title: Delayed gut colonization changes future insulin resistance and hepatic gene expression but not adiposity in high-fat diet induced obese mice

city: Frederiksberg C

first: Camilla

middle: Hartmann Friis

last: Hansen

address: Ridebanevej 9, 2nd floor

department: Faculty of Health Sciences

country: Denmark

institute: University of Copenhagen

summary: Since the first findings that germ-free mice appeared resistant to diet-induced obesity, an increasing number of studies have emphasized the role of the gut microbiota as a core regulator of host weight gain and metabolism. However, several studies have not been replicable and conflicting results have left the discussion surrounding causality elusive. Specifically, the importance of early microbial dysbiosis in later development of obesity and metabolic disorders has been a subject of debate. Male Swiss Webster mice raised under germ-free conditions were introduced to a specific-pathogen-free (SPF) facility for microbial colonization at 1 week (1W) and 3 weeks (3W) of age. They were compared with control animals (SPF) with a complete gut microbiota from birth. Liver RNAseq of 7 week old animals showed differential gene expression between the groups

overall_design: Mice were either normal (SPF) mice or germ free for the first three weeks of their life (W3)

first: Caroline

last: Mentzel


title: Quietly hiding: PD-L1 checkpoint expression in melanocyte stem cell quiescence and aging

status: Public on Apr 01 2024

city: Birmingham

first: Melissa

last: Harris

state: AL

address: 1300 University Blvd, CH464

department: Biology

country: USA

institute: University of Alabama at Birmingham

type: Expression profiling by high throughput sequencing

summary: Cellular quiescence is a reversible and tightly regulated stem cell function that is essential for healthy aging. However, the control elements of tissue-specific renewal, quiescence, and aging remain poorly understood. Using melanocyte stem cells (McSCs) to model and test the regulation of tissue-specific quiescence, we find that stem cell quiescence is neither a singular nor static process. McSCs display remarkable heterogeneity, with a fraction expressing the immune checkpoint protein PD-L1. Differential gene expression profiling identifies tissue-specific control of this immune privilege, specifically during melanocyte stem cell dormancy. In vitro quiescence assays confirm that inducing quiescence is sufficient to drive PD-L1 expression in melanoblasts and PD-L1 subsequently regulates aspects of melanoblast cell cycling. In vivo, a portion of McSCs appear to leverage this immune checkpoint as a key aspect of their dynamics during the dormant stage of the hair cycle. With age, this dynamic becomes unbalanced, tipping towards a higher proportion of PD-L1-expressing McSCs and a more deeply quiescent McSC pool. Collectively, these findings demonstrate that immune checkpoint expression is a physiological attribute of McSC quiescence and offer PD-L1-expressing quiescent stem cells as molecular targets for potential reactivation in regenerative and gerontological medicine.

overall_design: Dermis from postnatal day 0.5, 8-10-week, and 24-month mouse body skin was dissociated and processed using flow cytometry to obtain enriched populations of melanoblasts, adult quiescent melanocyte stem cells (qMcSCs) and aged qMcSCs, respectively. Cells of the melanocyte lineage were identified by their surface expression of the receptor KIT and the absence of the immune cell marker CD45. Melanoblasts in the P0.5 dermis are located within developing hair follicles. Enrichment for qMcSCs at both the adult and aged timepoints was achieved by isolating KIT+CD45- cells from mouse skin whose hair was in the telogen stage of the hair cycle. McSC enrichment at telogen is dependent on the fact that telogen hairs contain only McSCs and do not contain differentiated melanocytes. The telogen stage of the hair cycle was confirmed by the pinkness of the skin. Female mice were used for all melanoblast and McSC enrichments as it is technically challenging to dissociate and obtain cells of high quality from male skin. Melanoblasts and McSCs from several animals were pooled to generate enough RNA to serve as one biological replicate. Amplified cDNA was created from 20 ng total RNA using the Ovation RNA-Seq System V2 (Tecan Genomics). The cDNA was fragmented using a Covaris E210 before proceeding to library construction with 1000ng cDNA using TruSeq RNA Sample Prep Kit, version 2 (Illumina) using 10 PCR cycles. Libraries were pooled in equimolar ratio and sequenced together on a HiSeq 2500 with version 3 flow cells and sequencing reagents. At least 60 million 126-base read pairs were generated for each library. Data were processed using RTA 1.18.64 and CASAVA 1.8.2. RNA-Seq reads that passed the Illumina platform quality check were used for downstream analyses.

middle: L

first: Joseph

middle: W

last: Palmer


title: Cancer SLC6A6-mediated taurine uptake impairs CD8+ T cell antitumor immunity by upregulating immune checkpoints [mouse RNA-Seq]

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Xijing Hospital of Fourth Military Medical University

summary: Taurine is a supplement used to bolster immunity, but how taurine affects antitumor immunity remains largely unknown. We report that SLC6A6-mediated uptake of taurine by gastric cancer (GC) cells results in T cell exhaustion and cancer progression. SLC6A6 was correlated with GC aggressiveness and poor outcomes, and taurine uptake increased GC proliferation, survival, and cell motility. Taurine significantly increased CD8+ T cell infiltration and cytotoxic effector expression in GC tumors. Mechanistically, taurine deprivation in CD8+ T cells increased ER stress and the unfolded protein response, resulting in AT4 transcription, which acts as a switch for T cell exhaustion. SLC6A6 was transactivated by SP1 in GC cells, with a strong correlation between SP1 and SLC6A6 in GC patients. The SP1-SLC6A6 axis was triggered by chemotherapy. Our findings reveal that SLC6A6-mediated taurine consumption impacts immune evasion and propose that taurine supplementation might reinvigorate CD8+ T cell response and enhance therapy efficacy.

overall_design: Single CD45+ immune cells were obtained from taurine-treated MFC tumors from 615 mice and compared to their counterparts in saline-treated tumors.

first: Tianyu

last: Cao


title: Exploring the usefulness of urinary microRNA as a biomarker in pancreatic cancer and gastric cancer patients.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: By comparing urinary microRNA expression in representative cases of pancreatic and gastric cancer with that in healthy individuals, we were able to extract candidate biomarkers.

overall_design: In the study presented here, cell-free RNA was extracted from the urine of three pancreatic cancer cases (PC), three gastric cancer cases (GC), and three healthy volunteers (HV) as controls, respectively, and microRNA expression was analyzed.

first: Taisuke

last: Immaura

first: Shuhei

last: Komatsu


title: Single-cell multiplex chromatin and RNA interactions in aging human brain

city: La Jolla

first: Sheng

last: Zhong

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: The dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA (caRNA). Chromatin complex compositions change during cellular differentiation and aging, and are expected to be highly heterogeneous among terminally differentiated single cells. Here we introduce the Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within individual nuclei. Applied to 14 human frontal cortex samples from elderly donors, MUSIC delineates diverse cortical cell types and states. We observed the nuclei exhibiting fewer short-range chromatin interactions are correlated with an “older” transcriptomic signature and with Alzheimer’s pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci (cis eQTLs) and a promoter tends to be the cell type where these cis eQTLs specifically affect their target gene’s expression. Additionally, the female cortical cells exhibit highly heterogeneous interactions between the XIST non-coding RNA and Chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploring chromatin architecture and transcription at cellular resolution in complex tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this project, we applied MUSIC, a single cell technology can simultaneously detecting DNA and RNA multiplex interactions in the cell nucleus. We applied MUSIC to a mixed species library containing human embryonic cells (H1 cell line) as well as mouse embryonic cell line (E14). We also applied MUSIC to 14 human frontal cortex tissues.

first: Xingzhao

last: Wen

first: Zhifei

last: Luo

first: Wenxin

first: Riccardo

last: Calandrelli

first: Tri

middle: C

last: Nguyen

first: Xueyi

last: Wan

first: John

last: Lalith

first: Charles

last: Richard


title: Type III interferons induce pyroptosis in gut epithelial cells and delay tissue restitution  upon acute intestinal injury.

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

country: France

institute: CIML

summary: To determine the transcriptional programs initiated by IFN-λ to delay tissue restitution, we isolated intestinal crypts from the small intestine of VilCREIfnlr1fl/fl mice or WT littermates that have  been irradiated and performed targeted transcriptomics analysis

overall_design: WT mice and   VilCREIfnlr1fl/fl mice received 11 Gy ionizing radiation, with lead shielding of the upper body. Targeted transcriptomics was  performed  on  freshly  isolated  small  intestinal  crypts.Barcoded libraries were prepared using the Ion  AmpliSeq Transcriptome Mouse  Gene  Expression  Panel,  Chef-Ready  Kit  (A36412; Thermo  Scientific)

first: Benedetta

last: Sposito

first: Ivan

last: Zanoni

first: Achille

last: Broggi


title: Pentamethylquercetin induces Hep3B liver cancer cell apoptosis and cell cycle arrest via the ERK/NF-κB signaling pathway

city: Jinan

first: Yi

last: Han

address: 16766 Jingshi Road, Lixia District

institute: The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital

summary: In this study, we investigated the biological roles and potential mechanisms of pentamethylquercetin (PMQ), a natural polymethyl flavones, against Hep3B liver cancer cells. Cell viability and growth curves were determined using the cell counting kit-8 (CCK-8) assay; flow cytometry was used to detect cell cycle and apoptosis; colony formation assay and JC-1 staining were used to detect cell proliferation and mitochondrial membrane potential changes, respectively. Transcriptome sequencing and western blotting were respectively used to investigate transcription and expression changes in Hep3B cells treated with PMQ. Treatment with 30 and 100 μM PMQ more significantly inhibited cell growth and proliferation in Hep3B cells than in HepG2 and LO2 cells. PMQ induced Hep3B cell cycle arrest and apoptosis by significantly reducing CDK4, CDK6, Cyclin D1, Cyclin E1, Cyclin B1 and Bcl-2 expression and increasing Bax, CDK1 and cleaved PARP levels. Transcriptomic profiles and western blotting results revealed that the MAPK and TNF signaling pathways may be involved in PMQ-induced Hep3B apoptosis.

overall_design: Hep3B cells (three independent replicates per group) were treated with pentamethylquercetin(PMQ) (0, 100 μM) for 24 h.

