title: Pathogenesis of Achromobacter xylosoxidans respiratory infections: colonization and persistence in vivo and differential gene expression in cystic fibrosis sputum

city: Birmingham

first: Caitlin

last: Billiot

state: Alabama

address: 1918 University Blvd, MCLM 818

department: Pulmonary, Allergy, and Critical Care Medicine

institute: University of Alabama at Birmingham

summary: The goals of this study were to determine differential gene expression between Achromobacter xylosoxidans clinical isolate Ax 7 in a synthetic artificial sputum media compared to a rich media control (LB).

overall_design: Bacterial overnights of Ax 7 were subcultured into SCFM2 or LB and grown until stationary phase (10e10-10e11 CFU/mL) and RNA was extracted for gene expression analysis.

first: Billiot

last: Caitlin


title: Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution (RNA-seq)

status: Public on Dec 15 2023

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

type: Expression profiling by high throughput sequencing

summary: RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: The bacteria were grown up to mid-log phase, cultured in M9 minimal media with 0.2% glucose.  The experiments were conducted in biological duplicate.

first: Assiya

last: Taizhanova

first: Sang-Mok

last: Lee

first: Ye

last: Gao

first: Joon

middle: Y

last: Park


title: Determination of Shavenbaby target genes in mature Enterocytes (mECs)

status: Public on Dec 14 2023

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative de Toulouse

summary:
Shavenbaby (Svb) transcription factor is involved in the homeostasis of intestinal stem cells (ISCs), and the differentiation of their enteroblast progeny (EB) into enterocytes (EC). Svb is produced as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides SvbREP is processed into a shorter activator form (SvbACT) through partial proteasomal degradation of the REP domain.
In ISCs/EBs, Pri triggers SvbREP to ACT maturation, while SvbREP form accumulates in differentiated enterocytes. The absence of Svb promote the apoptosis of the intestinal stem cells. In ISCs/EBs, the ectopic expression of SvbREP form promotes the differentiation and the overexpression of SvbACT promotes hyperplasia. (Al Hayek, et al 2020)
Based on these functional analyses, Svb appears to control ISC/EB survival and behavior, balancing proliferation and differentiation through a molecular switch between its 2 antagonistic isoforms. In this study, we determine the Svb target genes in different cell types along the intestinal cell lineage.
This particular metadata sheet refers to early enterocytes (mEC) transcriptomic data (RNAseq) in control condition and upon modulation of Svb function.

overall_design: The samples correspond to control (mEC Ctrl), Svb-knock down ECs (mEC RNAiSvb), SvbACT constitutive form overexpression (mEC SvbAct). Three biological replicates were performed for each genotype (except for the Ctrl n=2), on different calendar days.

first: Alexandra

last: Mancheno-Ferris

first: Clement

last: Immarigeon


title: Determination of Shavenbaby target genes in Intestinal Stem Cells differenciation

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

overall_design: Refer to individual Series


title: Determination of Shavenbaby target genes in early Enterocytes (eECs)

summary:
Shavenbaby (Svb) transcription factor is involved in the homeostasis of intestinal stem cells (ISCs), and the differentiation of their enteroblast progeny (EB) into enterocytes (EC). Svb is produced as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides SvbREP is processed into a shorter activator form (SvbACT) through partial proteasomal degradation of the REP domain.
In ISCs/EBs, Pri triggers SvbREP to ACT maturation, while SvbREP form accumulates in differentiated enterocytes. The absence of Svb promote the apoptosis of the intestinal stem cells. In ISCs/EBs, the ectopic expression of SvbREP form promotes the differentiation and the overexpression of SvbACT promotes hyperplasia. (Al Hayek, et al 2020)
Based on these functional analyses, Svb appears to control ISC/EB survival and behavior, balancing proliferation and differentiation through a molecular switch between its 2 antagonistic isoforms. In this study, we determine the Svb target genes in different cell types along the intestinal cell lineage.
This particular metadata sheet refers to early enterocytes (eEC) transcriptomic data (RNAseq) in control condition and upon modulation of Svb function.

