_klf4_KO_RNAseq]

overall_design:
To investigate the gene expression regulation by KLF4 in in vivo pancreatic alpha cells.
Whole pancreatic islets  from C57B1/6J mouse pancreatic of the genotypes Klf4fl/fl;Gcg-iCre or Klf4+/+;Gcg-iCre
Using 3 mutant samples and 3 control samples differential gene expression analysis on this RNAseq were conducted using DESEQ2 with no batch correction.


title: The effect of microplastics on the nasal epithelial cells in obstructive lung diseases

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: The goal of this study was to evaluate the biological effect of microplastic fibres on nasal epithelium  from healthy subjects, as well as asthma and COPD pateients. We demonstrated the distinct biological response of asthmatic and COPD epithelial cells to microplastic fibers stimulation compared to healthy epithelial cells. ANKRD36, BCL2L15, C15orf48, CAPN14, FCGBP, FST, IL-19, MAFF, PGBD5, PKP1 and PTPRH are important markers of epithelial response after microplastic stimulation in obstructive lung disaeses. These mediators are linked to Th2 inflammation, alleviation of stress response, and, most notably, carcinogenesis. We demonstrated the distinct biological response of asthmatic and COPD epithelial cells to microplastic fibers stimulation compared to healthy epithelial cells. ANKRD36, BCL2L15, C15orf48, CAPN14, FCGBP, FST, IL-19, MAFF, PGBD5, PKP1 and PTPRH are important markers of epithelial response after microplastic stimulation in obstructive lung disaeses. These mediators are linked to Th2 inflammation, alleviation of stress response, and, most notably, carcinogenesis. Microplastic stimulation differently modified the response of airway epithelial cells in obstructive lung diseases than in controls. Asthmatic and COPD epithelial cells are more prone to damage after microplastic fibre exposure.

overall_design: A co-culture model (4 controls, 4 asthma, and 4 patients with COPD) employed nasal epithelial cells,  was exposed to polyamide fibres for 48h. The cells were cultured at an air-liquid interface (ALI) for 21 days in PneumaCult medium (StemCell) within a two-chamber system (Greiner Bio-One). Cells were then stimulated with microplastic fibres (200 µg/cm2).

first: Magdalena

last: Paplinska-Goryca

first: Paulina

last: Misiukiewicz-Stepien


title: RNA-seq of ex vivo differentiated osteoclasts of FLT3 ITD Ptprc KO mice and controls

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: The receptor tyrosine kinase FLT3 is expressed in myeloid and lymphoid progenitor cells. Here, the influence of the FLT3 ITD mutation and PTPRC inactivation on the bone remodeling was studied in mice.  Gene expression analysis of differentiated osteoclasts showed dysregulated signaling pathways influencing their differentiation as well as the coupling of bone resorption and formation.

overall_design: RNA-seq data comprises four osteoclast cell cultures seeded from CD11b-positve bone marrow cells of different C57BL/6J mice lines (wild type, Ptprc KO, Flt3 ITD KI, Flt3 KI Ptprc KO).  24 samples in 4 groups: wild type (4 samples), Ptprc KO (4 samples), Flt3 ITD KI (4 samples), Flt3ITD KI Ptprc KO (4 samples).

first: Carolin

last: Lossius

first: Akua

last: Annouh

first: Martin

last: Bens

first: Sandor

last: Nietzsche

first: Martina

last: Rauner

first: Lorenz

middle: C

last: Hofbauer

first: Jörg

last: Müller


title: METTL7A improves bovine embryo competence by attenuating oxidative stress

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: In vitro fertilization (IVF) is currently one of the most used assisted reproductive technologies to achieve a successful pregnancy. However, the acquisition of oxidative stress in embryo in vitro culture impairs its competence. Here, we demonstrated that the S-adenosyl-L-methionine (SAMe)-dependent thiol methyltransferase, methyltransferase-like protein 7A (METTL7A) improves the developmental potential of bovine embryos. We found exogenous METTL7A modulates expression of genes involved in embryonic cell mitochondrial pathways and promotes trophectoderm development. Surprisingly, we discovered that METTL7A alleviates mitochondrial stress and DNA damage and promotes cell cycle progression during embryo cleavage. In summary, we have identified a novel mitochondria stress eliminate mechanism regulated by METTL7A that occurs during the acquisition of oxidative stress in embryo in vitro culture. This discovery lays the groundwork for the development of METTL7A as a promising therapeutic target for IVF embryo competence.

overall_design: To investigate the role of METTL7A in bovine pre-implantation development, we overexpressed METTL7A by zygotic injection of in vitro transcribed METTL7A mRNA and conducted RNA-seq at 2-cell, 8-cell and blastocyst stages to profile differentially expressed genes.

first: Linkai

last: Zhu


title: Enhancing Human ACE2 Expression in Mouse Models for Improved COVID-19 Research

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

summary: Several humanized ACE2 (hACE2) mouse models have been developed for COVID-19 studies. Insertion of hACE2 at mouse Ace2 locus enables the utilization of endogenous promoter to drive its expression, better reflecting ACE2 abundance in various cell types and tissues. However, the relatively low expression of hACE2 in these mice may limit their fidelity in mimicking COVID-19 manifestations in humans and hinder their application in viral studies. In this study, we generated four hACE2 mouse models using different strategies for hACE2 expression. We found that the position of the β-globin intron within hACE2 cassette could have contrasting effects on hACE2 expression, with its placement downstream of hACE2 significantly increasing its transcription. Western blot analysis demonstrated that optimizing hACE2 codon usage further enhanced translation efficiency from all tested tissue. Consistent with elevated hACE2 expression, opt-hACE2 mice displayed more active immune response and severe COVID-19 phenotypes following SARS-CoV-2 challenging compared to other hACE2 mouse models. Thus, our study has elucidated the dual role of β-globin element in transgene expression, and highlighted that mice with optimized hACE2 codon preference could serve as a better model for SARS-CoV-2 studies.

overall_design:
To investigate the pathological outcomes of lungs in different hACE2 mouse models upon SARS-CoV-2 infection, we infected WPRE-hACE2, hACE2/β-globin, and opt-hACE2 mice with the original strain of the coronavirus from Wuhan (WIV04) , and harvest RNA samples of lungs at 3 day-post-infection (dpi).
we then performed RNA-seq, and compared the transcriptome changes of lungs between mock-infected and viral-infected mice from different models.

first: Wu

last: Haoyu

first: Hong

last: Guangliang


title: Loss ofPRICKLE1promotes abnormal endometrial epithelial architecture, reduced fertility, and decreased embryo implantation in mice.

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Successful embryo implantation requires coordinated changes in the uterine luminal epithelium, including structural alterations, apical-basal polarity shifts, intrauterine fluid resorption, and cellular communication. These processes, collectively termed plasma membrane transformation (PMT), are crucial but poorly understood, especially regarding their regulation by planar cell polarity (PCP) proteins. PCP proteins, essential for cell organization, are understudied in the context of uterine physiology. Prickle proteins, particularly Prickle1, play critical roles in cellular polarization and tissue morphogenesis. However, their function in the endometrial epithelium during embryo implantation is unknown. To investigate Prickle1's role in uterine physiology, we developed an endometrial epithelial conditional knockout (cKO) of Prickle1 using Lactoferrin-icre. PRICKLE1 ablation in the endometrial epithelium resulted in decreased fertility and embryo implantation by gestational day 4.5. Three-dimensional imaging revealed abnormal luminal folding, impaired luminal closure, and altered glandular structure in mutant uteri. Additionally, we observed decreased aquaporin-2 expression, disrupted cellular architecture, and protein expression and localization in mutant uteri. Evidence of epithelial-to-mesenchymal transition (EMT) was found within luminal epithelial cells, further linking PRICKLE1 loss to uterine pathologies. Furthermore, altered cellular division planes and increased multinucleated cells suggested a connection to EMT. Our findings highlight PRICKLE1's critical role in the PCP pathway within the uterus, revealing its importance in the molecular and cellular responses essential for successful pregnancy establishment.

overall_design: Whole uteri of Prickle1f/f Ltf-iCre cKO and control mice aged 6 months were isolated. Control samples (n=3) were pooled and cKO samples (n=3) were pooled.

first: Emily

last: Roberts

first: Aishwarya

last: Bhurke

first: Sornakala

last: Ganeshkumar

first: Ripla

last: Arora

first: Vargheese

last: Chennathukuzhi


title: 3D Bioprinting Lobule-like Hepatorganoids with Induced Vascularization for Orthotopic Implantation

city: Hangzhou

first: Zhichao

last: Ye

address: Huajiachi Campus

institute: Zhejiang University

summary: Orthotopic implantation tumor assays are frequently employed in tumor biology, drug screening, and personalized therapy researches. However, the limited representation of a complex tumor microenvironment in these implanted animal models hampers a comprehensive understanding of tumor progression and therapeutic response. In this research, we developed a 3D bioprinting method using gelatin methacryloyl (GelMA) hydrogel loaded with a prolonged released system of vascular endothelial growth factor (VEGF), embedding hepatocellular carcinoma cells, to fabricate lobule-like hepatorganoids that faithfully mimic the architecture of hepatic lobules. Moreover, we utilized GelMA hydrogel mixed with Matrigel, containing human umbilical vein endothelial cells (HUVECs), to induce vascularization on the organoids. Orthotopic implantation in mouse model was performed, allowing for an improved simulation of the vascularization process within hepatorganoids. Compared to control group, 3D bioprinted lobule-like hepatorganoids exhibited prolonged survival in mice, while serum analysis revealed significantly elevated levels of alpha-fetoprotein (AFP). Eventually, our findings demonstrate that this system effectively forms orthotopic implantion of liver tumors and facilitates vascularization, which may notably contribute to the understanding of tumor biology, drug screening, and personalized therapy.