first: Le

last: Zhang


title: Single-cell RNA profiling of the kidney in fructose overdose model using db/db mice

city: Otsu

first: Hiroaki

last: Tsuruta

state: Shiga

address: Tsukinowa

department: Department of Medicine

institute: Shiga University of Medical Science

summary: We have established a new fructose-overconsumption model using db/db mice, which showed more advanced kidney damage compared to the conventional db/db mouse model. To elucidate the mechanism of kidney injury caused by excessive fructose intake, we performed single-cell RNA analysis on the kidneys from this fructose-overconsumption model.

overall_design: Whole kideny of  db/m mice with fructose-free control diet, db/db mice with control diet and db/db mice with 60% fructose containing diet were isolated and analyzed using scRNAseq

first: Shinji

last: Kume


title: Bacterial Stress Bodies – Ancestral Condensates Regulating RNA Turnover and Protein Translation

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

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

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Refer to individual Series


title: Bacterial Stress Bodies – Ancestral Condensates Regulating RNA Turnover and Protein Translation III

summary: How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. Together, these functions ensure bacterial survival and recovery from N-starvation. Mammalian polyphosphate associates with P-bodies but not stress granules suggesting that polyphosphate’s interaction with select RNA binding proteins contributed to the evolution of functionally and compositionally distinct condensates in higher organisms.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA stability determined by RNA-seq of rifampicin treated wild-type and delta-ppk E. coli strains with Hfq-mCherry

first: Jian

last: Guan

first: Rebecca

last: Hurto

first: Akash

last: Rai

first: Christopher

last: Azaldegui

first: Luis

last: Ortiz-Rodriguez

first: Julie

middle: S

last: Biteen

first: P

first: Ursula

last: Jakob


title: Bacterial Stress Bodies – Ancestral Condensates Regulating RNA Turnover and Protein Translation II

overall_design: Determination of RNA bound by Hfq during nitrogen starvation via RIP-seq of RNA bound to Hfq-mCherry from wild-type and delta-ppk E. coli strains starved for nitrogen


title: Bacterial Stress Bodies – Ancestral Condensates Regulating RNA Turnover and Protein Translation I

overall_design: DNA-seq of DNA collected from Hfq-containing condensates collected from nitrogen starved wild-type and delta-ppk E. coli cells


title: Effect of depletion of TCF23 on myometrium transcriptome profile during late pregnancy

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

summary: TCF23 is a basic-helix-loop-helix transcription factor lacking a DNA binding domain with a C-terminal mediated inhibitory action. Tcf23 was significantly induced by progesterone but not estradiol in vitro and in vivo. To evaluate the biological role of Tcf23, we generated the Tcf23 knockout mouse. Although pregnant Tcf23 KO mice were able to maintain gestation until full term, a considerable proportion of KO females experienced delayed parturition, dystocia, and reduced litter outcomes, with a high incidence of resorption and fetal lethality. Morphological analysis of the pregnant uterus revealed aberrant disruption of both circular and longitudinal myometrial layers and disarrayed extracellular matrix at the conceptus sites in the KO mice. Transcriptome profile analysis of the KO myometrium demonstrated disruptions in cell adhesion, extracellular matrix (ECM), and gap junction signaling, indicating the crucial role of TCF23 in myometrial remodeling and preparation for contractility during late pregnancy. Altogether, our research highlights a novel cause for labor dysfunction mediated by loss of Tcf23 activity in murine uterine tissue.

overall_design: To investigate the function of TCF23 in the myometrium contraction, we generated TCF23 knockout mice by CRISPR/Cas9 technology. We then isolated the myometrium tissue from pregnant mice at gestational day 19 and performed RNA-seq of 3 different animals of each genotype. We conducted comparative gene expression profiling by analyzing data obtained from RNA-seq.

first: Fatma

middle: M

last: Minisy

middle: H

first: Hisashi

last: Oishi


title: RNA sequencing revealing the role of AMP-activated protein kinase signaling in mice myocardial ischemia reperfusion injury

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNA) and circular RNAs (circRNA) that sponge miRNAs could indirectly regulate gene expression, contributing to certain biological processes. This study aimed to investigate the role of non-coding RNAs in the pathogenesis of myocardial ischemia reperfusion-injury (MIRI). MIRI in male C57B/6J mice was induced by left anterior descending coronary artery ligation occlusion for 30 min, and 4 h of reperfusion. RNA sequencing was performed to obtain the mRNA and non-coding RNA expression profiles of the MIRI and sham groups. Bioinformatic methods were used to analyze the co-expression RNAs, miRNA binding sites and competitive endogenous RNA (ceRNA) pairs. Differentially expressed RNAs were identified with a cutoff fold change > 2 and p < 0.05. A total of 64 mRNAs were upregulated and 98 mRNAs were downregulated, and 10 lncRNAs were upregulated and 10 lncRNAs were downregulated. All altered (p < 0.05) mRNAs were selected for gene ontology and pathway analysis. The AMP-activated protein kinase (AMPK) signaling pathway was enriched in the downregulated genes, and the activation of AMPK was confirmed by Western blotting. The lncRNA co-expression network and ceRNA network base on genes in AMPK signaling pathway were then constructed, revealing that ENSMUST00000147762.7 and TUCP_000184 might be key regulators in MIRI induced AMPK activation. The expression levels of AMPK signaling-related RNAs and those involved in the ceRNA network were validated using qRT-PCR. Overall, this study identified potential new targets on AMPK signaling in MIRI.

first: Huankun

last: Sun

first: Jiaoni

last: Wang

first: Jiaqun

last: Que

first: Yangpei

last: Peng

first: Yongwei

last: Yu

first: Lei

first: Haihao

last: Ye

first: Kaiyu

last: Huang

first: Yangjing

last: Xue

first: Yingying

last: Zhou

first: Kangting

last: Ji


title: COPD basal cells are primed towards secretory to multi-ciliated cell imbalance driving increased resilience to environmental stressors

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

summary: We characterized primary human bronchial epithelial cells (pHBECs) from end-stage COPD and pulmonary healthy individuals. The transcriptomic profiles were assessed by single cell analysis in serial samples of pHBEC culture focussing on basal cell differentiation.

overall_design:
The serial single cell RNA sequencing analysis was performed by using the Drop-seq technology on seven different culture timepoints (day 0, 3, 5, 7, 14, 21, 28).
Raw data not provided due to patient privacy restrictions.

first: Mircea

middle: G

last: Stoleriu

first: Maximilian

last: Strunz

first: Herbert

last: Schiller

first: Anne

last: Hilgendorff


title: Single nuclei RNAseq of the periosteal response to bone fracture in mice

city: Créteil

first: Céline

last: Colnot

address: 8 rue du Général Sarrail

institute: INSERM U955

summary: Bone regeneration is a highly efficient process allowing scarless healing after injury. The periosteum, the outer layer of bones, is a critical source of skeletal stem/progenitor cells (SSPCs), as well as immune, endothelial and neural cells during bone repair. In our study, we generated a single-nuclei atlas of the murine periosteal response to bone fracture. We generated single nuclei datasets from uninjured periosteum and from injured periosteum and hematoma/fracture callus at days 5 and 7 post-injury from wild-type mice.

overall_design: Nuclei were extracted from uninjured periosteum, or injured periosteum and hematoma/callus at day 5 and 7 post-fracture. Nuclei were FACS-sorted and processed for single nuclei transcriptomics.

first: Simon

last: Perrin


title: NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: While dysfunction and/or death of light-detecting photoreceptor cells underlies most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids using induced pluripotent stem cells (iPSC) derived from a patient with genetic photoreceptor disease, an isogenic control, and an unrelated control. Organoids were sampled using single-cell RNA sequencing across the developmental window encompassing photoreceptor specification, emergence, and maturation; up to 260 days of in vitro differentiation. Using single-cell transcriptomics data, we reconstruct the rod photoreceptor developmental lineage and identify a branchpoint in development unique to the disease state that gives rise to a divergent rod photoreceptor cell population. We show that the rod-specific transcription factor NR2E3 is required for the proper expression of genes involved in phototransduction, including expression of the light-sensitive protein rhodopsin, which is absent in divergent rods. NR2E3-null rods additionally misexpress several cone-specific phototransduction genes at both the transcript and protein level. Using joint multimodal single-cell sequencing on late-stage retinal organoids, we further identify the specific putative regulatory sites where rod-specific factors act to steer rod and cone photoreceptor cell development. Importantly, these findings are strikingly different than that observed in rodent models of disease. Together, these data provide a roadmap of human photoreceptor development and leverage patient iPSCs to define the specific roles of rod transcription factors in photoreceptor cell emergence and maturation.

overall_design:
Three iPSC lines (ND [no disease] Control, NR2E3-null, and Isogenic Control) were differentiated to retinal organoids for 260 days. Samples were assayed by 3' scRNAseq at D40, D80, D120, D160 and D260 from all three lines. In a separate differentiation batch, NR2E3-null and Isogenic Control organoids were assayed by joint (RNA & ATAC) single-nucleus multimodal sequencing at D160 and D280. Multimodal runs yield paired scRNAseq and scATACseq libraries.
For AAV experiments, NR2E3-null organoids were cultured for 120 days. Organoids were treated with AAV carrying NR2E3-T2A-GFP or GFP or left untransduced as described. Organoids were harvested at D120 or following treatment at D160 and assayed by 3' scRNAseq. For ESCS Patient 2 experiment, an iPSC line from ESCS Patient 2 was differentiated to retinal organoids and assayed at D80 and D160 by 3' scRNAseq.
>>>Raw data were not provided for ATAC-seq Samples due to patient privacy concerns<<<

middle: K

first: Laura

middle: R

last: Bohrer

first: Budd

middle: A

last: Tucker


title: Tissue-specific reprogramming leads to angiogenic neutrophil specialization and tumor vascularization in colorectal cancer

city: Chicago

first: Ronen

last: Sumagin

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Polymorphonuclear neutrophil (PMN) tissue accumulation is an established feature of ulcerative colitis (UC) lesions and colorectal cancer (CRC). Given the emerging evidence of PMN phenotypic and functional heterogeneity, we analyzed the transcriptomic landscape of PMNs in blood and tissue during the spatiotemporal transition from inflammatory ulceration to CRC. Based on their transcriptional programs, PMNs were effectively stratified into distinct spatial compartments of peripheral blood, inflamed colon tissue, and the tumor niche. In silico pathway overrepresentation analysis, protein-network mapping, gene signature identification, and gene-ontology scoring revealed unique enrichment of angiogenic and vasculature development pathways in tumor-associated neutrophils (TANs). Functional studies utilizing ex vivo cultures, colitis-induced murine CRC, and patient-derived xenograft models demonstrated a critical role for TANs in promoting tumor vascularization. Spp1 (OPN) and Mmp14 (MT1-MMP) were identified by unbiased -omics and by mechanistic studies to be highly induced in TANs and function to critically regulate endothelial cell chemotaxis and branched network formation. TCGA dataset and clinical specimens confirmed enrichment of SPP1 and MMP14 in high-grade CRC but not in UC patients. Importantly, pharmacological inhibition of TAN trafficking or MMP14 activity effectively reduced tumor vascular density, leading to CRC regression. The current study identified a niche-directed PMN transcriptional reprograming and functional specialization, highlighting emerging PMN plasticity. Our findings define new TAN contributions to tumor vascularization, delineating a new therapeutic framework for CRC treatment focused on TAN angiogenic properties.