overall_design: The samples correspond to control (eEC Ctrl), Svb-knock down ECs (eEC RNAiSvb), SvbACT constitutive form overexpression (eEC SvbAct) and SvbREP constitutive isoform overexpression (eEC SvbRep). Three biological replicates were performed for each genotype, on different calendar days.


title: Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution

type: Genome binding/occupancy profiling by high throughput sequencing

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

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2


title: Determination of Shavenbaby target genes in Enteblast (EBs)

summary:
Shavenbaby (Svb) transcription factor is involved in the homeostasis of intestinal stem cells (ISCs), and the differentiation of their enteroblast progeny (EB) into enterocytes (EC). Svb is produced as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides SvbREP is processed into a shorter activator form (SvbACT) through partial proteasomal degradation of the REP domain.
In ISCs/EBs, Pri triggers SvbREP to ACT maturation, while SvbREP form accumulates in differentiated enterocytes. The absence of Svb promote the apoptosis of the intestinal stem cells. In ISCs/EBs, the ectopic expression of SvbREP form promotes the differentiation and the overexpression of SvbACT promotes hyperplasia. (Al Hayek, et al 2020)
Based on these functional analyses, Svb appears to control ISC/EB survival and behavior, balancing proliferation and differentiation through a molecular switch between its 2 antagonistic isoforms. In this study, we determine the Svb target genes in different cell types along the intestinal cell lineage.
This particular metadata sheet refers to enteroblast (EB) transcriptomic data (RNAseq) in control condition and upon modulation of Svb function.

overall_design: The samples correspond to control (EB Ctrl), Svb-knock down EBs (EB RNAiSvb ), SvbACT constitutive form overexpression (EB SvbAct) and SvbREP constitutive isoform overexpression (EB SvbRep). Three biological replicates were performed for each genotype, on different calendar days.


title: VGLL1 regulates extraembryonic lineage specification in human [CUT&TAG]

status: Public on Dec 18 2023

city: guangzhou

first: Wenjuan

last: Li

state: 广东

address: UCAS

department: GIBH

country: China

institute: UCAS

summary: Placenta abnormality is one of the key reasons for early pregnancy loss but the regulatory mechanisms underlying placenta formation are largely unknown. Here, we applied a human naïve pluripotent stem cell (PSC) derived TE model to explore the driven regulatory machinery. We demonstrate that VGLL1 (vestigial like family member 1) is crucial for TE self-renewal and TE-specific gene expression, thus suppressing VGLL1 leads to severely impaired cell proliferation and skewed TE induction. VGLL1 exerts its function through interacting with TEAD4 (TEA domain transcription factor 4) and colocalize at target gene promoters and enhancers. Further investigation uncovers the enrichment of H3K27ac active histone marks at genomic regions occupied by VGLL1-TEAD4 complex, indicates a close association between them. Overall, our data reveals the critical function model of VGLL1-TEAD4 in human TE derivation, highlighting a potential interspecies difference between human and mouse TE induction.

overall_design: Human naïve PSC were plated at a density of 100000 cells per well onextracellular matrix (ECM; Geltrex™)-coated 6-well plates and cultured with TE medium. Cells were collected for sequencing on day 5. For human TSC cells, cells cultured in TS-1 medium for five or six days were plated on Collagen IV coated 6-well plates and cultured with TSC medium. Cells cultured in TSC medium became morphologically stable after 2-3 passages.

first: Yueli

last: Yang


title: PGF2α induces a pro-labour phenotypical switch in human myometrial cells that can be inhibited with PGF2α receptor antagonists.