overall_design: Gene expression profiles of 3D bioprinted vascularized lobule-like hepatorganoids (VLH), 3D bioprinted HUVECs-hepatorganoids (HH), 3D bioprinted VEGF/hepatorganoids (VH), 3D bioprinted hepatorganoids (3DC) and 2D cultured huh7 (2DC) cells.


title: Gene expression analysis in canine interface dermatitis [DLE, MLE, DI-CLE]

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a comparative immunology case study of client-owned dogs to determine if immune and skin gene expression profiles in canine interface dermatitis.

overall_design: Gene expression was analyzed using 160 custom Nanostring probes to analyze 8 canines with DLE, 1 canine with MLE and 1 canine with DI-CLE compared to 5 healthy controls (leg margin excisions).

first: Shriya

last: Kannan

first: Nicholas

last: Robinson

first: Ramon

last: Almela


title: Gene expression analysis in canine

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

overall_design: Refer to individual Series


title: LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [ATAC-seq]

city: Toronto

first: Lamisa

last: Ataei

state: ON

address: 25 Orde St

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: In this study, we investigated the status of chromatin accessibility in naïve hES cells with DJ-LINE1 repression compared to control by Assay of Transposase Accessible Chromatin (ATAC)-seq.

overall_design: Naive H9 hES cells were maintained RSeT. Cells were transfected with gRNA plasmids in RSeT media added with 10 nM DZNep and 5nM TSA (RSeT+DT).  48 hours later, 50,000 sorted cells were directly processed for ATAC reaction and library preparation.

first: Miguel

last: Ramalho-Santos


title: LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [RNA-seq]

summary: In this study, we investigated whether RNA Pol II-mediated gene expression is affected by repression of DJ-LINE1. Guide RNAs targeting DJ-LINE1 or control genomic regions were transfected for 48h in CRISPRi naïve hESC.

overall_design: Naive H9 hES cells were maintained RSeT. Cells were transfected with gRNA plasmids in RSeT media added with 10 nM DZNep and 5nM TSA (RSeT+DT).  48 hours later, cells were directly processed for RNA extraction and RNA-seq library prep.


title: NKX2.2 and KLF4 cooperate to regulate α cell identity [MIN6_klf4_OE_ATACseq]

first: Lori

last: Sussel

overall_design:
To charcterize the the effect of Klf4 misexpression in beta cells on genomewide chromatin accessibility
Assays for transposase accessible chromatin (ATAC) were performed on live Min6 beta cells hat had been transfected with either a Klf4 expression plasmid or and epmty vector control plasmid.
ATAC-seq was done on 4 biological replicates for each transfection treatment. Peak calling was performed using MACS2 and diffbind was used to perform the differential accessibility analysis

first: Elliott

last: Brooks

first: Kristen

last: Wells

first: McKenna

last: Casey


title: Single cell lineage tracing of pulmonary endothelial cells in mouse model of Hereditary Hemorrhagic Telangiectasia 2

city: Los Angeles

first: Xiuju

last: Wu

state: CA

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: Arteriovenous malformations (AVMs) are characteristic of hereditary  hemorrhagic telangiectasia (HHT). We used single cell RNA sequencing (scRNA-seq) to trace pulmonary EC lineages in mice with endothelial-specific deletion of Alk1 gene.

overall_design: Lung VE-cadherin-cre tdTomato+ cells were isolated by fluorescence-activated cell sorting (FACS), and analyzed using scRNA-seq.

first: Wu

last: Xiuju

first: Zhao

last: Yan


title: The effects of ELF-1 on gene expression profiles of colonic tissue in DSS colitis at single cell level

city: Zhengzhou

first: Peng

last: Wang

address: Science Avenue

institute: Zhengzhou University

summary: The maintenance of intestinal homeostasis is closely related to the epithelial integrity and permeability.Elf-1 has been shown to play an important role in the development and maintenance of various hematopoietic lineages,as well as in the regulating the function of endothelial cells during tumor angiogenesis.Here, we characterized the intestinal cell landscape in DSS-induced model with Elf-1 deficiency at the single-cell level, and uncovered the disruption of intestinal immune homeostasis associated with Elf-1 deficiency.

overall_design: Colonic tissue were isolated from WT and Elf-1 knockout( Elf-1 KO) mice and analyzed with scRNA-seq


title: Molecular basis for condensin targeting to chromosomal loci [Hi-C]

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Faithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces and ensure the oriented attachment of kinetochores to microtubules at mitosis. Here we demonstrate that budding yeast condensin is recruited to pericentromeres through a direct interaction between its Ycg1 subunit and the pericentromeric adaptor protein, shugoshin (Sgo1). We identify a Short Linear Motif (SLiM), termed CR1, within the C-terminal region of Sgo1 which inserts into a conserved pocket on Ycg1. Disruption of this interface abolishes the Sgo1-condensin interaction, prevents condensin recruitment to pericentromeres and results in defective sister kinetochore biorientation in mitosis. Similar motifs to CR1 are found in known and potential condensin binding partners and the Ycg1 binding pocket is broadly conserved, including in mammalian CAP-G proteins. Overall, we uncover the molecular mechanism that targets condensin to define a specialized chromosomal domain.

overall_design: To determine how chromosome conformation changes in response to the absence of pericentromeric and rDNA condensin

first: Menglu

first: Adele

last: Marston


title: Angptl7+ chondrocytes and Sparc+ osteoblasts mediated the increased angiogenesis and abnormal remodeling of subchondral bone in the development of knee osteoarthritis

first: Yuan

last: Liu

state: Sichuan

address: No. 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

institute: SiChuan University West China Hospital

summary: With an increasing number of affected individuals and a trend towards younger age of onset, research on the treatment of knee osteoarthritis (KOA) is facing significant challenges. The pathogenesis of KOA is complex for being a multifactorial disease affecting the entire joint, and pathological remodeling of subchondral bone may be one of the key factors mediating the degeneration of the overlying cartilage. This study constructed a postmenopausal KOA mice model in bipedal mice to better understand how subchondral bone remodeling and cartilage degeneration interact during KOA development. The femoral condyle tissue, excluding the growth plate, was isolated from the distal epiphyseal line in KOA mice for single cell RNA sequencing and analysis. And a single-cell atlas of the osteochondral composite tissue, including chondrocytes, endothelia cells, osteoblasts, progenitor cells, and so on, was successfully constructed. Furthermore, three novel subtypes of chondrocytes, including Smoc2+ angiogenic chondrocytes, Angptl7+ angiogenic chondrocytes, and Col1a1+ osteogenic chondrocytes, were identified. Angptl7+ chondrocytes activated endothelia cells via the Fgf2-Fgfr2 interaction pathway, and promoted angiogenesis and vascular invasion in subchondral bone of KOA mice. The quantity of H-type vessels, which recruit numerous osterix+ osteoprogenitor cells and stimulate osteogenesis, exhibited an increase within the subchondral bone of mice with KOA. While Sparc+ osteoblast negatively regulated the bone mineralization and osteoblastic differentiation, aggravated the pathological remodeling of subchondral bone and KOA progression. These findings suggest that there are new avenues for potential therapeutic interventions in the treatment of KOA.

overall_design: To define cell populations and identify genome-wide gene expression patterns in the development of subchondral bone remodeling and cartilage degeneration. Ten femoral condyles from hindlimbs of 5 mice in each group at 22 weeks of age were isolated for scRNA-seq

first: Wacili

last: Da

first: Huiqi

last: Xie

first: Bin

last: Shen


title: Upregulation of the neuropeptide receptor calcitonin receptor-like in the spinal cord via MLL2 in a mouse model of paclitaxel-induced peripheral neuropathy

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Chemotherapy-induced peripheral neuropathy (CIPN) is a prevalent and severe side effect affecting cancer patients undergoing paclitaxel treatment. Growing evidence underscores the pivotal role of calcitonin-related peptide (CGRP) in the development of CIPN. Repeated administration of paclitaxel induces alterations in CGRP release from sensory neurons within the dorsal root ganglia (DRG). The density of the CGRP receptor is most prominent in the spinal horn, where it overlaps with the distribution of CGRP. However, the impact of chemotherapy medication on expression of the CGRP receptor in the spinal cord remains unclear, as well as the potential therapeutic benefits of a CGRP receptor antagonist in an animal model of CIPN. Using a mouse model of paclitaxel-induced mechanical hypersensitivity, we show upregulation of Calcitonin receptor-like receptor (Calcrl) mRNA expression in the spinal cord, an event that occurred in association with upregulation of the H3K4 methyltransferase MLL2. This effect of repeated paclitaxel administration was also linked to an increase in the recruitment of MLL2, thereby enhancing levels of the active mark H3K4me2 at the Calcrl promoter. Furthermore, administration of the CGRP receptor antagonist BIBN4096 mitigated mechanical and cold hypersensitivity in paclitaxel-treated mice. Together, these observations suggest the CGRP receptor in the spinal cord as a potential target for reducing paclitaxel-induced neuropathic pain in animal models.

overall_design: RNA-seq of the vehicle and paclitaxel-treated spinal cord samples (mouse).

first: Salvador

last: Sierra

first: Sara

last: Merz

first: Doan

last: On

middle: G

first: M

last: Imad Damaj

first: Javier

last: Gonzalez-Maeso


title: Short-read RNA-Seq experiment of major tissues from wild-type mice under fasting and fed treatments

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary:
Male C57BL/6 mice, sourced from the Jackson Laboratory, were acquired at 12 weeks of age. The mice were housed in groups of three per cage, with unrestricted access to water and a standard chow diet.
For the experimental treatments involving fasting and fed states (n = 3 per group), the mice were either provided continuous access to food or subjected to a 24-hour fasting period before euthanasia at 10 am for tissue collection.

overall_design: The tissues harvested included muscle, liver, heart, lungs, both white and brown adipose tissues, spleen, and kidney. These tissues were immediately preserved in liquid nitrogen post-sacrifice to maintain their integrity for subsequent analyses.