overall_design: Mice were subjected to multiple cycle of AOM/DSS. Blood or tumor-associated neutrophils were sorted and RNA-extracted at different disease timepoints (colitis, week 1; early CRC week 8, and advanced CRC week 13-14). We performed bulk RNAsequencing to characterize transcriptomic changes of neutrophils in cancer tissues and perform GO and GSEA analyses to identify angiogenic profiles of neutrophils. DEG analysis by DEseq2 and pairwise comparisons identified SPP1 and MMP14 as top upregulated genes in tumor neutrophils. We thus treated PDX models with MMP14 inhibitor and anti-OPN and extracted tumor cells for bulk RNAsequencing. Gene ontology and GSEA analyses identified collagen pathways and hypoxia pathways being enriched upon treatment with MMP14 inhibitor.

first: Triet

last: Bui

first: Lenore

last: Yalom

first: Matthew

last: Schipma

first: Brian

last: Wray


title: Ginsenoside Rd monomer alleviates ulcerative colitis by regulating miRNAs and target genes in macrophages

city: Harbin

first: Hui

last: Li

address: No.246 Xuefu Road

institute: 2nd affiliated hospital of Harbin Medical University

summary:
to discover the miRNAs involved in the production of cytokines by RAW264.7 cells  treated with LPS and ginsinoside Rd monomer
We then performed gene expression profiling analysis using data obtained from RNA-seq of RAW264.7 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RAW264.7 cells treated with LPS and Ginsenoside Rd monomer.

first: Bo

last: Qu


title: CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [Tetramer TCR-seq]

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

institute: Tokyo University of Science

summary: mRNA vaccines against the Spike glycoprotein of severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, it is unknown whether the repertoire of memory T cell clones changes between primary and secondary vaccinations. Here, we analyzed the kinetic profile of Spike-reactive T-cell clones before the first dose, one week after the first and second dose, and four weeks after the second dose of the BNT162b mRNA vaccine. Interestingly, a new set of Spike-reactive CD8+ T cell clones exhibited the greatest expansion following secondary vaccination and replaced the clones that had responded to the primary vaccination. Single-cell mRNA/protein/TCR analysis revealed that the first-responder clones exhibited a terminally differentiated phenotype, whereas second-responder clones exhibited an actively proliferating phenotype. These results show that Spike-reactive T cell responses induced by repetitive mRNA vaccination are augmented and maintained by replacement with newly-generated clones with proliferative potential.

overall_design: TCRseq was performed on Spike-specific CD8+ T cells determined by peptide-HLA tetramer assay on PBMC after Pfizer-BNT162b2 mRNA vaccination.

first: Masahiro

last: Kitabatake

first: Haruka

last: Abe

first: Peng

last: Xu

first: Mikiya

last: Tsunoda

first: Shigeyuki

last: Shichino

first: Atsushi

last: Hara

first: Noriko

last: Ouji-Sageshima

first: Chihiro

last: Motozono

first: Toshihiro

last: Ito

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Senescence-associatedmolecular signatures integrated with human gene co-expressionnetworks revealsCOL6A3 asnovelmediator [2]

city: new york city

first: Carmen

last: Argmann

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine

summary: We report expression profiles of various senescent cell types and modes of induction.

overall_design: 5 different non-transformed cell types from various origin were rendered senescent via ionising radiation and RNAseq was perfomed.  One strain (IMR90) was induced to senesce using various methods.  DEG Sen vs non-senescent cells were determined and compared accross all types of senescence.

first: Radoslav

last: SaviÄ

first: Priyanka

last: Patel

first: Eduard

last: Rogatsky

first: Jason

last: Kovacic

first: Johan

last: BjÃ¶rkegren

first: Jialiang

last: Yang

first: Robert

middle: N

last: OâBrien

first: Katyayani

last: Sukhavasi

first: Christopher

middle: B

last: Yohn

first: Zhidong

last: Tu

first: Simon

last: Koplev

first: Brittany

last: Dubose

first: Raili

last: Ermell

first: Eric

middle: E

last: Schadt

first: Mahru

last: An

first: Tetyana

last: Dodatko

first: Arno

last: Ruusalepp

first: Remi-Martin

last: Laberge


city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Fibroblast growth factor (FGF) 10 is essential for lung morphogenesis and polymorphisms in the Fgf10 region are linked with higher susceptibility towards COPD in human patients. We found that FGF10 signaling is impaired in lung septal wall compartment from COPD patients. Mice with impaired FGF10 signaling (Fgf10+/-) were more prone to develop cigarette smoke (CS)-induced emphysema and pulmonary hypertension (PH). Furthermore, FGF10 overexpression could successfully reverse cigarette smoke-induced emphysema and PH in mice.

overall_design: 14 groups with 4-5 biological replicates

first: Stefan

last: Hadzic

first: Norbert

last: Weissmann


title: Evaluating the effects of PTEN loss-driven cell transformation

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: We developed a unique in vitro transformation model utilizing PTEN CRISPR in the MCF10A human mammary epithelial cell line to study PTEN loss-induced transformation and profiled genome-wide expression in these cells to understand how PTEN loss alters the transcription landscape. We also examined changes in gene expression following inhibition of the p110b catalytic subunit of PI3 kinase, which is activated in the transformed cells. In addition, we profiled gene expression in MCF10A cells ectopically expressing PD-L1 (CD274), which is suppressed in cells harboring PTEN CRISPR.

overall_design: Examination of the effects of PTEN loss-driven transformation in mammary epithelial cells

first: Yubao

last: Wang

first: Thomas

last: Roberts


title: EGFR is a target of the tumor suppressor E3-ligase FBXW7

status: Public on Apr 03 2024

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

summary: FBXW7 is and E3 ubiquitin ligase and is highly mutated in colorectal cancer. We used human colon organoids with engineered FBXW7 hotspot mutations to investigate novel targets of E3 ligase activity with a combined transcriptomic and proteomic approach uncovering the EGFR-MAPK pathway as highly regulated by the E3 ligase activity.

overall_design: Human colon organoids were engineered to carry hotspot FBXW7 R505C mutation in combination or not with TP53 nonsense mutation with CRISPR-CAS9 Cytosine base editors. N=2 different clones with the same genetic background were passaged to single cells and seeded in BME with the same cell density. Cells were allowed to recover in full medium for 5 days before being washed and cultured for 48h in a medium depleted from EGF. The organoids were then recovered from BME and processed for RNA extraction and RNA-sequencing.

first: Matteo

last: Boretto

first: Maarten

last: Geurts

first: Shashank

last: Gandhi

first: Ziliang

last: Ma

first: Nadzeya

last: Staliarova

first: Martina

last: Celoti

first: Sangho

last: Lim

first: Gui-Wei

last: He

first: Rosemary

last: Millen

first: Else

last: Driehuis

first: Harry

last: Begthel

first: Lidwien

last: Smabers

first: Jeanine

last: Roodhart

first: Johan

last: van Es

first: Wei

last: Wu

first: Hans

last: Clevers


title: Gene expression profile of overgrown livers from genetic models involving YAP or MYC overexpression.

city: Cincinnati

first: Yunguan

last: Wang

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary:
We reasoned that when livers grow beyond their normal size, some growth regulating secreted factors will be suppressed and others will be overexpressed. To obtain overgrown livers, we used genetic models involving YAP or MYC overexpression
We the identified differentially expressed genes in both models and filtered out secreted factors by bioinformatically defined secreted protein list.

overall_design:
Col-TRE-YAPS127A; Rosa26-LSL-rtTA transgenic mice were given AAV-TBG-Cre between 8-10 weeks of age to induce rtTA expression in the liver. Upon dox administration, YAPS127A was induced for two or four weeks, then livers were collected.
We also used the LAP-tTA; TRE-MYC model of inducible liver specific MYC overexpression. MYC was induced at ~E8 by withdrawing dox water from pregnant mothers; livers were collected from offspring 4-weeks after birth.

first: Yu-Hsuan

last: Lin

first: Hao

last: Zhu


title: microRNA signature to support clinical-decision making in patients with suspected Obstructive Sleep Apnea

city: Lleida

first: David

last: de Gonzalo-Calvo

state: Lleida

address: Rovira Roure 80

country: Spain

institute: IRBLleida

summary: Plasmatic microRNA sequencing was conducted in specific matched subgroups of subjects (n = 53) with and without OSA using HTG EdgeSeq miRNA WTA Assay technology.

overall_design:
Obstructive sleep apnea (OSA) is a prevalent syndrome associated with significant morbidity and mortality. Recognizing and comprehensively characterizing the diverse pathogenetic pathways are pivotal steps to enhance outcomes. microRNA (miRNA) profiling represents a promising tool for elucidating pathogenetic mechanisms and developing disease-modifying interventions.