status: Public on Dec 13 2023

city: Coventry

first: Richard

middle: Jan

last: Stark

address: Gibbet Hill Campus, The University of Warwick

department: Bioinformatics RTP

country: United Kingdom

institute: University of Warwick

summary: Preterm birth is the leading cause of infant morbidity and mortality. There has been interest in developing prostaglandin F2α (PGF2α) antagonists as a new treatment for preterm birth although much of the rationale for their use is based on studies in rodents where PGF2α initiates labour by regressing the corpus luteum and reducing systemic progesterone concentrations. How PGF2α antagonism would act in humans that do not have a fall in systemic progesterone remains unclear. One possibility, in addition to an acute stimulation of contractions, is a direct alteration of the myometrial smooth muscle cell state towards a pro-labour phenotype. In this study we developed an immortalised myometrial cell line, MYLA, derived from myometrial tissue obtained from a pregnant, non‐labouring patient as well as a novel class of PGF2α receptor (FP) antagonist. We verified the functionality of the cell line by stimulation with PGF2α, which resulted in Gαq specific coupling and Ca2+ release that were inhibited by FP antagonism. Compared to four published FP receptor antagonists, the novel FP antagonist N582707 was the most potent compound (Fmax 7.67 ± 0.63 (IC50 21.26 nM), AUC 7.30 ± 0.32 (IC50 50.43 nM) and frequency of Ca2+ oscillations 7.66 ± 0.41 (IC50 22.15 nM)). RNA‐sequencing of the MYLA cell line at 1, 3, 6, 12, 24 & 48 hours post PGF2α treatment revealed a transforming phenotype from a fibroblastic to smooth muscle mRNA profile. PGF2α treatment increased expression of MYLK, CALD1 and CNN1 as well as the pro-labour genes OXTR, IL6 and IL11 which were inhibited by FP antagonism. Concomitant with inhibition of a smooth muscle, pro-labour transition, FP antagonism increased the expression of the fibroblast marker genes DCN, FBLN1 and PDGFRA. Our findings suggest that in addition to the well described acute contractile effect, PGF2α transforms myometrial smooth muscle cells from a myofibroblast to smooth muscle, pro-labour like state, and that the novel compound N582707 has potential for prophylactic use in preterm labour management beyond its use as an acute tocolytic drug.

overall_design: RNA-Seq data collected from immortalised myometrial cell line (MYLA) cells treated with either 1 μM PGF2α or vehicle equivalent control at time 0 followed by harvesting cells at 1 hour, 3 hours, 6 hours, 9 hours, 12 hours, 24 hours, and 48 hours. Biological replicates of each time/treatment were made in triplicate.

first: Isabel

last: Hamshaw

first: Anne

last: Straube

first: Laura

last: Baxter

first: Mohammad

last: Tauqeer Alam

first: Walter

middle: J

last: Wever

first: Jun

last: Yin

first: Yong

last: Yue

first: Philippe

last: Pinton

first: Aritro

last: Sen

first: Gregory

middle: D

last: Ferguson

first: Andrew

middle: M

last: Blanks


title: RT-qPCR analysis in zebrafish Viperin KO fish under VHSV infections

status: Public on Dec 12 2023

city: Jeju

last: Shanaka

address: Ara-dong

department: Marine life Sciences

institute: Jeju National University

summary: For this experiment, WT and Viperin KO fish were used and fish were injected with either PBS or VHSV and the gene expression was analyzed

overall_design: qPCR expression analysis of zebrafish immune genes under VHSV infection.

first: K

middle: A

first: Jehee

last: Lee


title: Loss of thymocyte competition underlies the tumor suppressive functions of the E2a transcription factor in T-ALL

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

country: USA

institute: The University of Chicago

summary: T lymphocyte acute lymphoblastic leukemia (T-ALL) is frequently associated with increased expression of the E protein transcription factor inhibitors TAL1 and LYL1. In mouse models, ectopic expression of Tal1 or Lyl1 in T cell progenitors, or inactivation of E2a, is sufficient to predispose mice to develop T-ALL. How E2a suppresses thymocyte transformation is currently unknown. Here, we show that early deletion of E2a, prior to the DN3 stage, was required for robust leukemogenesis and was associated with alterations in thymus cellularity, T cell differentiation, and gene expression in immature CD4+CD8+ thymocytes. Introduction of wild-type thymocytes into mice with early deletion of E2a prevented leukemogenesis, or delayed disease onset, and impacted the expression of multiple genes associated with transformation and genome instability.  Our data indicate that E2a suppresses leukemogenesis by promoting T cell development and enforcing inter-thymocyte competition, a mechanism that is emerging as a safeguard against thymocyte transformation.  These studies have implications for understanding how multiple essential regulators of T cell development suppress T-ALL and support the hypothesis that thymus cellularity is a determinant of leukemogenesis