first: Chengfei

last: Jiang


title: ATAC-Seq experiment of major tissues from wild-type mice under fasting and fed treatments

summary:
Male C57BL/6 mice, sourced from the Jackson Laboratory, were acquired at 12 weeks of age. The mice were housed in groups of three per cage, with unrestricted access to water and a standard chow diet.
For the experimental treatments involving fasting and fed states (n = 3 per group), the mice were either provided continuous access to food or subjected to a 24-hour fasting period before euthanasia at 10 am for tissue collection. The tissues harvested included muscle, liver, heart, lungs, both white and brown adipose tissues, spleen, and kidney. These tissues were immediately preserved in liquid nitrogen post-sacrifice to maintain their integrity for subsequent analyses.

overall_design: The nuclei were isolated tissues from pooled frozen tissues and sent for ATAC-Seq library preparation.The ATAC-Seq DNA library generations were processed using Kaestner lab’s pipeline.The purified DNAs were amplified using TruSeq i7 index primers (Illumina) via PCR. The library quality and quantity were evaluated using Bioanalyzer and Qubit, and the final library was sequenced at NHLBI DNA Sequencing and Genomics Core.


title: LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

first: Lamisa

last: Ataei

summary: In this study, we constructed UMI-4C profiles of 5 different genomic loci (viewpoints) in two H9 human hES cell lines - naïve and primed - in order to study the 3D chromatin contact maps of these selected loci.

overall_design: Naive H9 hES cells were maintained RSeT and Primed H9 hES cells were maintained in mTeSR. UMI-4C was performed following previous reports by Schwartzman et al. with some modifications.

first: Simon

last: Monis

first: Miguel

last: Ramalho-Santos


title: Bruton’s tyrosine kinase inhibition re-sensitizes multidrug-resistant DLBCL tumors to venetoclax

city: miami

first: Jonathan

middle: H

last: Schatz

state: Florida

address: 1580 NW 10th Ave 1st floor

department: Department of Medicine

institute: university of miami

summary: Disparate mechanisms of pathogenesis have thwarted implementation of precision medicine approaches for the treatment of diffuse large B-cell lymphoma (DLBCL), the most frequently diagnosed hematologic malignancy in the United States. Though curable with combination chemoimmunotherapy in many newly diagnosed patients, DLBCL carries persistently poor prognosis for those with relapsed or refractory (rel/ref) disease, despite recent advances in immunotherapy. Here, we build on recent findings implicating gain-of-function mutations in the BCL10 signaling protein as drivers of resistance to Bruton’s tyrosine kinase (BTK) inhibitors. We show mutant BCL10-driven DLBCL models are resistant to multiple additional drug classes, demonstrating urgency to derive mechanistically rooted treatment strategies to overcome undruggable BCL10 mutants that form stable BTK-independent signaling filaments upstream of NF-kB activation. BCL10 mutants promote a cytokine-reinforced positive feedback loop of lymphomagenesis driving not just NF-kB but multiple additional pathways converging on diffuse activation of oncogenic transcription factors. Up-regulation of multiple anti-apoptotic genes promotes increased mitochondrial membrane potential, a key factor underlying multidrug resistance. Increased expression of BCL2, BCL2L1 (BCL-XL), and BCL2A1 (BFL1) drives resistance to the BCL2 inhibitor venetoclax, but further investigation revealed expression is overcome by the potent non-covalent BTK inhibitor pirtobrutinib. Venetoclax plus pirtobrutinib synergized in overcoming resistance and potently killed BCL10- mutant DLBCL tumors in vitro and in vivo. BTK therefore retains key roles protecting DLBCL tumors from apoptosis even when direct downstream activation of the BCL10 signaling complex activates NF-kB independently.

overall_design: To investigate the role of BCL10 mutations in diffuse large B cell lymphoma, we established RIVA cell lines with BCL10 mutations and vector in a doxycycline inducible plvx-Tetone vector. We then performed gene expression analysis using data obtained from RNA-seq of RIVA cells containing empty vector and BCL10 mutations after 24 hours of doxycycline induction.

first: Caroline

middle: A

last: Coughlin

first: Dhanvantri

last: Chahar

first: Marianna

last: Lekakis

first: Abdessamad

middle: Y

last: Alaoui

first: Lingxiao

last: Li

first: Evan

last: Roberts

first: Natalia

last: Camps Gallego

first: Claude-Henry

last: Volmar

first: Ola

last: Landgren

first: Shaun

last: Brothers

first: Anthony

middle: J

last: Griswold

first: Catalina

last: Amador

first: Daniel

last: Bilbao

first: Francesco

last: Maura


title: Distinct Cellular Mechanisms Underlie Chemotherapies and Their Combinations with PD-L1 Checkpoint Inhibitor in Triple-Negative Breast Cancer [TNBC]

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Panjiayuan nanli #17, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: The combination of immune checkpoint blockade (ICB) and chemotherapy holds promise for treating triple-negative breast cancer (TNBC), yet the underlying mechanisms remain incompletely understood. Here, we integrated previously published and newly generated single-cell RNA sequencing (scRNA-seq) data to investigate the tumor immune microenvironment (TIME) in advanced TNBC patients receiving various therapies, including paclitaxel, nab-paclitaxel, and their combinations with an anti-PD-L1 antibody atezolizumab. Notably, compared to atezolizumab plus paclitaxel, atezolizumab plus nab-paclitaxel primarily rewired TCF7+ stem-like effector memory CD8 T cells (Tsem) and CD4 follicular helper T (Tfh) cells. Nab-paclitaxel, but not paclitaxel, predominantly modulated the myeloid compartment, expanding mast cells and pro-inflammatory macrophage subsets. Our analyses in human TNBC and murine models highlighted the crucial role of mast cells in orchestrating anti-tumor immune responses, likely by recruiting and activating T cells and B cells. In vivo experiments demonstrated that activating mast cells alongside PD-L1 blockade significantly attenuated tumor progression, suggesting mast cells as a promising adjunct for enhancing ICB therapy efficacy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
In this study, we obtained 78 tumor biopsy samples derived from 44 TNBC patients. Within this cohort, 16 patients received nab-paclitaxel plus atezolizumab, 12 received nab-paclitaxel, 9 received paclitaxel plus atezolizumab, and 7 received paclitaxel.

***************************************************************
Submitter states that missing raw data will be uploaded to China Genomic Sequence Archive (GSA), according to the Regulations on the Management of Human Genetic Resources in China.
***************************************************************

first: Hongyan

last: Chen

first: Hongnan

last: Mo

first: Ning

last: Zhao

first: Binghe

last: Xu

first: Zemin

first: Zhihua

last: Liu

first: Fei

last: Ma


title: Sequencing to Explore the Mechanism Network of N-acetyltransferase 10 (NAT10) Promoting Colorectal cancer in human colorectal cancer cell SW620 [RIP-seq]

city: Wu Han

first: Gongcai

last: Tao

state: Hu Bei Province

address: No. 9, Zhangzhidong Road, Wuchang District

department: Department of Gastrointestinal Surgery

institute: Renmin Hospital of Wuhan University

summary: N-acetyltransferase 10 (NAT10), the only known mRNA ac4C “writer,” plays a significant role in several human diseases, including CRC and gastric cancer. As NAT10 can activate or repress important signaling pathways, such as the EMT pathway, DNA damage repair, or apoptosis, by catalyzing the ac4C modification of oncogene mRNA, targeting NAT10 shows great potential for inhibiting cancer cell malignant progression in vitro and in vivo. This complex network of colorectal cancer progression mediated by NAT10 remains to be identified, which can expand cancer therapy options. To identify potential NAT10-regulated ac4C targets, we checked RIP-Transcriptome Sequencing in human colorectal cancer cell SW620.

overall_design: To identify potential NAT10-regulated ac4C targets which has interaction with NAT10, we checked RIP-Transcriptome Sequencing to find the interaction between NAT10 and its target in human colorectal cancer cell SW620.

first: Dan

last: Song

first: Chenhong

last: Wang

first: Mingzhen

first: Yanxin

last: An

first: Yongbin

last: Zheng


title: Direct RNA sequencing experiment of major tissues from wild-type mice under fasting and fed treatments

first: Haiming

last: Cao

first: Chengfei

last: Jiang


title: Sequencing to Explore the Mechanism Network of N-acetyltransferase 10 (NAT10) Promoting Colorectal cancer in human colorectal cancer cell SW620

summary: N-acetyltransferase 10 (NAT10), the only known mRNA ac4C “writer,” plays a significant role in several human diseases, including CRC and gastric cancer. As NAT10 can activate or repress important signaling pathways, such as the EMT pathway, DNA damage repair, or apoptosis, by catalyzing the ac4C modification of oncogene mRNA, targeting NAT10 shows great potential for inhibiting cancer cell malignant progression in vitro and in vivo. This complex network of colorectal cancer progression mediated by NAT10 remains to be identified, which can expand cancer therapy options. To identify potential NAT10-regulated ac4C targets, we checked mRNA sequencing in human colorectal cancer cell SW620.

overall_design: To identify potential NAT10-regulated ac4C targets, we established NAT10 knocking-down cell lines in SW620 by shRNA. Then we performed gene expression profiling analysis using data obtained from mRNA-seq in NAT10 knocking-down SW620 cells and its control cells.