Plasma miRNAs were quantified through RNA sequencing (HTG Molecular Diagnostics, Inc, Tucson, AZ, USA) in 53 matched patients with and without OSA (selected using nearest neighbor propensity score matching by age, sex and body mass index (BMI))

first: Thalia

last: Belmonte


title: Gene expression profile at the single-cell level of tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells or WT CD8+ T cells

city: Yangsan

first: YUNA

last: JO

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan National University

summary: To investigate the function of Nrf2-deficient CD8 T cells in the regulation of anti-tumor response, we established adoptive transfer models. We then performed gene expression profiling analysis using data obtained from single-cell RNA-seq(scRNA-seq) of Nrf2-deficient and WT CD8 T cells in the tumor.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for Nrf2-deficient and WT CD8+ T cells in the solid tumor

first: Yuna

last: Jo

first: Changwan

last: Hong


title: Transient galanin expression shapes peripheral‑to‑central connectivity in the somatosensory thalamus during whisker development

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

summary:
Purpose:
We aimed to resolve if there is a matched expression of neuropeptide receptor(s) and their ligand(s) between the sensory trunk of the trigeminal nerve (Pr5) and the ventrobasal hypothalamus on postnatal day 7 (P7) in mice. We hypothesized that a coincidence of neuropeptide expression and release from the ventrobasal thalamus and the cognate receptor(s) for the specific neuropeptide(s) in trigeminal neurons could allow for novel hypotheses be built on intercellular communication between peripheral axons and their postsynaptic targets in the thalamus. Thereby, this work can be informative of the developmental integration of the whisker pathway, one of the major sensory modalities in laboratory rodents. To this end, we used single-cell RNA-seq on cells dissociated from the ventrobasal thalamus and Pr5 on P7.
Results:
We tested this hypothesis by single-nucleus RNA-seq performed in parallel on the ventrobasal thalamus and Pr5 at P7. At this developmental stage, the ventrobasal thalamus contained two subtypes of Slc17a6+(glutamatergic) neurons, one subtype of Gad1/Gad2+ (GABA) neurons, astroglia, oligodendrocytes, and vascular components (n = 923 nuclei isolated from n = 3 pups of mixed sex). Slc17a6+ neurons, which we recognize as cortically projecting glutamate neurons, co-expressed molecular components underpinning barrel map formation (e.g., Grin1, Adcy1, Prkaca,99 Ache, Slc6a4) and a significant amount of the thalamocortical neuronal marker Cck, while other neuropeptides/hormones were absent or barely present (e.g., Npy, Sst). At the same time, we harvested n = 731 nuclei from the Pr5 by micro-excision at P7, of which ∼98% expressed Slc17a6, thus qualifying, in total or in part, as centrally-projecting sensory neurons. This neuronal cohort harbored axon guidance molecules, and neuropeptide receptors.
Conclusions:
We suggest that neuropeptides, particularly galanin, could participate in guidance decisions of Pr5 axons given the complementarity of ligand-receptor expression patterns, and that Galr1 expression could be a time locked feature for those neurons that actively undergo neuritogenesis at a given time.

overall_design: To resolve if there is a matched expression of neuropeptide receptor(s) and their ligand(s) between the sensory trunk of the trigeminal nerve (Pr5) and the ventrobasal hypothalamus on postnatal day seven (P7) in mice we obtained 10X Genomics single nucleus samples of those regions from juvenile mice (n = 3, C57BL/6JRj of mixed sex).

first: Zsófia

last: Hevesi

first: Joanne

last: Bakker

first: Evgenii

middle: O

last: Tretiakov

first: Csaba

last: Adori

first: Thomas

last: Krausgruber

first: Sabrina

last: Ladstätter

first: Christoph

last: Bock

first: Tomas

last: Hökfelt


title: Hepatocyte regeneration is driven by embryo-like DNA methylation  reprogramming

city: Jerusalem

first: Batia

last: Azria

state: Israel

address: Jerusalem

country: Israel

institute: Hebrew university of Jerusalem

summary: As a result of partial hepatectomy (Phx), the remaining liver tissue undergoes a process of renewed proliferation that leads to rapid regeneration of the liver. By following the early stages of this process, we observed dramatic programmed changes in the DNA methylation profile, characterized by both de novo- and de- methylation events, with a subsequent return to the original adult pattern as the liver matures. Strikingly, these transient alterations partially mimic the DNA methylation state of embryonic hepatoblasts (E16.5), indicating that hepatocytes actually undergo epigenetic de-differentiation. Furthermore, Tet2/Tet3-deletion experiments demonstrated that these changes in methylation are necessary for carrying out basic embryonic functions, such as proliferation, a key step in liver regeneration. This implies that unlike tissue-specific regulatory regions that remain demethylated in the adult, early embryonic genes are programmed to first undergo de-methylation, followed by re-methylation as development proceeds. The discovery of this built-in system may open new targeting opportunities for regenerative medicine.

overall_design: Methylation profiling by high throughput sequencing of control liver, 7 d after Phx, 2 m after Phx and of TET2/3 DKO liver 7d after Phx.

first: Tal

middle: F

last: Michaeli

first: Ofra

last: Sabag

first: Rimma

last: Fok

first: Nathalie

last: Abudi

first: Rinat

last: Abramovitch

first: Jonathan

last: Monin

first: Yuval

last: Gielchinsky

first: Howard

last: Cedar

first: Yehudit

last: Bergman


title: Pro-inflammatory diet exacerbates colitis and alters gut microbiota

city: Guangzhou

first: Caiguang

last: Liu

address: No. 58 Zhongshan Road 2, Guangzhou, Guangdong Province, P.R. China.

institute: The First Affiliated Hospital, Sun Yat-sen University

summary:
To elucidate the underlying mechanisms of pro-inflammatory diet in regulating intestinal inflammation.
We performed gene expression profiling analysis using data obtained from RNA-seq of colon tissues from mice treatment with or without pro-inflammatory diet.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colon tissue from mice treatment with or without pro-inflammatory diet.

first: Xiaojun

last: Zhuang

first: Zhirong

last: Zeng


title: Graded FGF activity patterns distinct cell types within the apical sensory organ of the sea anemone Nematostella vectensis

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Bilaterian animals have evolved complex sensory organs comprised of distinct cell types that function coordinately to sense the environment. Each sensory unit has a defined architecture built from component cell types, including sensory cells, non-sensory support cells, and dedicated sensory neurons. Whether this characteristic cellular composition is present in the sensory organs of non-bilaterian animals is unknown. Here, we interrogate the cell type composition and gene regulatory networks controlling development of the larval apical sensory organ in the sea anemone Nematostella vectensis. Using single cell RNA sequencing and imaging approaches, we reveal two unique cell types in the Nematostella apical sensory organ, GABAergic sensory cells and a putative non-sensory support cell population. Further, we identify the paired-like (PRD) homeodomain gene prd146 as a specific sensory cell marker and show that Prd146+ sensory cells become post-mitotic after gastrulation. Genetic loss of function approaches show that Prd146 is essential for apical sensory organ development. Using a candidate gene knockdown approach, we place prd146 downstream of FGF signaling in the apical sensory organ gene regulatory network. Further, we demonstrate that an aboral FGF activity gradient coordinately regulates the specification of both sensory and support cells. Collectively, these experiments define the genetic basis for apical sensory organ development in a non-bilaterian animal and reveal an unanticipated degree of complexity in a prototypic sensory structure.

overall_design: scRNA-Seq

first: Keith

last: Sabin

first: Matthew

last: Gibson


title: Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors

city: La Jolla

first: Kay

last: Tye

address: 10010 N Torrey Pines Rd

department: Systems Neurobiology Laboratory

institute: Salk Institute

summary: The amygdalostriatal transition zone (ASt) is anatomically poised to provide a shortcut between corticolimbic and basal ganglia circuitry, and mediate behavioral responses to stimuli in parallel with the amygdala. Like the amygdala, the ASt receives converging sensory input from thalamic and cortical pathways. However, the projections of the ASt are distinct from canonical outputs of the amygdala complex, and are integrated with striatal circuits involved in action selection. Despite this intriguing circuit connectivity, the function of the ASt is almost completely unknown. In the present study, we collected cellular resolution recordings of genetically-defined neurons during a valence discrimination task to interrogate the functional role of ASt circuitry, and characterized the transcriptomic profile of the ASt in comparison to neighboring regions. We find that ASt neurons, and specifically, ASt neurons expressing dopamine receptor 2 (D2+), robustly encode sustained conditioned responses to cues of negative valence. Selective inhibition of D2+ ASt neurons was found to cause a striking reduction in conditioned fear responses. We also used single-nucleus RNA sequencing to generate a comprehensive profile of gene expression in ASt neurons, and found that the ASt is genetically distinct from adjacent GABAergic brain regions. RNAscope labelling also confirmed there is a greater proportion of D2+ neurons than D1+ neurons in the ASt, a unique feature compared to other regions of the striatum. Together, our findings provide the first evidence the ASt is a critical structure for encoding learned associations to direct motivated behavior.

overall_design: Comparative single-cell gene expression profiling of pooled amygdalostriatal transition area, central amygdala, dorsal striatum, and tail of striatum samples using snRNA-seq

first: Fergil

last: Mills

first: Christopher

last: Lee

first: James

last: Howe


title: Transcriptomic analysis of primary hepatocytes and total livers from WT mice fed with CSAA or CDAA-HSHC diet during 2 weeks.

city: Lille

first: Ludivine

last: Clavreul

address: Bd du Pr Jules Leclecq

institute: INSERM UMR1011

summary: Mouse primary hepatocytes (PH) and total livers (TL) prepared from C57Bl6 male adult mice which were fed either a CDAA supplemented cholesterol with glucose and fructose or a CSAA diet during 2 weeks.

overall_design: 3 independent preparations of PH and 4 independent preparations of TL were performed and used to prepare RNA which was then processed for analysis using Clariom S Assay, mouse microarrays according to standard procedures.

first: Réjane

last: Paumelle-Lestrelin


title: Epigenome analysis of wild type and Nsd2 gene-edited mice

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: Genome wide DNA methylation profiling of thymocytes from wild type and Nsd2 knock out (KO) and Nsd2 knock in (KI). The 906th Proline of Nsd2 was substituted to Leucine in Nsd2 KI by gene editing. The Illumina Infinium Mouse methylation Beadchip was used to obtain DNA methylation profiles across approximately 270,000 CpGs in thymocytes. Samples included 2 wild type, 2 heterozygous knock out, 1 heterozygous knock in, and 1 homozygous knock in.