overall_design: CD45.1+ CD4+CD8+ thymocytes were isolated from Ctrl and E2a-deficient mice at 4 or 8 weeks of age, or from E2a-/- mice that were sublethally irradiated and transplanted with wild-type competitor cells 4 weeks after transplantation.

first: Geoffrey

last: Parriott


title: Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

type: Methylation profiling by genome tiling array

summary: Therapy resistance is a major limitation for treatment efficacy in colorectal cancer. Circulating tumor cells (CTCs) and epigenetic modifications, such as DNA methylation, are involved in the development of acquired resistance during treatment. The aim of this work was to characterize the DNA methylation landscape of colon CTCs during cancer progression and the development of therapy resistance. We analyzed nine permanent colon CTC-derived cell lines, which were collected at baseline (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]) from peripheral blood samples of a patient with metastatic colon cancer. The DNA methylome of these nine CTC lines was analyzed by EPIC arrays.


title: Depletion of Nrf2 in pancreatic cancer cells shifts arginine metabolism into the phosphocreatine energy system

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

summary:
Depletion of Nrf2 leads to an increase in cellular ROS, reduced glutathione and thiols, and profound reprogramming of metabolism. Unbiased transcriptome analyses show that key enzymes of glycolysis, pentose phosphate pathway, and glutathione cycle are significantly downregulated, while enzymes of arginine and medium-chain fatty acids metabolism are upregulated. Besides glutamine, pancreatic cancer cells deficient of Nrf2 axis become highly dependent on arginine, which is channelled into the synthesis of phosphocreatine and polyamines. Key enzymes of the creatine pathway, gatm and ckb, are more expressed and more active in Nrf2(-/-) than in WT cells. This metabolism shift creates an energy buffer that enables pancreatic cancer cells to handle increased energy demand. Metabolomic analysis showed that 12% of the creatine pool is phosphorylated in Nrf2(-/-) cells, while the level drops to < 0.1% in WT cells. The inhibition of the creatine pathway with cyclocreatine in Nrf2(-/-) cells, reduces by 43% the ATP level and by 70% invasion rate in matrigel. Furthermore, we found that combination therapies that can target simultaneously the creatine pathway and the KRAS G12D-Nrf2 axis produce a stronger anticancer effect than monotherapies. Taken together, our data provide the basis for the rationale design of new combination therapies against pancreatic cancer.
The KRAS G12D-Nrf2 axis controls redox homeostasis and metabolism in PDAC cells. Suppression of KRAS G12D-Nrf2 decreases glycolysis, PPP and glutathione cycle and promotes a metabolic shift of arginine into the synthesis of phosphocreatine

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Panc-1 cells and its KO derivatives (NRF2 KO).

first: Himanshi

last: Choudhary

first: Annalisa

last: Ferino

first: Ylenia

last: Cortolezzis

first: Francesca

last: D’Este

first: Marina

last: Comelli

first: Valentina

last: Rapozzi

first: Eros

last: Di Giorgio

first: Luigi

middle: E

last: Xodo


title: Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide

city: Zurich

first: Shana

middle: J.