title: Cellular translational enhancer elements that recruit eukaryotic initiation factor 3

city: Heidelberg

first: Jiří

last: Koubek

address: INF 345

department: ZMBH

institute: Heidelberg University

summary: Translation initiation is a highly regulated process which broadly affects eukaryotic gene expression. Eukaryotic initiation factor 3 (eIF3) is a central player in canonical and alternative pathways for ribosome recruitment. Here we have investigated how direct binding of eIF3 contributes to the large and regulated differences in protein output conferred by different 5′-untranslated regions (5′-UTRs) of cellular mRNAs. Using an unbiased high-throughput approach to determine the affinity of budding yeast eIF3 for native 5′-UTRs from 4,252 genes, we demonstrate that eIF3 binds specifically to a subset of 5′-UTRs that contain a short unstructured binding motif, AMAYAA. eIF3 binding mRNAs have higher ribosome density in growing cells and are preferentially translated under certain stress conditions, supporting the functional relevance of this interaction. Our results reveal a new class of translational enhancer and suggest a mechanism by which changes in core initiation factor activity enact mRNA-specific translation programs.

overall_design: DMS-seq of yeast 5'-UTRs

first: Jiri

first: Shivani

last: Bhandarkar

first: Jaswinder

last: Kaur

first: Cole

middle: T

last: Lewis

first: Rachel

last: Niederer

first: Andrei

last: Stanciu

first: Colin

middle: E

last: Aitken

first: Wendy

middle: V

last: Gilbert


title: RNA signatures followed by immunization of multiantigenic adenovirus-based vaccine candidate against mycobacterium tuberculosis

city: Cheongju-si, Chungcheongbuk-do

first: Jin-Seung

last: Yun

address: 212, Osongsaengmyoung 2-ro, Osong-eup, Heungdeok-gu

country: South Korea

institute: Korea National Institute of Health

summary: We here report that recombinant multiantigenic adenovirus based vaccine candidate induces immunogenicity and protective effectiveness. RNA-seq transcriptome analysis on whole blood of vaccine canddate vaccinated mice collected pre-, 1 week post-, and 4 weeks postinfection revelaed differentially expressed genes associated with immune and inflammaotry responses, especially belonging to the Wnt signaling pathway. Our results suggest that immunization with vaccine candidate promotes strong boosting effects in BCG-primed mice, presenting itself as a new vaccine candidate.

overall_design: To investigate the RNA signature induced by vaccine candidate, mice were vaccinated with BCG pasteur 1173P2 via the subcutaneous route at 5-6 weeks of age, and after 10 weeks, immunized twice with vaccine candidate at 4 week intervals. Three weeks after the final immunization, mice was challeged with Mycobacterium tuberculosis H37Rv strain using a Glas-col aerosol generator. To evalute RNA signature, whole blood of mice was collected at pre-challenge, 1 week post-challenge, 4 weeks post-challenge.

first: Hye-Sook

last: Jeong


title: Molecular basis for condensin enrichment at pericentromeres [Brn1_ChIP-seq]

first: Daniel

last: Robertson

overall_design: To determine whether direct Sgo1-Ycg1 binding is responsible for condensin (Brn1) recruitment to pericentromeres

first: Menglu

first: Adele

last: Marston


title: Sequencing to Explore the Mechanism Network of N-acetyltransferase 10 (NAT10) Promoting Colorectal cancer in human colorectal cancer cell SW620 [ac4CRIP]

first: Gongcai

last: Tao

summary: N-acetyltransferase 10 (NAT10), the only known mRNA ac4C “writer,” plays a significant role in several human diseases, including CRC and gastric cancer. As NAT10 can activate or repress important signaling pathways, such as the EMT pathway, DNA damage repair, or apoptosis, by catalyzing the ac4C modification of oncogene mRNA, targeting NAT10 shows great potential for inhibiting cancer cell malignant progression in vitro and in vivo. This complex network of colorectal cancer progression mediated by NAT10 remains to be identified, which can expand cancer therapy options. To identify potential NAT10-regulated ac4C targets, we checked ac4CRIP Sequencing in human colorectal cancer cell SW620.

overall_design: To identify potential NAT10-regulated ac4C targets, we established NAT10 knocking-down cell lines in SW620 by shRNA. Then we checked ac4CRIP Sequencing to find the interaction between NAT10 and the mRNA of its target in NAT10 knocking-down SW620 cells and its control cells.

first: Dan

last: Song

first: Chenhong

last: Wang

first: Mingzhen

last: Ma

first: Yanxin

first: Yongbin


title: Molecular basis for condensin enrichment at pericentromeres

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

overall_design: Refer to individual Series


title: Molecular basis for condensin enrichment at pericentromeres [Sgo1_ChIP-seq]

overall_design: To determine whether mutate the predicted Sgo1-Ycg1 binding sites influence Sgo1 pericentromeric localisation


title: m6A methyltransferase Mettl3 is essential for neuronal homeostasis and sleep via modulating Npy in mice

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road268

institute: zhejiang university

summary: To unravel the underlying mechanisms how neuronal Mettl3 loss induces the activation of microglia, we performed RNA-sequencing (RNA-seq) with the thalamic tissues of 2- and 4-month-old Ctrl and cKO mice, respectively.

overall_design: we performed bulk RNA sequencing (RNA-seq) with both ctrl and cKO mice brain in 2month and 4month to reveals the altered gene expression relating to microglia

first: Qihang

last: Sun


title: Airway Organ Tissue Equivalent (OTE) Platform for Modeling Chlorine Gas Toxicology.

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

summary: The purpose of this study was to assess gene expression changes in airway OTE tissues following chlorine exposure (CE).

overall_design: OTEs were exposed to medical air (MA) or 20 ppm chlorine gas (Cl2) for 30 min. At 0, 6, 12 or 24 hours post-exposure, OTEs were collected and snap-frozen in liquid nitrogen for gene expression studies.

first: Sean

last: Murphy

first: Anthony

last: Atala

first: Kimberly

middle: D

last: Reeves

first: Hannah

last: Ainsworth

first: Laura

last: Cox

first: Carl

last: Langfeld


title: The Pollutant Perfluorohexane Sulfonate (PFHxS) Reduces Serum Thyroxine but Does Not Alter Thyroid Hormone Action in the Postnatal Rat Brain

city: Research Triangle Park

first: Katherine

middle: Lynn

last: O'Shaughnessy

address: 109 TW Alexander Drive

institute: United States Environmental Protection Agency

summary: Per- and polyfluoroalkyl substances (PFAS) are surfactants utilized in an array of commercial products including nonstick cookware, stain resistant textiles, personal care products, and firefighting foam. Despite their widespread use, concerns regarding the safety of these compounds have been raised. One of the most reproducible effects of some PFAS is their ability to reduce serum thyroid hormones (THs) such as thyroxine (T4) and triiodothyronine (T3) in animal models. As THs are required for normal brain development, PFAS may also be developmental neurotoxicants. Here, we examine the endocrine and neurodevelopmental consequences of perfluorohexane sulfonate (PFHxS) exposure in pregnant, lactating, and developing rats, and compare its effects to the goitrogen propylthiouracil (PTU). We show that PFHxS dramatically reduces maternal serum T4, nearly equivalently to PTU (-55 and -51%, respectively). However, only PTU increases thyroid stimulating hormone (TSH). The lactational transfer of PFHxS is significant and reduces pup serum T4 across the postnatal period. However, only PTU drastically reduces brain THs. Evaluation of brain TH action by phenotyping, RNA-Sequencing, and quantification of radial glia cell morphology supports that PTU interrupts brain TH signaling while PFHxS has limited to no effect. Overall, these data show that PFHxS induces abnormal serum TH profiles in dams and pups; however, there were no indications of hypothyroidism in the postnatal brain. We suggest the stark differences between the neurodevelopmental effects of PFHxS and a typical goitrogen may be due, in part, to the ability of PFHxS to interact with thyroid hormone distributing proteins like transthyretin.

overall_design: We investigated the transcriptional effects of PFHxS versus Control and PTU (known goitrogen) versus Contol on postnatal day 6 (PN6). This tissue is the ventricular/subventricular zone of the rat brain processed for bulk RNA-Seq using Illumina NovaSeq.

first: Kiersten

last: Bell

first: Aubrey

last: Sasser

first: Mary

last: Gilbert

first: Cal

last: Riutta

first: Jermaine

last: Ford

first: James

last: McCord

first: Carmen

last: Wood


title: Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection

city: Ithaca

first: Michelle

last: Liu

state: NY

address: 618 Tower Road

institute: Cornell University

summary: Malignant testicular germ cells tumors (TGCTs) are the most common solid cancers in young men. Current TGCT diagnostics include conventional serum protein markers, but these lack the sensitivity and specificity to serve as accurate markers across all TGCT subtypes. MicroRNAs (miRNAs) are small non-coding regulatory RNAs and informative biomarkers for several diseases. In humans, miRNAs of the miR-371-373 cluster are detectable in the serum of patients with malignant TGCTs and outperform existing serum protein markers for both initial diagnosis and subsequent disease monitoring. We previously developed a genetically engineered mouse model featuring malignant mixed TGCTs consisting of pluripotent embryonal carcinoma (EC) and differentiated teratoma that, like the corresponding human malignancies, originate in utero and are highly chemosensitive. Here, we report that miRNAs in the mouse miR-290-295 cluster, homologs of the human miR-371-373 cluster, were detectable in serum from mice with malignant TGCTs but not from tumor-free control mice or mice with benign teratomas. miR-291-293 were expressed and secreted specifically by pluripotent EC cells, and expression was lost following differentiation induced by the drug thioridazine. Notably, miR-291-293 levels were significantly higher in the serum of pregnant dams carrying tumor-bearing fetuses compared to that of control dams. These findings reveal that expression of the miR-290-295 and miR-371-373 clusters in mice and humans, respectively, is a conserved feature of malignant TGCTs, further validating the mouse model as representative of the human disease. These data also highlight the potential of serum miR-371-373 assays to improve patient outcomes through early TGCT detection, possibly even prenatally.

overall_design: Gene expression profile was generated for an independent murine embryonal carcinoma cell line (EC3) and their thioridazine-differentiated counterparts (TR3) with three biological replicates.

first: Amanda

last: Loehr

first: Robert

last: Weiss


title: SMARCA4 Inhibits Breast Tumor progression through Transcriptional Activation of GTPase Activating Factor ARHGAP29 and RHOA Suppression [ATAC]