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to the Illumina Infinium Mouse methylation Beadchip

first: Kenihiro

last: Hata


title: Protective effects on melphalan-induced mouse intestinal injury treated by Human Umbilical Cord-derived Mesenchymal Stem Cells

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

institute: the Second Hospital of Dalian Medical University

summary:
Autologous peripheral hematopoietic stem cell transplantation (autoHSCT) is one front-line therapy with high-dose melphalan for multiple myeloma (MM). Patients with MM who receive conditioning regimen with melphalan usually suffer from severe gastrointestinal symptoms, as one of nonhematological toxicities.
Aim: It is an urgent demand to develop an effective methods to repair the intestinal injuries in patients with MM receiving conditioning regimen with high-dose melphalan for autoHSCT. Therefore, the protective effects of Human umbilical cord derived-mesenchymal stem cells (hucMSCs) is investigated after infusion into mouse model with melphalan-induce gastrointestinal injuries.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control small intestine cells and its treatments (melphalan, melphalan+MSC, and MSC+melphalan).

first: Yifei

last: Ren

first: Xuehong

last: Zhang


title: Genome-wide maps of chromatin state in thymocytes from Nsd2-edited mice

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed high-throughput profiling of histone modifications in mouse thymocytes in which Nsd2 were deleted (KO) or Nsd2 were substituted as following c.2717C>T; p.Pro906Leu that is an orthologous substitution of human NSD2 c.2714C>T; p.Pro905Leu (KI). We found that lysine 36 dimethylation were generally decreased in KO and KI. These were associated with regulation of gene expression.

overall_design: Examination of histone H3 lysine 36 dimethylation in mice thymocytes.

first: Kenichiro


title: CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [scTCR-seq, CITE-seq]]

first: Hiroyasu

last: Aoki

summary: mRNA vaccines against the Spike glycoprotein of severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, it is unknown whether the repertoire of memory T cell clones changes between primary and secondary vaccinations. Here, we analyzed the kinetic profile of Spike-reactive T-cell clones before the first dose, one week after the first and second dose, and four weeks after the second dose of the BNT162b mRNA vaccine. Interestingly, a new set of Spike-reactive CD8+ T cell clones exhibited the greatest expansion following secondary vaccination and replaced the clones that had responded to the primary vaccination. Single-cell mRNA/protein/TCR analysis revealed that the first-responder clones exhibited a terminally differentiated phenotype, whereas second-responder clones exhibited an actively proliferating phenotype. These results show that Spike-reactive T cell responses induced by repetitive mRNA vaccination are augmented and maintained by replacement with newly-generated clones with proliferative potential.

overall_design: Single-cell CITE-seq combined with TCRseq was performed on non-naive CD4+ and CD8+ T cells collected from PBMC of two participants 7 days after the second dose of Pfizer-BNT162b2 mRNA vaccine.

first: Masahiro

last: Kitabatake

first: Haruka

last: Abe

first: Peng

last: Xu

first: Mikiya

last: Tsunoda

first: Shigeyuki

last: Shichino

first: Atsushi

last: Hara

first: Noriko

last: Ouji-Sageshima

first: Chihiro

last: Motozono

first: Toshihiro

last: Ito

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [AIM Bulk TCR-seq]

overall_design:
TCRseq was performed on Spike-reactive CD4+ and CD8+ T cells determined by AIM assay on PBMC of 15 participants seven days after Pfizer-BNT162b2 mRNA vaccination.
-------------------------
Submitter states  GSE210227 "was not used in the final revision".


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [CB vs mPB scRNA-seq]

city: NY

first: Tomer

last: Itkin

address: 1300 York Avenue, A-869

department: Medicine

institute: Weill Cornell Medicine

summary: Single cell RNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from cord blood (CB) and mobilized peripheral blood (mPB) donors, after co-culture with vascular niche cells, to uncover differential transcriptional output between HSPC derived from CB and mPB origins.

overall_design: Human CB and mPB HSPCs were harvested isolated and sorted. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resorted and processed for 10X Chromium scRNA-seq analysis.

first: Sean

last: Houghton

first: Shahin

last: Rafii


title: CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [Bulk TCR-seq]

city: Noda

institute: Tokyo University of Science

overall_design: TCRseq was performed on CD4+ and CD8+ T cells collected from PBMC of 38 participants before and after Pfizer-BNT162b2 mRNA vaccination.


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [snRNA/ATACseq HSPC Multiome]

summary: Multiome single nuclei RNA/ATAC-seq analysis was performed on sorted population of SLAM LSK HSPCs to uncover transcriptional determinants regulating HSPCs in distinct transitional states.

overall_design: SLAM LSK HSPCs were harvested isolated and sorted from flushed and crushed murine tibias and femurs. SLAM LSK HSPCs pooled from 20 mice were analyzed by multiome 10X sequencing procedure.


title: Effect of depletion of HOIP on gene expression during B16-F10 melanoma tumor development in immunedeficinet mice.

city: Kyoto

first: Kazuhiro

last: Iwai

address: Yoshida Konoecho, Sakyo-ku

institute: Kyoto university

summary: To investigate the cooperative function LUBAC E3 ligase complex during tumor development, we established HOIP-knockout B16-F10 murine melanoma cell lines.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of the established 4 control or 4 HOIP-KO s.c tumors 2 weeks after innoculation.
Comparative gene expression profiling analysis of RNA-seq data for control and HOIP-KO B16-F10 tumors.

first: Katsuhiro

last: Sasaki


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [scRNA-seq  cocultured HSPCs]

summary: Single cell RNA-seq analysis was performed on sorted population of LSK HSPCs with different genetic background and phenotype, after co-culture with vascular niche cells, to uncover differential transcriptional output following genetic manipulation.

overall_design: LSK HSPCs were harvested isolated and sorted from flushed and crushed murine tibias and femurs. LSK HSPCs (WT, Fli-1ROSAΔ , Fli-1ROSAΔN1-ICiOE, and N1-ICiOE) were introduced into co-culture with vascular niche ECs. 4-OHT was introduced into cultures to induce genetic manipulation. Cultures were harvested and LSK HSPCs were resorted and processed for 10X Chromium scRNA-seq analysis.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ompR mutant of K. pneumoniae ATCC43816 Transcriptomes.

city: Beijing

first: Lijun

last: Wang

state: Beijing Shi

address: Shuangqing Road 30#

department: Department of Basic Medical Science

institute: Tsinghua University

summary: Purpose: This study aims to compare the transcriptome profiling (RNA-seq) of ompR mutant to that of WT and to evaluate the transcrptional regulation of OmpR in K. pneumoniae in exponential phase.

overall_design: mRNA profiles of  K. pneumoniae ATCC43816 wild-type (WT) and ompR knockout mutant were generated by deep sequencing, in duplicate, using Illumina Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with RSEM using the Expectation Maximization (EM) algorithm. TPM method is used to calculated expression level.


title: Real-time quantitative PCR analysis of mice kidney after administration of Lu-177-octreotate, Lu-177-octreotate + A1M and A1M

city: Gothenburg

first: Charlotte

last: Andersson

address: Gula Stråket 2B

department: Department of Medical Radiation Science

country: Sweden

institute: University of Gothenburg

summary: This work aimed to examine the regulation of apoptosis-related genes in kidney cortex and kindey medulla one and seven days after administration of 177Lu-octreotate with and without A1M and of A1M alone. C57BL/6N mice were injected with either 177Lu-octreotate + PBS, A1M + PBS or 177Lu-octreotate + A1M. Also, a control group was sham-treated with saline. Half of the animals in each treatment and control group were terminated by cardiac puncture one-day post-injection (1 dpi), and the remaining animals were terminated at 7dpi. Kidneys were dissected at the time of termination, snap-frozen in liquid nitrogen and stored at -80°C.

overall_design: Three biological replicated were included in each test group at both 1 dpi and 7dpi, and three biological replicates were included in corresponding controls. An equal amount of total RNA (40 µg) was extracted from all samples, and 200 ng of total RNA was reversed transcribed into cDNA per sample.

first: C

first: K

last: Simonsson

first: E

last: Shubbar

first: M

last: Gram

last: Helou

last: Forssell-Aronsson


title: Transcritpomic analyses of CARD14 WT and psoriatic gain-of-function CARD14 E138A mutant over time

city: London

first: Tolar

last: Pavel

address: Gower St

country: United Kingdom

institute: UCL

summary: CARD14 gene mutations have been shown to be a causitive factor for psoriasis in human patients. CARD14 signalling is poorly understood and very little is known about how it regulates NF-kB activation. Basic research is therefore required to better understand the mechanisms by which is brings about pathology in a gain-of-function state. Analyses of CARD14 mutant versus WT transcription over time in a relevant cell type (keratinocyte) was pursued as one of several means to better understand CARD14-driven psoriasis.

overall_design: CARD14E138A-3xFLAG HaCaT-TR, CARD14WT-3XFLAG HaCaT-TR keratinocytes were seeded  for tetracycline incubations of 0, 3, 6, and 9 h. Cells were lysed and RNA isolated (RNeasy kit, QIAGEN, #74106). mRNA was then purified using a poly-A KAPA mRNA Hyper Prep kit (Roche) and sequenced on an Illumina HiSeq4000 instrument.

first: Paul

last: O'Sullivan

first: Stefan

last: Boeing

first: Steven

last: Ley


title: CD8+ T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance

first: Hiroyasu

last: Aoki

address: 2669 Yamazaki

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

overall_design: Refer to individual Series


title: Deep sequencing and fitness calculation for plasmids carrying the CREATE cassette from the enriched tolerant strains  under different pressures by using  Illumina protocol

city: Tianjin

first: Yangyang

last: Zheng

address: 135 Yaguan Road, Jinnan District, Tianjin

institute: Tianjin University

summary: We  report using global regulator libraries based on the CRISPR-enabled trackable genome engineering (CREATE) method to engineer tolerance against multiple inhibitors in Escherichia coli. Deep mutagenesis libraries were rationally designed, constructed, and screened to target 34,340 mutations across 23 global regulators.These libraries were divided into G1, G2, G3, G4 and G5 sub-groups according to different gene functions (such as active sites, DNA binding sites, and predicted functional sites) . And we successively screened the libraries under different stress conditions (acetate, NaCl, furfural, high temperature and  isobutanol), and enriched mutants able to tolerate multiple inhibitors. In order to determine the tolerance-conferring mutations screened under different stress conditions, deep sequencing and fitness analysis were used to detect the recombinant strains with good performance.