last: Sturla

address: Schmelzbergstrasse 9

department: D-HEST

country: Switzerland

institute: ETH Zurich

summary: Temozolomide kills cancer cells by forming  O6-methylguanine (O6-MeG), which leads to apoptosis due to mismatch-repair overload. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair mechanisms, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution.   We analyzed O6-MeG formation and repair with regards to sequence contexts and functional genomic regions in glioblastoma-derived cell lines and evaluated the impact of MGMT transfection. O6-MeG signatures were highly similar to mutational signatures of patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O6-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O6-MeG accumulation in highly expressed genes, suggesting an additional transcription-associated contribution to its repair. These data provide high resolution insight on how O6-MeG formation and repair is impacted by genome structure and regulation. Further, O6-MeG-seq is expected to enable  future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.

overall_design: We used a novel DNA modification sequencing stragegy, O6‑MeG‑seq, to assess O6-methylguanine in LN-229 cells exposed to temozolomide. We used an MGMT-transfected LN-229 cell line and the transfection control cell line further referred to as wild-type (WT). They were exposed to temozolomide or solvent control once (1x) or repetitively (3x). There are 3 biological replicates per condition plus temozolomide-exposed naked DNA serving as positive control.

first: Jasmina

last: Büchel

first: Cécile

last: Mingard

first: Vakil

last: Takhaveev

first: Patricia

middle: B

last: Reinert

first: Giulia

last: Keller

first: Tom

last: Kloter

first: Sabrina

last: Huber

first: Maureen

last: McKeague


title: Role of UPF1-LIN28A interaction during early differentiation of pluripotent stem cells

city: Seoul

first: Jungwook

last: Hwang

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

institute: Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea

summary: Two RNA binding proteins, UPF1 and LIN28A, have well-known functions in posttranscriptional regulations and stem cell differentiation. Most studies on UPF1 and LIN28A have focused on the molecular mechanism in differentiated cells and stem cell differentiation, respectively. We revealed that LIN28A directly interacts with UPF1, which happens before UPF1 forms a complex with UPF2, thereby resulting in the reduction of UPF1 phosphorylation and inhibition of nonsense-mediated mRNA decay (NMD). Our studies reveal that cell fate is determined by transcriptome regulation through UPF1-LIN28A interaction in hPSCs.

overall_design: Examination of the influence of UPF1-LIN28A interaction in hPSCs and differentiated cells

first: Seungwon

last: Jung

first: SeungHwan

last: Ko

first: Narae

last: Ahn

first: Jinsam

last: Lee

first: Chang-Hwan

last: Park


title: ONT-cappable-seq for P23-45 bacteriophage 5 min post-infection

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

summary: We performed the long-read RNA sequencing technique ONT-cappable-seq on RNA samples of T. thermophilus infected with phage P23-45 5 minutes post-infection. Using this approach, we obtained the primary transcriptome at the early infection stage and sequenced it in full-length. Based on this data, we were able to identify viral transcription start sites and termination sites and uncover distinct promoter motifs.

overall_design: Full-length transcriptional profiling of T. thermophilus infected with phage P23-45 at 5min post-infection using ONT-cappable-seq.

first: Leena

last: Putzeys

first: Maarten

last: Boon

first: Maria

last: Sokolova


first: Donghyuk

last: Kim

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


title: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA-polymerases encoded by P23-45 bacteriophage

summary: By doing ChIP-seq with antibodies against two P23-45 RNA polymerases gp64 and gp96 we showed that both RNA polymerases interact with the phage genome at the early stage of infection. Gp96 interacts with pre-early P23-45 genes, while gp64 interacts with pre-early, early and some middle-stage genes.

overall_design: Thermus thermophilus HB8 cells were infected with P23-45 bacteriophage at a high multiplicity of infection. Next, cells were collected at 5, 20, and 40 minutes post infection with the phage. Chromatin immunoprecipitation followed by DNA-sequencing (ChIP-seq) was performed using antibodies against P23-45 RNA polymerases gp64 and gp96 (first 1540 amino acid residues). Samples without addition of antibodies were used as controls for input DNA.