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: The chromatin-remodeling SWI/SNF complex emerged as a potent suppressor of tumor spheroid growth. SMARCA4 was identified as a top candidate to suppress TNBC growth in 3D tumor spheroid model using genome-wide CRISPR screen. Specifically, the loss of the SWI/SNF ATPase subunit SMARCA4 promotes tumor spheroid growth with reduced compactness, and enhanced the growth in breast primary tumors and metastasis across multiple breast cancer models. Further investigations revealed its function in inhibiting the RHOA pathway. SMARCA4 is required for the transcription of Rho GTPase activating factor ARHGAP29, achieved through direct binding to its promoter to provide DNA accessibility. The loss of SMARCA4 resulted in reduced ARHGAP29 levels and hyperactive RHOA signaling. This subsequently disrupted cell adhesion, facilitated a loose spheroid structure and promoted spheroid growth.

overall_design: Whole genome chromatin accessibility profiles for SMARCA4 manipulated derivatives of TNBC SUM159 cells were determined using ATACseq. The panel of 4 derivative samples include NTC (non-targeting control), KD1 (SMARCA4 knockdown), KD1+SMARCA4 (rescue) and KD1+Vec (rescue control)

first: Zheng

last: Sun

first: Yibin

last: Kang


title: Lung Immunophenotyping of Fat-1 mice Post Chronic Organic Dust Exposure

city: Fort Collins

first: Tara

last: Nordgren

state: CO

address: 1380 Centre Ave.

department: Environmental and Radiological Health Sciences

institute: Colorado State University

summary: We characterized the transcriptomic profile of whole left lung homogenate in dust exposed Fat-1 and C57Bl/6 (WT) mice in male and female mice.

overall_design: 3 lungs for each group (Sex, Genotype, Exposure) were run on the Myeloid Mouse panel provided by Nanostring.

first: Logan

last: Dean


title: Hypoxia dysregulates circadian rhythm and causes synapse elimination defects in astrocytes

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

summary: In this study, we used human cortical organoids (hCOs) derived from induced pluripotent stem cells (iPSCs) to examine how hypoxia exposure interferes with astrocyte synapse engulfment at 6 months in culture and 10 months in culture, equivalent to mid fetal- or neonatal-equivalent stages of development, respectively. We identified that hypoxia inhibits the synaptosome engulfment by human astrocytes at both developmental stages, with a more pronounced phenotype in 10 months astrocytes. Transcriptional analyses revealed disruptions in circadian rhythm pathways in hypoxic astrocytes, but not neurons, and PER2 luciferase assays (PER2::LUC) validated the presence of circadian rhythms and their disruption by hypoxia in intact hCOs, with more pronounced rhythms in 10 months hCOs.

overall_design: We performed differential gene expression and Gene Ontology analysis using bulk RNA-seq of day 200 and day 300 human cortical organoid exposed to control or hypoxic conditions.

first: Li

last: Li

first: Shin

last: Chi Hong

first: Voss

last: Anna

first: Shadrach

last: Jen-Lee

first: Htun

last: Saw

first: Puno

last: Alyssa

first: Nagar

last: Dhriti

first: Ramirez

last: Nephy

first: Rojo

last: Daniela

first: Gibson

last: Erin

first: Kaltschmidt

last: Julia

first: Sloan

last: Steven

first: Chung

last: Won-Suk

first: Pasca

last: Anca


title: MT-100, a human Tie2 agonist antibody, significantly improves penile neurovasculature in diabetic mice via novel target Srpx2

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

summary: Diabetes is an incurable, long-term, chronic disease that can lead to a variety of complications, including angiopathy, peripheral neuropathy, kidney disease, erectile dysfunction (ED), and infections. The angiopoietin-Tie 2 signaling pathway plays a critical role in blood vessel development, formation, remodeling, and peripheral nerve regeneration. Therefore, activation strategies of the Tie2 signaling pathway have been developed as potential therapies for ischemic and inflammatory vasculoneural diseases. Here, we developed a human Tie2 agonist antibody (MT-100) that not only resists Angpt2 antagonism and activates Tie2 signaling, but also regulates a novel target, Sushi Repeat Containing Protein X-Linked 2 (Srpx2), to survival of vascular and neuronal cells, reduces the production of reactive oxygen species (ROS), activates the PI3K/AKT/eNOS signaling pathway, increases the expression of neurotrophic factors (NGF, BDNF, and NT3), and ultimately improves the erectile function of diabetic mice. Our findings not only provide new conclusive evidence that the human Tie2 agonist antibody MT-100 may be a promising therapeutic strategy for the treatment of diabetic ED but also create substantial clinical applications for other complications associated with diabetes.

overall_design: Control (normal mice) (n=4), DM+NC (diabetic mice+negative control) (n=4) and DM+MT-100 (diabetic mice+MT-100) (n=4)

first: Fang-Yuan

last: Liu

last: Lee

first: Guo

middle: N

last: Yin

first: Jeong-Ki

last: Min

first: Ji-Kan

last: Ryu


title: Single-cell RNA sequencing of peripheral blood mononuclear cells reveals complex cellular signalling signatures of type 2 diabetes mellitus

city: hefei

first: Dongjin

last: zhao

state: anhui

address: 117 Meishan Road, Hefei City, Anhui Province, China

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

summary: The onset of the Type 2 diabetes mellitus (T2DM) is related to autoimmunity. Exploring biomarkers of T2DM based on single-cell sequencing technology can provide new insights for the molecular mechanisms. B cells, T cells, monocytes/macrophages, platelets, neutrophils, NK cells and cDC2s were grouped into 7 subclusters. Furthermore, T cells and monocytes/macrophages might be significantly correlated with the clinical characteristics of T2DM patients. RPL27 and AC018755.4 expression were strongly negative correlated with HbA1c. CD4+ T cells are mainly in the memory activation stage, and CD8+ T cells are effectors. The 50 genes whose expression varied with developmental time were associated with cytoplasmic translation, cell‒cell adhesion mediated by integrin, and the regulation of the inflammatory response. The GSEA results showed that the marker genes were enriched in the HALLMARK_INTERFERON_GAMMA_RESPONSE and HALLMARK_TNFA_SIGNALING_VIA_NFKB. Meanwhile, TNFRSF1A is the most core genes in network interaction . Further analysis revealed ligand‒receptor pairs, including MIF- (CD74 + CD44), MIF- (CD74 + CXCR4), ANXA1-FPR1 and LGALS9-CD45. Conclusions: Our study revealed that the transcriptional map of immune cells from PBMCs provided a framework for understanding the immune status via scRNA-seq analysis.

overall_design: We profiled 43,971 cells and 20,228 genes from peripheral blood mononuclear cells (PBMCs) of T2DM patients (Mod, treat) and healthy controls (Con) by single-nucleotide RNA sequencing.

first: Jindong

last: Zhao

first: Zhaohui

last: Fang


title: Pharmacological Downregulation of De Novo Active and Essential lncRNA SMILO via Inhibition of FLI1 Transcription Factor in Multiple Myeloma. [RNA-seq]

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

country: Spain

institute: CIMA

summary: Background: Despite the advances in therapeutic strategies, Multiple Myeloma (MM) remains incurable. Our recent research has detected 1556 de novo active chromatin regions in MM in comparison to healthy B cells. These regions were associated to 1059 coding genes and 89 lncRNAs, which play important roles in MM pathobiology (Ordoñez. Genome Research 2020; Carrasco-León. Leukemia 2021). The modulation of these genes could be essential for the development of novel therapeutic strategies to improve the response of MM patients.  Aims: We aimed to pharmacologically regulate these de novo active genes in an attempt to modulate the abnormal transcriptome of MM. Methods: Given that de novo chromatin activation marks were mainly located at acetylated promoter and enhancer regions, JQ1 Bromodomain and Extraterminal Domain Inhibitor (BETi) was used. Three MM cell lines (KMS-11, RPMI8226 and KMS-12) were treated at 1µM during 72h and then, RNA-seq, ChIP-seq of H3K27ac and ATAC-seq were performed. For the identification of the regulatory proteins of de novo active genes Reverse-ChIP was carried out. Protein inhibitions were conducted using CRISPR-Cas9, and protein and mRNA levels were analyzed by Western Blot and RT-qPCR, respectively. Results: After JQ1 treatment, the RNA-seq revealed a significant downregulation of more than ten percent of de novo active genes, indicating that JQ1 can negatively modify the expression of de novo active genes in MM. Interestingly, SMILO, a de novo active and essential lncRNA in MM, presented one of the greatest inhibitions, surpassing even described BETi targets (Fig. 1A). Considering that pharmacological regulation of the lncRNAs has been widely proposed as a therapeutic approach, we decided to use JQ1 to further explore the mechanism of regulation of this lncRNA. Through ChIP-seq and ATAC-seq analysis, we verified that this decrease was not due to changes in chromatin activation and accessibility produced by JQ1 in MM cells, suggesting that JQ1 may displace the transcriptional machinery, such as Transcription Factors (TFs), from de novo active regions and specifically from those related to SMILO. Interestingly, the Reverse-ChIP study revealed the binding of 16 proteins in the SMILO region. Among these, we selected as our candidate the TF FLI1, because FLI1: 1) was overexpressed in MM in comparison to healthy B cells; 2) presented a positive correlation of expression with SMILO; 3) MM patients with higher expression of FLI1 presented worse Progression Free Survival (PFS) and Overall Survival (OS) both in univariate and multivariate analyses considering classical genetic alterations of MM (Fig. 1B) and 4) FLI1 showed a significant decrease in H3K27ac at the promoter region after JQ1 treatment (Fig. 1C), which correlated with a great decrease in FLI1 protein levels. To ascertain that FLI1 is causally involved in the expression of SMILO, FLI1 was silenced using CRISPR-Cas9 technology, which substantially depleted FLI1 protein levels giving rise to a significant reduction of the expression of SMILO (Fig. 1D). All these results explain the mechanism by which JQ1 downregulates SMILO via the downregulation of the TF FLI1 (Fig. 1E).  Summary/Conclusion: Our study highlights the innovative ability of BETi molecules to modulate the expression of lncRNAs. We underscore the involvement of FLI1 in the regulation of SMILO, a de novo active and essential lncRNA in MM, opening the door to the development of novel therapeutic strategies based on RNA directed therapies.