overall_design: Mutations on chromosomes were consistent with those carried by the CREATE plasmids. Firstly, the CREATE plasmids of tolerant strains were extracted separately. Following extraction, the CREATE plasmids were used as templates for PCR using Illumina-compatible primers designed with Golay barcodes . CREATE library fragments were amplified in 16 cycles of PCR. At the first PCR step, each experimental sample was ligated with a unique barcode used to track the mutations. After that, PCR products were confirmed by electrophoresis and purified using an Agarose Gel DNA Extraction Kit. Deep sequencing was performed according to the Illumina protocol for amplicon sequencing.   The editing cassette was used to quantify fitness associated with different mutations in the library. Fitness associated with all mutations in the library was calculated using log2-fold enrichment. Synonymous mutations of every homology arm were regard as a part of each corresponding library. Synonymous mutations were used to determine the standard deviation and mean value of the log2-fitness change of wild-type cells. Then, a mean ± 2σ cutoff (i.e., p=0.05 assuming a normal distribution) was used to estimate strongly enriched mutations in the selections. The confidence interval of 95% was used to calculate statistically significant differences between samples. Differences with p ≤ 0.05 were considered statistically significant.

first: Alaksh

last: Choudhury

first: Xin

last: Song

first: Zhiwen


title: Gene expression in splenic B cells or thymocytes from mice with Nsd2 was edited

first: Tomoko

last: Kawai

summary: We performed RNA-Seq on primary splenic B cells and thymocytes that were collected from wild type and Nsd2-edited mice.

overall_design: Transcriptome profiles of 13 to 15 weeks old wild type (WT) and Nsd2 knock in or knock out mice

first: Kenichiro

last: Hata


title: Bleomycin-injured alveolospheres

city: Kashiwa

first: BIN

last: WU

address: #304, 6-6-2, Kashiwanoha

department: Research

institute: ImmunoGeneTeqs


title: Single-cell RNA sequencing analysis of murine lung epithelial cells and fibroblasts derived from bleomycin-injured alveolospheres

summary: Pulmonary fibrosis is a devatating lung disease with limited effective treatment. Because fibrotic responses are considered to be regulated by complex cellular and molecular circuits, it is difficult to demonstrate a causal relationship of cells, molecules, and cell-cell interactions with diseases in vivo. To overcome this issue, we established bleomycin (BLM)-stimulated alveolosphere model as an ex vivo culture model. To clarify whether our ex vivo model recapitulates the cellular and molecular response to BLM-induced lung injury, we performed single-cell RNA-seq (scRNA-seq) analysis of the BLM-stimulated alveolospheres generated by co-culturing murine lung epithelial cells and lung fibroblasts.

overall_design: Alveolopheres were generated by co-culturing primary mouse CD326 positive lung epithelial cells and Cd140a positive lung fibroblasts. To clarify transcriptomic changes of BLM-injured alveolospheres at single-cell level, we stimulated alveolospheres with bleomycin (0.1 ug/ml) in a culture media from day 8 to day 10 post co-cultured. After that, bleomycin was removed from the culture media and the alveolospheres were further cultured until day 14 post co-cultured. scRNA-seq analysis was performed at day 10 and day 14 post co-cultured.

first: Bin

last: Wu

first: Shigeyuki

last: Shichino

first: Tatsuro

last: Ogawa

first: Rina

last: Matsukiyo

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: Evaluating the H2O2-induced tRNA expressions change in Streptococcus oligofermentans

first: Huichun

last: Tong

address: NO. 3, Yihao Yuan, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: The tRNA gene expression change was evaluated by whole genomic microarray chip in Streptococcus oligofermentans challenged by H2O2.

overall_design: Mid-exponential anaerobically grown Streptococcus oligofermentans was treated with or without 0.5 mM H2O2 for 30 min, then the cells were collected, total RNA extracted and subjected to Microarray hybridization. Two oligonucleotide were designed for each gene. The experiments were repeated for two  times.


title: The proteomic and transcriptomic profiles of gastric mucosa from health volunteers

city: Shenzhen

first: Yuhao

last: An

state: Guangdong Province

address: 16 Lanjing Road, Kengzi Street, Pingshan District

institute: Shenzhen Bay Lab

summary: As the important layer of the stomach wall, gastric mucosa is related to many functions of digestion. According to the anatomical location, the human stomach is divided into seven regions. In order to get an entire profiling of the 7 regions at proteomic and transcriptomic levels, we collected 7 biopsies from each health volunteer, 49 total were used for integrative analysis, and measured the regional-specific gene products to define the reference intervals of gene expression for outliers screening and prognostic gene detection. Collectively, we presented profiling of normal gastric mucosa at different levels and defined reference ranges of gene expression to study the specific characteristics of abnormal and cancer samples, providing a better understanding of stomach physiological function in studies of gastric disease mechanism.

overall_design: Following the histoanatomy of human stomach in medicine, we collected the gastric mucosa biopsies from the health volunteers without H. pylori infection. To keep the omic data at different expression levels have a consistent location for further comparison, after tissue homogenization, the powder was split into two parts for protein and mRNA extraction. Finally, the transcriptomic data was generated by RNAseq.


title: Metformin treatment on Fusobacterium nucleatum

city: Shanghai

first: Xiaowen

last: Huang

address: 145 Middle Shandong Road, Shanghai 200001, China

institute: Shanghai Jiao Tong University, Shanghai Cancer Institute,Shanghai Institute of Digestive Disease

summary: High throughput RNA sequencing  For RNA sequencing, F. nucleatum was incubated with 1 mM or 5 mM metformin for 7 hours, when the bacterium were under logarithmic phase. Total RNA of F. nucleatum was stabilized with RNA protect Bacteria Reagent (QIAGEN, Germany) and extracted using a QIAGEN RNeasy kit (QIAGEN, Germany) following the manufacturer’s instructions.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

overall_design: Examination of the alterations in Fusobacterium nucleatum gene expression by metformin treatment.

first: Xialu

last: Hong

first: Hua

last: Xiong


title: Effect of 630nm LED red light on rheumatoid arthritis

city: Harbin

first: Wuqi

state: Heilongjiang

address: Baojian Road

department: Department of Microbiology

institute: Wu Lien-Teh Institute

summary: Photobiomodulation (PBM) is praised as a promising physical therapy, which has many advantages, such as noninvasive, painless. The 630nm LED-stimulated-MH7A cells were sequenced for analyzing the mechanism of PBM. As a result,1181 differentially expressed genes were identified.

overall_design: RNA-seq of MH7A cells treated with TNFα treatment or TNFα treatment and LED-15min/3times

first: Hao

first: Caiyun

last: Meng

first: Fengmin

last: Zhang


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [Bulk HSPC RNA-seq]

first: Tomer

last: Itkin

summary: Presetting of adaptive hematopoiesis by Fli-1 entails reciprocal niche sensing of Notch/VEGF-A pathways to supersede Spi1-driven dormancy. RNA-seq analysis for WT and Fli-1 KO HSPCs was performed to uncover changes in transcriptional output following Fli-1 deletion.

overall_design: RNA sequencing of WT and Fli-1 KO HSPCs after 6d in co-culture with a vascular niche post Fli-1 deletion induction.

first: Sean

last: Houghton

first: Shahin

last: Rafii


title: Transcriptome of Paraquat-induced Pulmonary Fibrosis

city: Nanjing

first: LU

last: FAN

state: Jiangsu

address: No. 300 Guangzhou Road

department: Department of Emergency

institute: Jiangsu Province Hospital, the First Aﬃliated Hospital of Nanjing Medical University

summary:
PURPOSE: Pulmonary fibrosis (PF) is a pathological state presenting at the progressive stage of heterogeneous interstitial lung disease (ILD). The molecular mechanisms are incompletely understood. We built a mouse model of lung fibrosis induced by paraquat. Using transcriptome analysis, we identified differentially expressed proteins (DEGs) and provided further functional analysis.
METHODS: We built a mouse model of lung fibrosis through intratracheal instillation of paraquat. After instillation, mice were kept for 7 and 28 days, respectively. we performed time-series RNA sequencing (RNA-Seq) on the lung samples from paraquat treated mice and saline control. The DEGs were verified by qPCR.
RESULTS: The transcriptome data found a total of 1345 of differentially expressed genes (DEGs) up-regulated and 844 DEGs down-regulated significantly in paraquat group on day 7. There were 511 DEGs up-regulated and 179 DEGs down-regulated remarkably on day 28 after PQ instillation (Fold Change ≥2 and Q value ≤0.001). We verified 6 significantly changed genes by qPCR, proving the accuracy of RNA-seq.
CONCLUTION: Our transcriptomic study assigns genes for fibrogenesis and reveals their dynamic changes from lung injury to repair, providing new insights for the and development of biomarkers and treatment in fibrotic diseases.

overall_design: Lung mRNA profiles of paraquat-induced pulmonary fibrosis

first: Lu

last: Fan

last: Sun

first: Jingsong


title: Transcriptome analysis of endometrium cells in Equus asinus

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

summary: Deoxynivalenol (DON) and zearalenone (ZEA) are the most common mycotoxins, which are damage to the reproductive system of human and animal. Endometrium cells perform vital roles of female reproduction. In the present study, transcriptomic was conducted on different dosage (0 μM, 10 μM and 30 μM) of DON and ZEA treatment donkey endometrium cells. Transcriptomic analysis showed 7386 differentially expressed genes (DEGs) were identified between DON 10 μM treatment group and control group, with 3655 up regulated and 3731 down; 8694 DEGs were identified between DON 30 μM treatment group and control group, with 4532 up regulated and 4162 down; 1768 DEGs were identified between ZEA 10 μM treatment group and control group, with 763 up regulated and 1005 down; and 3311 DEGs were identified between ZEA 30 μM treatment group and control group, with 1501 up regulated and 1810 down. In DEGs, Caspase-1, GSDMD-NT, ESR 1, PRDX 4, NOX 1, MSH 6 and CD 44, were expressed changed in DON and ZEA treatment group, which related to pyroptosis, hormone secretion, oxidative stress and cancerous. It is unprecedented that DON induced cell death by pyroptosis. This study provides valuable genetic resources for understanding the mechanisms and pathways of the toxin effect of DON and ZEA for Equus asinus’ endometrium cells.