first: Ekaterina

last: Goldobina

first: Anastasia

last: Chaban


title: SARS-CoV-2 produces a microRNA, CoV2-miR-O8, in patients with COVID-19 infection

status: Public on Dec 11 2023

city: Bedford Park

first: Jonathan

last: Gleadle

state: SA

address: 3D226 Renal Lab, Flinders Medical Centre, Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

type: Non-coding RNA profiling by high throughput sequencing

summary: SARS-CoV-2 can generate viral microRNAs (v-miRNAs) that target host gene expression. This study used small RNAseq to identify the v-miRNAs present in COVID-19 patients' nasopharyngeal swabs. The study identified a specific conserved v-miRNA sequence (CoV2-miR-O8) unique to SARS-CoV-2 that is highly present in COVID-19 patients' samples, interacts with Argonaute, and has features consistent with Dicer and Drosha generation. CoV2-miR-O8 is predicted to target specific human genes and can be detected by RTPCR assays in patients.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: small RNA-seq analysis on RNA extracted from nasopharyngeal swabs obtained from patients with COVID-19 infection ascertained by a routine diagnostic RT PCR assay

first: Elise

last: Tucker

first: Soon Wei

last: Wong

first: Darling

last: Rojas-Canales


title: Role of SRSF5 in HeLa cells

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt


title: T. thermophilus infected with phage P23-45


title: Identification of Candidate Master Regulators of the Response to Early Heat Stress in Climate-adapted Wheat Landraces via Transcriptomic and Co-expression Network Analyses

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

institute: Centre for Novel Agricultural Products, University of York

summary: Climate change is not only causing a rise of global temperature but also more variable climates. In major wheat-producing countries, spring temperatures have increased up to 40°C in recent years. Considering the wheat optimal growth temperature of around 20°C, wheat is particularly prone to damage by heat stress. To combat this threat, it is imperative to understand the response of wheat to early heat stress. This research is focus on understanging the transcriptional reprogramming of wheat when exposed to heat stress during the three-leaf stage. Differential expression and weighted gene co-expression network analysis have been used here before and after the stress to to identify candidate master-regulators of this transcriptional response.

overall_design: Thirteen wheat landraces where used to asses the wheat transcriptomic response to 14-days heat stress during the early stages of development (3-leaf stage). The experiment was performed by growing the plant until 3 leaf-stage (22°C/16°C (day/night) on an 18 hour day/night cycle) and then submitting the plants to 14 days of 35°C/30°C (day/night) and three days of recovery (22°C/16°C (day/night) on an 18 hour day/night cycle) after that. Four replicates, per treatment, per landrace accession were used in this experiment. mRNA-Seq analysis was performed on RNA material collected at the 3-leaf stage and after the heat stress.

first: Liam

last: Barratt

first: Ian

last: Bancroft

first: Andrea

last: Harper


title: Microenvironment-induced CREPT expression by cancer-derived small extracellular vesicles primes field cancerization

status: Public on Dec 10 2023

city: Xiamen City

first: Yuting

last: Lin

state: -- Please Select --

address: Xiamen University, Xiang'an District, Xiamen City, Fujian Province, China

institute: XIAMEN UNIVERSITY

summary: Cancer local recurrence increases the mortality of patients, and might be caused by field cancerization, a pre-malignant alteration of normal epithelial cells. It has been suggested that cancer-derived small extracellular vesicles (CDEs) may contribute to field cancerization, but the underlying mechanisms remain poorly understood. In this study, we aim to identify the key regulatory factors within recipient cells under the instigation of CDEs. In vitro experiments were performed to demonstrate that CDEs promote the expression of CREPT in normal epithelial cells. TMT-based quantitative mass spectrometry was employed to investigate the proteomic differences between normal cells and tumor cells. Loss-of-function approaches by CRISPR-Cas9 system were used to assess the role of CREPT in CDEs-induced field cancerization. RNA-seq was performed to explore the genes regulated by CREPT during field cancerization. CDEs promote field cancerization by inducing the expression of CREPT in non-malignant epithelial cells through activating the ERK signaling pathway. Intriguingly, CDEs failed to induce field cancerization when CREPT was deleted, highlighting the importance of CREPT. Transcriptomic analyses revealed that CDEs elicited inflammatory responses, primarily through activation of the TNF signaling pathway. CREPT, in turn, regulates the transduction of downstream signals of TNF by modulating the expression of TNFR2 and PI3K, thereby promoting inflammation-to-cancer transition. CREPT not only serves as a biomarker for field cancerization, but also emerges as a target for preventing the cancer local recurrence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To investigate the role of CREPT in CDEs-treated non-malignant epithelial cells, we utilized two mammary epithelial cell lines, namely MCF10A and NMuMG, and employed the CRISPR-Cas9 system to knockout the CREPT gene in these cells, resulting in the generation of four cell lines: MCF10A, MCF10AKO, NMUWT, and NMUKO.
Then we performed gene expression profiling analysis using data obtained RNA sequencing of these four cell lines under conditions with or without CDEs treatment.
Comparative analysis of gene expression profiles based on RNA-Seq data in the cells with and without CDEs treatment. Subsequently, the differences in the expression profile changes between the cells with and without CREPT expression were evaluated.