overall_design: To investigate the pharmacological regulation of de novo active genes in Multiple Myeloma, we treated three human MM cell lines with the JQ1 Bromodomain and Extraterminal Inhibitor. KMS-111, KMS-12 and RPMI8226 cell lines were treated at 1µM and 72h. We performed the experiment in duplicate and then, the  changes in the transcriptome were analysed by RNA-seq.

first: N

last: Gómez-Echarte

first: A

last: Carrasco-León

first: E

last: Miranda

first: L

last: Garate

first: B

last: García-Torre

last: Gimenez-Camino

last: Urizar-Compains

last: Barrena

first: D

last: Olaverri

first: P

last: Aguirre

last: Ariceta

first: S

last: Alonso-Moreno

last: Belver

first: JI

last: Martín-Subero

last: San José-Enériz

first: F

last: Prosper

first: X

last: Agirre


title: Hepatic and Pancreatic Changes in Response to Prenatal Diet Restriction with Postnatal Exposure to a High Fat/high fructose Diet in the Adult Male and Female Rat Offspring

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: This study aimed to investigate the impact of prenatal calorie restriction followed by a mismatch with postnatal excess calories on the hepatic transcriptome and its potential association with adult-onset non-alcoholic fatty liver disease (NAFLD).

overall_design: We isolated hepatic transcript from the liver of 6 months old rats fed with High fat and high fructose diet (HFhf) throughout or 50% caloric restricted during gestation followed by either regular chow diet (IUGR-RC) or HFhf diet till the end of the experiment (IUGR-HFhf). Control group (CON) was fed with regular chow diet throughout. Snap frozen and subsequently powdered tissue were used to extract total RNA and RNA seq library was prepared using Kapa Stranded RNA sequencing kit with Ribo-erase. Libraries were sequenced by the HiSeq-4000

first: Bo-Chul

last: Shin

first: Amit

last: Ganguly

first: Liesbeth

last: Maggiotto

first: Manal

last: Habib

first: Sherin

last: Devaskar


title: Chronic Lymphocytic Leukemia in African Ancestry Population is Characterized by Increased Genomic Instability

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: Despite the considerable effort to characterize the genomic landscape of chronic lymphocytic leukemia (CLL), published data have been almost exclusively derived from patients of European Ancestry (EA), with significant underrepresentation of minorities, including patients of African Ancestry (AA).  Furthermore, although over a decade has passed since the initial observations of AA CLL patients suggesting an increased frequency of adverse prognostic factors and inferior clinical outcomes when compared to EA CLL, the differences between populations remain poorly understood.  To begin to address this gap, we explored whether ancestry differences exist in the genetic and transcriptomic features of 157 AA and 440 EA individuals diagnosed with CLL.  In our study focused on 59 putative driver genes, we found an increased frequency of mutations in driver genes in AA CLL, including mutations in genes of the DNA damage repair (DDR) pathway.  Telomere erosion was also increased in AA CLL, amplifying the notion of increased genomic instability in AA CLL.  Furthermore, we found enrichment of the Tumor Necrosis Factor-alpha (TNFα) Signaling via NF-κB pathway in AA CLL compared to EA CLL, suggesting that tumor promoting inflammation plays an important role in AA CLL.  In summary, we found higher frequency of mutations in genes from the DDR pathway along with shorter telomers and higher transcription of NFkB pathway genes. These results suggest that genomic instability is more prevalent in AA CLL than EA CLL.  Future studies are needed to show that it may be a driver of poor prognosis among AA CLL patients.

overall_design: The RNA portion of the study included 58 CLL individuals with African Ancestry (AA) and 292 CLL individuals with European Ancestry (EA). Baseline clinical characteristics, Rai stage, and IGHV-mutation status were abstracted from medical records by each participating institution. Peripheral blood mononuclear cells (PBMC) were obtained from all individuals.  Extraction of RNA was performed either directly from PBMCs presenting a tumor cell population >80% or following the enrichment of CD5+/CD19+ clonal cells in cases with purity <80%.

first: Cecilia

last: Bonolo de Campos

first: Chantal

last: McCabe

first: Laura

last: Bruins

first: Daniel

last: O'Brien

first: Sochilt

last: Brown

first: Renee

last: Tschumper

first: Cristine

last: Allmer

first: YuanXiao

last: Zhu

first: Kari

last: Rabe

first: Sameer

last: Parikh

first: Neil

last: Kay

first: Huihuang

last: Yan

first: James

last: Cerhan

first: John

last: Allan

first: Richard

last: Furman

first: J

middle: B

last: Weinberg

first: Danielle

last: Brander

first: Diane

last: Jelinek

first: Marta

last: Chesi

first: Susan

last: Slager

first: Esteban

last: Braggio


title: A key netwrok hub gene GRN confers chemo resistance in H2081 SCLC cells.

city: New York

first: Seungyeul

last: Yoo

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: NCI-H2081 is a cisplatin sensitive cell line. We over-expressed GRN protein in the cell to test whether GRN expression confers chemo-resistance into the cells. GRN over-expression is sufficient to confer chemo-resistance to small cell lung cancer (NCI-H2081). Genes differentially expressed in GRN-overexpressed cells compared to control cells were identified by DESeq2 (FDR < 0.01). Down-regulated genes were enriched for neuroendocrine signatures including ASCL1.

overall_design: mRNAs from parental and engineered NCI-H2081 cells with either GFP or GRN were extracted and differentially expressed genes are identified.

first: Ayushi

last: Patel

first: Jun

first: Hideo

last: Watanabe


title: Pharmacological Downregulation of De Novo Active and Essential lncRNA SMILO via Inhibition of FLI1 Transcription Factor in Multiple Myeloma.

first: Nahia

last: Gomez-Echarte


title: Skatole attenuates osteoarthritis by protecting chondrocytes and mediating macrophage repolarization through regulating the NFκB/MAPK signaling pathway and metabolic reprogramming

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

summary: Osteoarthritis (OA) is the most common joint disease, but there are currently no disease-modifying OA drugs (DMOADs) yet approved by the regulatory agencies. Regulating macrophage polarization can alleviate synovial inflammation and then repair articular cartilage damage, providing a new target for OA treatment. Here, we found that Skatole can modulate macrophage polarization and attenuate OA. Skatole hindered M1 macrophage polarization while promoting M2 macrophage polarization. Mechanistically, Skatole activated Stat6, suppressed the phosphorylation of IKK, IκBα, and p65 in NFκB signaling pathway, and inhibited MAPK signaling activation. RNA-seq analysis revealed that Skatole downregulated the expression of inflammation-related genes, while upregulating genes involved in glutathione metabolism and oxidative phosphorylation, thereby reducing ROS levels and inhibiting M1 macrophage polarization. Moreover, conditional medium (CM) from M1 macrophages treated with Skatole balanced anabolism and catabolism in mouse chondrocytes while inhibiting cell apoptosis. Intriguingly, in IL1β-treated chondrocytes, Skatole directly suppressed inflammation and catabolism, without significantly affecting cell apoptosis or anabolism; In vivo experiments showed that Skatole increased M2 polarization and decreased M1 polarization of synovial macrophages, alleviated synovitis, and lessend articular cartilage damage in destabilization of medial meniscus (DMM)-induced OA mice. Our finding suggest that Skatole has the potential to function as a DMOAD.

overall_design: Compare the differentiation of gene expression between macrophages treated with DMSO, DMSO+LPS and LPS+Skatole.


title: Single cell RNA analysis of lung endothelial cells in mouse model of Hereditary Hemorrhagic Telangiectasia 2

city: Los Angeles

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

summary: Arteriovenous malformations (AVMs) are characteristic of hereditary  hemorrhagic telangiectasia (HHT). We used single cell RNA sequencing (scRNA-seq) to analyzed the pulmonary ECs in mice with endothelial-specific deletion of Alk1 gene.

overall_design: Lung VE-cadherin+ and CD45- cells were isolated by fluorescence-activated cell sorting (FACS), and analyzed using scRNA-seq.

first: Wu

last: Xiuju


title: Runt-related Transcription Factor 1 (RUNX1) is a mediator of acute kidney injury

city: Madrid

first: Ana Belen

last: Sanz

address: Avda. Reyes Catolicos 2

institute: IIS-Fundacion Jimenez Diaz

summary: Treatment for acute kidney injury (AKI) is suboptimal. A better understanding of its pathogenesis may lead to new therapeutic approaches. Kidney transcriptomics analyses of murine folic acid-induced AKI (FA-AKI) identified Runx1 as the most upregulated RUNX family gene. RUNX1 overexpression in FA-AKI was validated at the mRNA and protein levels and localized mainly to tubular cell nuclei. Bacterial lipopolysaccharide (LPS)-induced cytokine storm-AKI also upregulated kidney RUNX1. Increased tubular and interstitial RUNX1 expression were also observed in human AKI. In cultured murine tubular cells, the proinflammatory cytokine TWEAK and LPS increased RUNX1 and IL-6 expression. Mechanistically, RUNX1 bound to the Il-6 gene promoter while RUNX1 targeting with either the chemical inhibitor Ro5-3335 or a specific small interfering RNA (siRNA) prevented the TWEAK- and LPS-induced upregulation of IL-6 through a RUNX1/NFκB p50 pathway. TWEAK and LPS also induced RUNX1 binding to the promoter of Cdkn1a which encodes the cyclin-dependent kinase inhibitor p21 and increased p21 expression. In vivo, preventive Ro5-3335 improved kidney function and reduced inflammation and p21 expression in both FA-AKI, and in cytokine storm-AKI. However, administration of Ro5-3335 after the insult only improved kidney function in cytokine storm-AKI. Kidney transcriptomics identified inflammatory genes and the transcription factor Yap1 as key targets of Ro5-3335 in cytokine storm-AKI. In conclusion, RUNX1 contributes to AKI by driving the expression of genes involved in inflammation and represents a novel therapeutic target in AKI.