overall_design: Total mRNA profiles of DON and ZEA treated endometrium cells were generated by deep sequencing, in triplicate.

first: Guoliang


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing  [Bulk EC RNA-seq]

summary: RNA-seq analysis for WT and Fli-1 KO ECs was performed to assess changes in transcriptional output following Fli-1 deletion.

overall_design: RNA sequencing of WT and Fli-1 KO ECs after 6d in co-culture with a vascular niche post Fli-1 deletion induction.


title: JAK Activity Regulates Mesoderm Cell Fate and Cardiac Differentiation by controlling MESP1 expression

status: Public on Mar 31 2024

first: su

last: yao

address: 1239 Siping Road

institute: Tongji university

summary: Cardiac development requires precise gene expression programs at each developmental stage guided by multiple signaling pathways and transcription factors (TFs). MESP1 is transiently expressed in mesoderm, and is essential for subsequent cardiac development, while the precise mechanism regulating its own transcription and mesoderm cell fate is not fully understood. Therefore, we developed a high content screen assay to identify regulators of MESP1 expression in mesodermal cells differentiated from human pluripotent stem cells (hPSCs). The screen identified CYT387, a JAK1/JAK2 kinase inhibitor, as a potent molecule that can significantly increase MESP1 expression. CYT387 was also found to enhance cardiomyocyte differentiation from hPSCs in vitro. Mechanistical studies found that JAK inhibition promotes MESP1 expression by reducing cytoplasmic calcium concentration and subsequently activating canonical WNT signaling. Our study identified a role of JAK signaling in early mesoderm cells, and sheds light on the connection between the JAK-STAT pathway and transcriptional regulation of MESP1, which expands our understanding of mesoderm and cardiac development.

overall_design: To investigate how JAK regulates MESP1 expression, we performed bulk RNA-Seq of CYT387 and DMSO treated mesoderm cells.

first: Su

last: Yao

first: ke

last: wei


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing  [Bulk H3K27ac ChIP]

summary: H3K27ac ChIP-seq analysis for WT and Fli-1 KO HSPCs was performed to uncover changes in chromatin H3K27ac modifications following Fli-1 deletion.

overall_design: H3K27ac ChIP sequencing of WT and Fli-1 KO HSPCs after 6d in co-culture with a vascular niche post Fli-1 deletion induction.


title: Targeting SOX4/PCK2 signaling suppresses neuroendocrine differentiation of castration-resistant prostate cancer

city: shanghai

first: jing

state: shanghai

address: Rm 1515, Bldg 17, 160 Pujian Rd, Shanghai 200127, China

institute: Shanghai jiaotong university

summary:
Background: Neuroendocrine prostate cancer (NEPC), a lethal subset of prostate cancer, is characterized by loss of AR signaling and resulting resistance to AR-targeted therapy during neuroendocrine transdifferentiation, for which the molecular mechanisms remain unclear. Here, we report that SRY-Box transcription factor 4 (SOX4) is upregulated in NEPC, which induces neuroendocrine markers, neuroendocrine cell morphology, and NEPC cell aggressive behavior.
Methods: To understand the function of SOX4 in the development and progression of NEPC, we detected malignancy characterization after over-expression or knock-down of SOX4 in prostate cancer cells. Xenograft tumors representing NEPC subtypes were analyzed by pathologists.  Protein expression profiles were validated in patient tumor tissue. Diagnoses were complemented by transcriptome sequencing and ATAC sequencing of specific cell lines and public clinical datasets.
Results: SOX4 expression was significantly elevated in NEPC. Activating SOX4 in non-NEPC cells induced NE transdifferentiation, while silencing it in NEPC cells impeded NEPC progression. SOX4 promote neuroendocrine characteristics by inducing PCK2-mediated metabolism changing.
Conclusions: Elevated SOX4 drives NE transdifferentiation in PCa via PCK2-mediated . Altogether, these findings highlight SOX4 as a novel molecule to drive NEPC progression and suggest that it might be a potential therapeutic target for NEPC.

overall_design:
To investigate the role of SOX4 in the differentiation of  prostate cancer cell lines, we established DU145-shSOX4 cell line and DU145-oeSOX4 cell line to investigate whether SOX4 knockdown could repress the neuroendocrine transdifferentiation of NE-like cells.
We then performed gene expression profiling analysing data obtained from RNA-seq of  DU145-shCon and DU145-shSOX4 cells. We also performed ATAC seq to explore  the chromatin accessibility in   DU145-oeSOX4  compared with DU145-Vector cells.

last: Jing

first: Zhen

middle: k

last: Tao


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [Bulk ATAC-Seq]

summary: ATAC-seq analysis for WT and Fli-1 KO HSPCs was performed to uncover changes in chromatin accessibility following Fli-1 deletion.

overall_design: ATAC sequencing of WT and Fli-1 KO HSPCs after 6d in co-culture with a vascular niche post Fli-1 deletion induction.


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [scRNA-seq engrafted HSPCs]

summary: Single cell RNA-seq analysis for WT and Fli-1 KO engrafted HSPCs (Lineage negative CD45.2+) was performed to assess changes in transcriptional output in HSPCs following Fli-1 deletion and Notch1 overexpression and to determine distribution of cells among the different hematopoietic populations.

overall_design: Single cell RNA sequencing of WT and Fli-1 KO Notch1 OE lineage depleted HSPCs after 4 month of in vivo engraftment preceded by 6 days of co-culture with a vascular niche.

first: Brandon

last: Hadland


title: Stiffness Assisted Cell-Matrix Remodeling Trigger Mechanotransduction Regulatory Programs to Induce Stem Cell Differentiation

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy, Medical Research and Education Building II Suite 4344

department: Department of Molecular and Cellular Medicine

institute: Texas A&M University

summary: The interplay of transcription and epigenetics in response to biophysical factors is important in the design of engineered matrix platforms that seek to direct cellular fate. We present a nanoparticle crosslinker to reinforce hydrogels and study the impact on hMSC transcription through RNA-seq. The study provides insight into how environmental stiffness drives global intracellular signaling through PI3AKT transction and chromatin remodeling to enable YAP/TAZ activity.

overall_design: Examination of matrix stiffness impact on transcriptome and epigenome to modulate hMSC fate

first: Anna

middle: L

last: Kersey

first: Daniel

last: Cheng

first: Kaivalya

last: Deo

first: Christina

last: Dubell

first: Ting-Ching

last: Wang

first: Manish

last: Jaiswal

first: Min Hee

last: Kim

first: Tanmay

last: Lele

first: Akhilesh

last: Gaharwar

first: Aparna

last: Murali

first: Sarah

last: Hargett


title: RNA-seq of AtPIN5 overexpressing tobacco BY-2 cells

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: This RNA-seq is a part of the paper describing the role of PIN5 in generating auxin sinks.  https://www.biorxiv.org/content/10.1101/2024.01.24.576992v1

overall_design: Gene expression analysis of stable transgenic BY-2 cell line inducibly expressing AtPIN5. RNA was isolated from two-day-old cells,  1 µM β-estradiol (diluted in DMSO) was added at the beginning of the subculture interval. Cells treated with DMSO were used as a control. Cells were cultured in standard BY-2 medium.

last: Müller

first: Jan

last: Petrášek

first: Kamil

last: Růžička

first: Milada

last: Čovanová


title: Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing

first: Tomer

last: Itkin

address: 1300 York Avenue, A-869

institute: Weill Cornell Medicine

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

sample_organism:
Homo sapiens
Mus
Mus musculus

platform_organism:
Homo sapiens
Mus
Mus musculus

overall_design: Refer to individual Series


title: FER kinase governs invasive tumor growth through dynamic control of oncogenic growth factor receptor activity

city: Utrecht

first: Peter

last: Haughton

address: Heidelberglaan 100

department: Pathology

institute: UMCU

summary: EGFR antagonism using monoclonal antibodies remains the only approved and targeted first line treatment option for non-resectable head and neck squamous cell carcinoma (HNSCC), yielding a modest 13% response rate. While it is clear that alternative growth factor receptor (GFR) signals govern refractory behavior towards EGFR antagonism, it remains unknown which upstream mechanisms control subcellular GFR activation. Here, we show that FER, a non-receptor tyrosine kinase, controls invasive tumor growth through dynamic GFR activation and recycling. Using patient derived organoid (PDO) models HNSCC we demonstrate that FER is essential for invasive growth in collagen extracellular matrix (ECM) networks. We show that inactivation of FER impairs growth factor dependent phosphorylation of EGFR-Y1068 and MET-Y1234/5. Additionally, FER controls ligand dependent endocytic recycling, and endocytic velocity, implying multifactorial functional regulation of proximal receptors during HNSCC invasion. Loss of function experiments using either genetic intervention or a FER PROteolysis-TArgeting Chimera (PROTAC) strategy in PDO-based xenograft mouse models, demonstrate that FER is essential for invasive growth and metastasis of HNSCC. Finally, we demonstrate direct clinical relevance by showing that FER expression levels correlate with poor survival in HNSCC patients. In sum, we conclude that FER is a master regulator of HNSCC invasive growth and metastasis, and nominate FER as a prominent candidate for targeted clinical intervention in HNSCC patients.

overall_design: Single-cell mRNA sequencing was performed on a tongue squamous cell carcinoma patient derived organoid line (T4), cultured in a collagen type-I (invasive) matrix in the absence (dox neg) or presence of doxycyline to induce a FER knockdown (dox pos).

middle: D

first: Wisse

last: Haakma

first: Sandra

last: Tavares

first: Lotte

last: Enserink

first: Garik

last: Galustjan

first: Sjors

last: Koppes

first: Else

last: Driehuis

first: Hans

last: Clevers

first: Yanchun

last: Zhang

first: Gaofeng

last: Fan

first: Stefan

last: Willems

first: Patrick

middle: W

last: Derksen


title: Allosteric regulation by c-di-AMP modulates global signal integration in Actinobacteria