first: Hanguo

last: Jiang


title: Plasma miRNAs as biomarkers of epilepsy

city: Warsaw

first: Kinga

last: Szydlowska

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary:
Epilepsy frequently develops as a result of brain insult, for example brain injury or stroke. Currently there are no tools allowing us to predict which trauma patients will eventually develop epilepsy. There is evidence that microRNAs levels are altered in plasma, making them attractive candidates for peripheral biomarkers of epilepsy.
We analyzed miRNA levels in plasma samples using Affymetrix microarrays 4.1 and performed comparative analysis of samples. We performed 3 comparisons: i) control animals vs. Status epilepticus animals, ii) animals which developed first spontaneous seizure around 7 days post stimulation (EARLY), or later after 21days post stimulation (LATE), iii) animals that had developed seizures at given timepoint (EPI) and animals that did not experience seizures by given timepoint (NONEPI).

overall_design: We draw the blood from rats after electrical stimulation of amygdala, which induces status epilepticus, at 4 timepoints: 14, 30, 60 and 90 days after status epilepticus. Later RNA was isolated from all the samples at the same time and microarray 4.1 were used in agreement with the producer's protocol, to test levels of each miRNA.

first: Katarzyna

last: Lukasiuk


title: Single-cell transcriptomics and in vitro lineage tracing reveals differential susceptibility of human iPSC-derived midbrain dopaminergic neurons in a cellular model of Parkinson’s disease.

status: Public on Dec 08 2023

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

summary: Advances in stem cell technologies open up new avenues for modelling development and diseases. The success of these pursuits however rely on the use of cells most relevant to those targeted by the disease of interest, for example, midbrain dopaminergic neurons for Parkinson’s disease. In the present study, we report the generation of a human induced pluripotent stem cell (iPSC) line capable of purifying and tracing nascent midbrain dopaminergic progenitors and their differentiated progeny via the expression of a Blue Fluorescent Protein (BFP).  This was achieved by CRISPR/Cas9 assisted knock-in of BFP and Cre into the safe harbour locus AAVS1 and an early midbrain dopaminergic lineage marker gene LMX1A, respectively. Immunocytochemical analysis and single cell RNA sequencing of iPSC-derived neural cultures confirms developmental recapitulation of the human fetal midbrain and high quality midbrain cells. By modelling Parkinson’s disease-related drug toxicity using 1-Methyl-4-phenylpyridinium (MPP+), we showed preferential reduction of BFP+ cells, a finding demonstrated independently by cell death assays and single cell transcriptomic analysis of MPP+ treated neural cultures. Together, these results highlight the importance of disease relevant cell type in stem cell modelling.

overall_design: single cell RNA sequencing data of of human induced Pluripotent Stem Cells (iPSC) derived into dopaminergic (DA) neurons. iPSC-DA were either challenged with MPP+ and non challenged (basal) for 3 main groups given their sorting status. The dataset consist of a total of 6 samples, three groups of cells according to their sorting status: non sorted (NS), sorted BFP positive (LMX1A+) and sorted BFP negative, and two treatment conditions (basal or treated with MPP+).