overall_design:
To invetigate the role of RUNX1 in cytokine storm-AKI (CS-AKI), we perfomed an animal model of cytokine storm by i.p. LPS injection. One group of mice received a dose of  an inhibitor of RUNX1, Ro5-3335, before LPS injection. All mice were sacrificed at 24 hours later.
We used C57BL/6 female mice (Charles River Laboratories, Ecully, France), 12- to 14-week-old, and 19-21 gr of weight
We then performed gene expression profiling analysis usining data from RNA-seq of 4 different experimental groups: Control, Ro5-3335, CS-AKI and CS-AKI+Ro5-3335.

first: Miguel

last: Fontecha-Barriuso

first: Natalia

last: Villar-Gomez

first: Juan

last: Guerrero-Mauvecin

first: Julio

last: Martinez-Moreno

first: Susana

last: Carrasco

first: Diego

last: Martin-Sanchez

first: María

last: Rodríguez-Laguna

last: Sanchez-Niño

last: Ruiz-Ortega

first: Alberto

last: Ortiz

first: Ana


title: Transcriptomic profiling of adipocytes in response to cold reveals unique properties  of Cxcl12 as a brown adipocyte secreted chemokine

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Beyond its thermogenic potential, brown adipose tissue (BAT) performs important endocrine  functions that regulate metabolism. However, the BAT microenvironment and the factors involved in BAT homeostasis and adaptation to cold remain poorly characterized. We therefore aimed to study secreted factors from active brown adipocytes that may be involved in adipocyte function and/or may orchestrate inter-cellular communications. For this, mRNA levels in mature adipocytes of brown, beige and white adipose depots from mice exposed to 21 days of cold were evaluated using RNA sequencing, and bioinformatic analysis was used to predict for potentially secreted factors. Cxcl12 was found to be the most cold-induced C-X-C chemokine in BAT, and Cxcl12 mRNA expression analysis by qPCR and fluorescence in-situ hybridization revealed its enrichment in brown adipocytes upon cold. Cold increased CXCL12 secretion from BAT, yet its level in plasma remained unchanged indicating a potential local action. Cxcl12 knockdown in mature brown adipocytes impaired thermogenesis, estimated by norepinephrine (NE)-induced Ucp1 gene expression, glycerol release and mitochondrial respiration despite unaltered β-adrenergic signaling, suggesting Cxcl12 regulates adipocyte function independently from the β-adrenergic pathway. Importantly, unaltered adipocyte characteristics upon Cxcl12 loss may indicate CXCL12 primarily regulates the NE-induced adipocyte activation. Furthermore, CXCL12 might exert inter-cellular crosstalk via its capacity to promote macrophage chemotaxis and neurite outgrowth. Here we present CXCL12 as a novel brown adipocyte, cold-induced secreted factor involved in adipocyte function and inter-cellular crosstalk within BAT.

overall_design:
For the aims of our study we evaluated mRNA levels in mature adipocytes of brown, beige  and white adipose depots from mice exposed to 21 days of cold using RNA sequencing. Bioinformatic analysis was subsequently used to predict for potentially secreted factors.
Mice were first held at thermo neutral conditions for 21 days. Thereafter half of the mice  where transferred to cold exposure for 21 days while the rest (control group) where kept for the same amount of time at thermo neutral conditions. Adipocyte tissue was then harvested from all mice, RNA was isolated from the tissue and sequenced.

first: Marina

last: Agueda-Oyarzabal

first: Kaja

last: Plucinska

first: Marie

last: Isidor

first: Oksana

last: Dmytriyeva

first: Axel

last: Pontoppidan

first: Jo

last: Henningsen

first: Patricia

last: Petersen

first: Erin

middle: L

last: Brown

last: Rupar

first: Marco

last: Tozzi

first: Thue

middle: W

last: Schwartz

first: Romain

last: Barrès

first: Camilla

last: Schéele

first: Brice

last: Emanuelli


title: single cell RNA sequencing analysis of infected or bystander (noninfected) monocytes during M. marinum infection

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

institute: Technical University of Denmark

summary: Mice were infected with wild type, EspK::tn, or deltaRD1 (completely ESX-1-deficient) Mycobacterium marinum. 14 days post infection, infected and uninfected monocytes from the infected tissue were sorted for single cell RNA sequencing analysis.

first: Kristina

last: Munke

first: Julia

last: Lienard

first: Clément

last: Da Silva

first: Julien

last: Vandamme

first: Katie

last: Laschanzky

first: Thorsten

last: Joeris

first: William

last: Agace

first: Fredric

last: Carlsson


title: Pharmacological Downregulation of De Novo Active and Essential lncRNA SMILO via Inhibition of FLI1 Transcription Factor in Multiple Myeloma. [ATAC-seq]

first: Nahia

last: Gomez-Echarte

first: N

last: Gómez-Echarte

first: A

last: Carrasco-León

first: E

last: Miranda

first: L

last: Garate

first: B

last: García-Torre

last: Gimenez-Camino

last: Urizar-Compains

last: Barrena

first: D

last: Olaverri

first: P

last: Aguirre

last: Ariceta

first: S

last: Alonso-Moreno

last: Belver

first: JI

last: Martín-Subero

last: San José-Enériz

first: F

last: Prosper

first: X

last: Agirre


city: 南京市

first: zhen

last: xu

institute: 南京鼓楼医院

summary: Candida albicans, as an opportunistic pathogen, exhibits aberrant changes in patients with inflammatory bowel disease and dominate the colonic mucosal immune response. However, the causative agent in Candida albicans is not clear. We found that Candida albicans in IBD patients had characteristic gene expression, and PMA1 was significantly increased, compared with that in healthy controls. We used a Crispr-Cas9-based fungal strain editing system to knock out the PMA1 gene and demonstrated the important role of PMA1 in Candida albicans-aggravating colitis. Proteomic analysis showed that PMA1 is carried by extracellular vesicles of Candida albicans. Then we found PMA1-containing EVs modulated the migration of cDC2 from the lamina propria to mesenteric lymph nodes, and induced TH17 cell differentiation during colitis. Our results showed that PMA1-containing EVs promote maturation, cytokine secretion and migration of cDC2, thus promoting TH17 differentiation. Moreover, we suggested that the CARD9 expression in DCs is required for recognition of PMA1 within EVs, CARD9 deletion in DCs abrogates cytokine secretion induction by PMA1. Metabolite sequencing analysis results showed that CARD9 can activates glycolysis in DCs. As an adaptor protein, CARD9 can combined with G3P aa2-146 domain through its CARD region. These findings reveal the specific pathogenic factor of Candida albicans–host interactions in colitis progression and highlight new diagnostic and therapeutic targets for diseases of inflammatory origin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. albicans in healthy people and patients with UC

first: Zhen

last: Xu


title: The effect of PNPO-OE in Multiple myeloma cells ARP1 and H929

city: Jiangsu Nanjing

first: Deng

middle: Zhen

last: Dong

address: Xianlin Roud 138

institute: Nanjing University of Chinese Medicine

summary: To explore the function of PNPO, we constructed ARP1 and H929 pTSB-EV/PNPO-OE cell lines via lentivirus packaging. We found different genes change between EV and OE cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ARP1 and H929 EV or PNPO-OE cells

first: Zhendong

last: Deng


title: SMARCA4 Inhibits Breast Tumor progression through Transcriptional Activation of GTPase Activating Factor ARHGAP29 and RHOA Suppression [RNA]

first: Yong

last: Wei

overall_design: Total RNA samples were collected from non-targeting shRNA control (NTC) and SMARCA4 knockdown derivatives (KD1 and KD2) of human triple negative breast cancer (TNBC) cell SUM159 cultured in both  2D and 3D spherioid culture system. The whole transcriptome profiling were determined using RNAseq. Three repeats of each 3D samples were profiled while single sample pair for 2D culture is used.

first: Zheng

last: Sun

first: Yibin

last: Kang


title: Pharmacological Downregulation of De Novo Active and Essential lncRNA SMILO via Inhibition of FLI1 Transcription Factor in Multiple Myeloma. [ChIP-Seq]

first: Nahia

last: Gomez-Echarte

first: N

last: Gómez-Echarte

first: A

last: Carrasco-León

last: Miranda

last: Garate

last: García-Torre

last: Gimenez-Camino

last: Urizar-Compains

last: Barrena


title: Reference Long-read Isoform-aware Transcriptomes of Activated Human CD4 T cells (PacBio Iso-Seq, matched to Illumina RNA-Seq Data)

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of T cell functional plasticity as it relates to human health and disease. However, To our knowledge, no long-read transcriptome reference exists for activated human CD4 T cells. To begin to fill this gap, we purified CD4 T cells from the peripheral blood of a healthy female donor and activated these cells with anti-CD3/CD28 beads to generate populations of early activated (4hr), mid-activated (16hr), blasting (48hr) and proliferating (120hr) CD4 T cells. From each of these time points, we obtained high-quality RNA (RIN>9) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis, which we hope will serve as a reference for future transcriptomic studies of these populations. UCSC genome browser tracks for these samples can be accessed at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=on&position=chr1:206,903,317-206,921,941&hubUrl=http://162.215.210.70/~tracks/Mitchell_IsoSeq_Stim/hub.txt

overall_design: CD4 T cells were enriched to >98% purity from the peripheral blood mononuclear cells of a healthy female donor. Purified CD4 T cells were activated with anti-CD3/CD28 Dynabeads for 4hr (early activated), 16hr (mid-activated), 48hr (blasting) and 120hr (proliferating). RNA was extracted from populations at each time point and used for Pacific Biosciences Iso-Seq long-read sequencing in parallel with Illumina RNA-Seq short-read sequencing. The resulting datasets are offered here as reference transcriptomes for studies of these populations.