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

summary: C-di-AMP is primarily associated with the regulation of carbon utilization as well as other central traits, central metabolism, and bacterial stringent response to environmental changes. Elevated c-di-AMP levels result in aberrant physiology for most c-di-AMP synthesizing organisms, drawing particular attention to the importance of the c-di-AMP homeostasis and the molecular mechanisms pertaining to nucleotide metabolism and signal transduction. Here we show that c-di-AMP binds the GntR-family regulator DasR, uncovering a direct link between c-di-AMP and GlcNAc signaling. Further, we show c-di-AMP functions as an allosteric activator of DasR activity. GlcNAc is necessary for cell-surface structure from bacteria to humans, as well as a signal for bacterial development and antibiotic production. DasR is a global repressor that oversees GlcNAc metabolism and antibiotic production, which enables Actinobacteria to cope with stress and starvation. Our in vivo studies reveal the important biological role of allosteric regulation by c-di-AMP in metabolic imbalance and the transduction of a series of signals. Notably, DasR also controls intracellular c-di-AMP level through direct repression on disA. Overall, we identify a function of allosteric regulation between c-di-AMP and DasR in global signal integration and c-di-AMP homeostasis in bacteria, which is likely widespread in Actinobacteria.

overall_design: Saccharopolyspora erythraea WT and OdisA strains grown in TSB medium are used for ChIP-seq

first: Zhi-Yao

last: Peng

first: Liu-Chang

last: Zhao

first: Zong-Qin

last: Chen

first: Yu

last: Fu

first: Bang-Ce

last: Ye


title: Genome-wide maps in H9C2 cells with or without PAGln treatment (100 μM)

first: Lufeng

last: Zheng

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

summary: Analysis of H9C2 cells following PAGln treatment or not. PAGln regulates various mRNA expression in H9C2 cells.Results provide insight into the role of PAGln-involved mechanisms underlying PAGln-mediated effects on coronary artery disease (CAD).

overall_design: MRNA profiles of H9C2 cells treated with or without PAGln were generated by deep sequencing, in two repeats, using Illumina NovaSeq 6000.

first: Hang

last: Xu


title: Nanopore-based full-length transcriptome sequencing of yak (Bos grunniens) testis

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: Alternative splicing (AS) is strictly regulated during cell differentiation and development. AS events are common in the testis, but the splicing regulation in spermatogenesis is still unclear. In this experiment, the third-generation ONT sequencing was used to sequence the full-length transcriptome of testicular tissue, and 40,038 new transcripts were obtained, and the proportion was almost close to the number of known transcripts identified. A total of 7,645 fused transcripts, 15,355 ASs, 25,798 SSRs, and 35,503 lncRNAs were detected. Through gene co-expression network analysis, the key pathways and Hub genes in each stage of yak testicular development were confirmed. The effects of alternative splicing and splicing variation on mammalian spermatogenesis will provide new insights into the potential application of alternative splicing in the treatment of male infertility.

sample_organism:
Bos grunniens
Bos grunniens x Bos taurus

overall_design: The full-length transcriptomes of four developmental stages of yak and adult cattle-yak testis were obtained by ONT sequencing technology,

first: Xingdong

last: Wang

first: Shaoke

last: Guo

first: Jie

last: Pei

first: Xian


title: A hominoid-specific signaling axis setting the tempo of synaptic maturation

first: Dong

last: Jian

address: 393 Middle Huaxia  Road

institute: shanghaitech university

summary: Compared to that of other mammals, human cortical neurons exhibit higher dendritic complexity and synaptic density, and the maturation process is much protracted. However, the molecular mechanism governing these specific features is unclear. Here, we report that the hominoid-specific gene TBC1D3, a core duplicon in the human genome, promotes dendritic arborization and maintains the slow pace of synaptogenesis. Furthermore, to gain insights into the mechanism by which the TBC1D3-MICAL1-ATRX complex determines the slow pace of spinogenesis, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) experiment using an ATRX antibody targeting the C-terminal region in cultured mouse cortical neurons.

overall_design: Contol neurons (DIV14), TBC1D3 neurons (DIV14),  M1 neurons (DIV14), and young neurons were conducted ChIP-seq experiment using an ATRX antibody.

first: Jian

last: Dong

first: Zhen-ge

last: Luo


title: GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation

status: Public on Mar 28 2024

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

summary: Mutations in transcription factor Growth Factor Independence 1B (GFI1B) cause inherited bleedings with varying intensity possibly caused by different effects on the transcriptional function of GFI1B. We studied transcriptomic changes of normal and GFI1BT174N,H181Y,R184P,Q287* mutants in megakaryoblast MEG01 cells using RNA-sequencing. Compared to normal GFI1B each variant affected different gene modules with limited overlap between variants. Remarkably, GFI1BQ287* specifically activated a myeloid-associated gene module. Based on this finding we studied megakaryocyte differentiation using normal and GFI1BQ287* patient-derived induced pluripotent stem cells (IPSC) followed by single cell RNA-sequencing. This revealed a 45-fold decrease in the megakaryocyte/myeloid cell ratio in the GFI1BQ287* versus control condition. Moreover, myeloid specific genes were expressed within GFI1BQ287* but not normal megakaryocytes. Finally, we studied how megakaryocyte development was affected by inhibiting binding of GFI1B to Lysine Specific Demethylase 1 (LSD1), an interaction required for megakaryocyte development. Treatment of both MEG01 cells and normal IPSC-derived developing megakaryocytes with the small-molecule inhibitor GSK-LSD1 resulted in profound activation of myeloid gene programs within megakaryocytes, while the IPSC-derived megakaryocyte/myeloid ratio dropped two-fold. We conclude that GFI1B and LSD1 suppress myeloid differentiation allowing for proper megakaryocyte development. LSD1 inhibitor and GFI1BQ287*-mediated perturbation of this function causes myeloid skewing during megakaryocyte development.

overall_design: To determine transcriptomic changes induced by GFI1B variants we retrovirally expressed GFI1BT174N, H181Y, R184P, Q287* next to normal GFI1B and an empty vector in megakaryoblast MEG01 cells followed by RNA-isolation and in triplicate RNA-sequencing 4 days later.

first: Jeron

last: Venhuizen

first: Maaike

last: van Bergen

middle: H

first: Bert

last: van der Reijden


title: Human Cortical Kidney Sections

city: Birmingham

first: James

last: George

state: Alabama

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

summary: Acute kidney injury (AKI) is a major health burden in the United States. Macrophages have been shown to mediate AKI in murine models. Murine kidneys contain multiple subpopulations of kidney resident macrophages (KRM) that are transcriptionally and spatially distinct. We hypothesized the human kidney contains orthologous KRM subpopulations, both transcriptionally and spatially. We utilized kidney sections from donors diagnosed with mild to moderate AKI in order to increase the translatability of murine research to clinical settings.

overall_design: Visium samples include 10 micron sections of human kidneys.

first: Elise

last: Erman

first: Kyle

last: Moore

first: Matthew

last: Cheung

first: Jennifer

last: La Fontaine

first: Zhengqin

last: Yang

first: Reham

last: Soliman

first: Anupam

last: Aqarwal


title: A functional 3D full-thickness model for comprehending the interaction between airway epithelium and connective tissue in cystic fibrosis.

status: Public on Mar 29 2024

city: Napoli

first: Paolo

middle: Antonio

last: Netti

address: Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53

department: IIT - Center for Advanced Biomaterials for Healthcare

country: Italy

institute: IIT

summary: Patients with cystic fibrosis (CF) experience severe lung disease, including persistent infections, inflammation, and irreversible fibrotic remodelling of the airways. Although therapy with transmembrane conductance regulator (CFTR) protein modulators reached optimal results in terms of CFTR rescue, lung transplant remains the best line of care for patients in an advanced stage of CF. Indeed, chronic inflammation and tissue remodelling still represent stumbling blocks during treatment, and underlying mechanisms are still unclear. Nowadays, animal models are not able to replicate clinical features of the human disease and the conventional in vitro models lack a stromal compartment undergoing fibrotic remodelling. To address this gap, we show the development of a 3D full-thickness model of CF with a human bronchial epithelium differentiated on a connective airway tissue. We demonstrated that the epithelial cells not only underwent mucociliary differentiation but also migrated in the connective tissue and formed glandular structures. The presence of the connective tissue stimulated the pro-inflammatory behaviour of the epithelium, which activated the fibroblasts embedded into their own extracellular matrix (ECM). By varying the composition of the model with CF epithelial cells and a CF or healthy connective tissue, it was possible to replicate different moments of CF disease, as demonstrated by the differences in the transcriptome of the CF epithelium in the different conditions. The possibility to faithfully represent the crosstalk between epithelial and connective in CF through the full thickness model, along with inflammation and stromal activation, makes the model suitable to better understand mechanisms of disease genesis, progression, and response to therapy.

overall_design: The epithelial and connective compartments of an in vitro 3D cystic fibrosis full-thickness model were analyzed by RNAseq. The full-thickness model was developed with a cystic fibrosis epithelium and a cystic fibrosis connective airway tissue (cystic fibrosis) or a cystic fibrosis epithelium and a normal connective airway tissue (hybrid). The epithelium from these full-thickness models was compared with the cystic fibrosis epithelium differentiated in the absence of the connective tissue. The FT CF EPI was the cystic fibrosis epithelium from the cystic fibrosis full-thickness model; the HFT EPI was the cystic fibrosis epithelium from the hybrid full-thickness model; The HBE was the cystic fibrosis human bronchial epithelium differentiated on porous inserts without the connective tissue; the FT CF CAT was the connective tissue from the cystic fibrosis full-thickness model; the HFT CAT was the connective tissue from the hybrid full-thickness model.

first: Claudia

last: Mazio

first: Laura

middle: S

last: Scognamiglio

first: Costantino

last: Casale

first: Valeria

last: Panzetta

first: Francesco

last: Urciuolo

first: Luis

middle: J

last: Galietta

first: Giorgia

last: Imparato