first: Cassandra

middle: R

last: Woolley

first: Julia

last: Chariker

first: Zachary

middle: M

last: VanWinkle

first: Caleb

middle: S

last: Whitley

first: Easton

last: Ford

first: Elizabeth

last: Hudson

middle: C

first: Melissa

last: Smith

first: Thomas

last: Mitchell


title: Reference Transcriptomes of Activated Human CD4 T cells

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

overall_design: Refer to individual Series


title: The Transcriptome of MHV  or PVM Infected RAW264.7 Cell

city: Beijing

first: Yun

last: Liu

address: Panjiayuan Street

institute: Institute of Laboratory Animals Science,CAMS & PUMC

summary: In the current in vitro research, murine macrophage RAW 264.7 cell were infected by mouse hepatitis virus, a coronavirus existed in mouse. The transcriptome analysis showed the differential expressed genes(DEG) related  to important cellular physiological activity. In addition, DEGs related to metabolism and histone modification were detected, which might correlate with the trained immunity of macrophages. The current in vitro viral infection study showed the key innated immunity character of macrophages, which suggest the replacement value of viral infection cells model, to reduce the animal usage in preclinical researches.

overall_design: Cells from ATCC were cultured in  DMEM medium  with 10% fetal bovine serum (FBS) at 37 °C with 5% CO2. Before viral infection，the medium was changed to DMEM with 1%FBS. 800 TCID50 were added per well. At 3, 6, 12, 24, 48hour post infection(hpi.), the culture medium was discarded, and the attached cells were washed with PBS and harvested in Trizol reagent.Transcriptome sequencing was carried out byNovo Zhiyuan Co., Ltd. (Beijing, China).

first: Tingting

last: Feng


title: SKP-SC-EVs-derived miRNA-30a-5p promote angiogenesis in peripheral nerve regeneration by targeting Lif and ANGPT2

city: nantong

first: songlin

last: zhou

state: jiangsu

address: 19 qixiu road

institute: Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education

type: Non-coding RNA profiling by high throughput sequencing

summary: Ischemia and hypoxia caused by vascular injury aggravate nerve injury. The extracellular vesicles from skin precursor-derived Schwann cells  (SKP-SC-EVs) have proven to be beneficial to the regeneration of peripheral nerve injury, but whether SKP-SC-EVs can repair injured peripheral nerves by promoting angiogenesis remains unclear. Here, we found that SKP-SC-EVs enhanced the angiogenesis, which were verified by the transparency of tissue engineered nerve graft (TENG) and ultrasonic blood flow imaging. In vitro we verified that SKP-SC-EVs promote the proliferation, migration and tube formation of human umbilical vein endothelial cells (HUVECs), which were traditionally used for the evaluating angiogenesis capacity. Furthermore, the expression pattern of microRNA (miRNA) in SKP-SC-EVs was profiled and functional experiments were screened. Notably, miR-30a-5p was selected because of the remarkably pro-angiogenic ability in vivo and in vitro, which was similar to the effects of SKP-SC-EVs. Luciferase reporter assay and functional experiments revealed miR-30a-5p contained in SKP-SC-EVs promoted angiogenesis by targeting ANGPT2 and LIF in the insufficient of VEGFa. Taken together, miR-30a-5p enriched in SKP-SC-EVs may be a key regulator of angiogenesis for the cell-free treatment for peripheral nerve injury.

overall_design: Examination of the expression pattern of microRNA in SKP-SC-EVs

first: Songlin

last: Zhou

first: Qiang

first: Mengru

last: Zheng

first: Mingzhi

last: Du


title: Reference Short-Read Transcriptomes of Activated Human CD4 T cells (Illumina RNA-Seq, Matched to PacBio Iso-Seq Data)

middle: H

middle: A


title: Comparing nephrotoxicity of the calcineurin inhibitors, cyclosporine A and tacrolimus, identifies their differential effects within the renal compartments, rat model

city: Berlin

first: Hasan

last: Demirci

address: Philippstr. 12

department: Institute for Functional Anatomy

institute: Charité - Universitätsmedizin Berlin

summary: Chronic calcineurin inhibitor (CNI) nephrotoxicity is a major drawback in current immunosuppressive regimens. In the chronic setting, arteriolar hyalinosis, decreased glomerular filtration rate, interstitial fibrosis and tubular dedifferentiation are the major adverse side effects. Regimens with cyclosporine A (CsA) and tacrolimus (Tac) have been compared before the background of potentially more harmful effects of CsA. Conversely, CsA is still widely used in transplant recipients and has been considered for replacement of Tac in posttransplant diabetes.To identify regulatory mechanisms in CsA and Tac nephrotoxicity in rat, we used quantitative transcriptomics

overall_design: Adult (10 to12 weeks) male Wistar rats were divided into groups receiving cyclosporine  A  (CsA; target trough plasma level 3 mg/ml) and the respective vehicle (saline), or tacrolimus (Tac; target trough plasma level 3.5 ng/ml) and the respective vehicle (25% DMSO/75% PEG500), via subcutaneously implanted osmotic minipumps (Alzet,  2ML4,  Cupertino,  California) for 28 days. Kidneys were harvested and bulk RNA-seq was performed.

first: Sebastian

last: Bachmann

first: Ismail

last: Hassanin

first: Duygu Elif

last: Yilmaz


title: Gene expression profiling data following overexpression of TRIM8  in lung cancer cell lines (A549, CL1-0, H358)

city: Taichung

first: Jian-Wei

last: Chen

address: 145 Xingda Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

summary: Lung cancer is the cancer with the highest mortality rate in the world.  Ubiquitination is a post-translational modification that is widely present in cells to regulate the level of intracellular proteins, and is closely related to cancer progression. TRIM8 as an E3 ligase is one of the members of ubiquitination. In order to characterized the function of TRIM8 in lung adenocarcinoma, we overexpressed TRIM8 in different p53-type cell lines (A549, CL1-0 and H358)

overall_design: Gene expression profiling of A549, CL1-0, and H358 lung cancer cells were transfected with pcDNA3.1-TRIM8 plasmid or pcDNA3.1 as mock control.

first: Jeremy

middle: J

first: Chi-Hsuan

last: Wei

first: Chia-Wei

last: Weng

first: Chih-Ying

last: Wu

first: Hsuan-Yu

first: Gee-Chen

last: Chang


title: Gene expression analysis in canine erythema multiforme [EM]

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a comparative immunology case series study of client-owned dogs to determine if immune and skin gene expression profiles in spontaneous canine erythema multiforme (EM) mirror those observed in human patients.

overall_design: Gene expression was analyzed using 160 custom Nanostring probes to analyze 3 canines with EM compared to 5 healthy controls (leg margin excisions).

first: Ramon

last: Almela

first: Nicholas

last: Robinson


title: Maternal obesity alters the placental transcriptome in a fetal sex-dependent manner

city: Winston-Salem

first: Jeannie

last: Chan

address: Medical Center Boulevard

institute: Wake Forest School of Medicine

summary:
This study used a mouse model of diet-induced obesity with fetal overgrowth to investigate molecular changes in the placentas of obese dams.
Obese and control dams were euthanized on embryonic day 18.5 to collect placental samples for RNA sequencing.

overall_design:
RNA-Seq was carried out to compare gene expression in the placentas of obese (n=10) and control (n=10) dams.
Obese and control groups each had an equal number of male and female fetuses.

first: Fredrick

last: Rosario

first: Laura

last: Cox

first: Thomas

last: Jansson


title: Single-cell sequencing revealed the remodeling of the brain microenvironment by breast cancer metastasis

city: Wuxi

first: Wei

last: Tian

address: Zhongshan Road

institute: Wuxi No.2 People's Hospital

summary: To infer the effects of metastatic breast cancer cells on brain microenvironment, a murine model of TNBC brain metastasis was established, and brain tissues were obtained for scRNA-seq from the experimental group and the control group.

overall_design: A murine model of breast cancer brain metastasis for scRNA-seq


title: RNA-sequencing analysis to investigate genes regulated by ASAP1 in RD cells

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

summary: In this study we identified genes whose expression is altered by knock down of ASAP1 expression in RD cells in the presence or absence of the MEK inhibitor trametinib

overall_design: RD cells were transfected with control siRNA or ASAP1 siRNA, followed by treatment with vehicle (DMSO) or trametinib (MEK inhibitor) for 2 or 3 days.

first: Katie

last: Hebron

first: Marielle

last: Yohe


title: Chip sequencing after ER stress induced in HCC cells using tunicamycin

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

summary: We report the application of the CHIP sequencing-based technology in the high-throughput analysis of histone modifications in HepG2 cells. Endoplasmic reticulum stress related super enhancers were identified and their regulatory target genes were predicted.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H3K27ac in HepG2 cells.

first: Guoping

last: Sun

first: Jiatao

last: Liu


title: Enhanced growth and productivity of useful metabolites by indole-3-propionic acid treatment in Lemna aequinoctialis culture

status: Public on Feb 11 2025

city: Dongjak-gu

first: Ye-Been

last: Lee

state: Seoul

address: 84, Heukseok-ro

institute: Chung-ang university

summary: Analysed at the gene expression level, IPA administration in Lemna aquaequinoctialis affected broad transcriptome changes, which also provide important information on its interaction with the metabolome.

overall_design: Transcriptome obtained by grinding lyophilised Lemna aequinoctialis.

first: Hyung-Kyoon

last: Choi