first: Lucia

middle: F

last: Cardo

first: Zongze

last: Li

first: Caleb

last: Webber

first: Meng


title: Single-cell RNA landscape of osteoimmunology microenvironment in Osteoporotic Vertebral Compression Fracture (OVCF) and Kümmell's Disease (KD)

status: Public on Dec 09 2023

city: Guangzhou

first: Yude

last: Xu

state: Guangdong

address: No. 396, Tongfu Middle Road

institute: Guangzhou Red Cross Hospital

summary: KD known as avascular necrosis after OVCF. we used scRNA-seq analysis to investigate the osteoimmunology microenvironment and cellular composition in OVCF and KD.

overall_design: A total of two human samples were analyzed, including one OVCF and one KD patient with vertebral fracture bone tissue

first: Suixiang

last: Huang

first: Zhencong

first: Libing

last: Dai

first: Hao

last: Wu

first: Peigeng

last: Wang

first: Xiguan

last: Yao

first: Wei

last: Luo

first: Yiming

last: Liu

first: Weichao

last: Yang

first: Yi

last: Feng

first: Haixiong

last: Miao

first: Jiake

first: Dongping

last: Ye


title: Nascent-seq of HeLa cells after rapid depletion of SRSF5 using hGRAD for 2h, 8h and 16h

first: Michaela

last: Müller-McNicoll

summary: We used HeLa cells expressing GFP-tagged SRSF5 and the rapid depletion plasmid hGRAD from genomic loci. SRSF5 depletion was started after addition of Doxycyclin and was allowed for 2h, 8h and 16h. One hour before harvesting, cells were incubated with 4-sU for exactly 1 hour to label newly transcribed RNAs. 4-sU-labelled RNAs were biotinylated and purified over streptavidin beads and transformed into an RNA-seq library. We compared differential expression and intron retention between T0 and the other time points.

overall_design: We sequenced 2 biological replicates for all four timepoints (T0, T2, T8 and T16) with 150-bp paired end reads and 100 Million reads per replicate.


title: Transcriptome-wide mapping of RNA:protein interactions of SRSF5 in HeLa cells

summary: We performed SRSF5 iCLIP2 in HeLa cells expressing endogenously GFP-tagged SRSF5.

overall_design: 5 biological replicates were subjected to the iCLIP2 procedure with UV-crosslinking at 254 nm. For IPs an anti-GFP antibody was used. No UV treatment served as negative control.


title: Global blood miRNA profiling unravels early signatures of immunogenicity of Ebola vaccine rVSVΔG-ZEBOV-GP

city: Leiden

first: Eleonora

last: Vianello

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary:
We characterized the intracellular miRNAs, isolated from whole blood cells (WB), induced by vaccination against Ebola.
We identified early miRNA signatures associated with the ZEBOV-specific IgG antibody responses at day 28 or 360 post-vaccination.

overall_design: We isolated total RNA including miRNA from whole blood from 48 healthy individuals receiving the rVSVΔG-ZEBOV-GP vaccine or placebo. Timepoints day 0 (baseline before vaccination), and days 1, 2, 3, and 7 post-vaccination have been considered. We performed miRNA-seq. We then identified differentially expressed miRNAs by comparing rVSVΔG-ZEBOV-GP vaccines vs placebo controls. Next, we correlated baseline and early miRNAs with the ZEBOV-specific IgG antibody titer measured at day 28 and day 360 by performing Pearson Correlation. We used Machine Learning algorithms to identify the best early miRNA signatures able to discriminate high and low antibody levels at day 28 and day 360. Finally, we identified a miRNA antibody predictive signature associated with immune-related target mRNAs and corresponding pathways.

first: Josefine

last: Persson

first: Björn

last: Andersson

first: Suzanne

last: van Veen

first: Thomaz

last: Lüscher Dias

first: Francesco

last: Santoro

first: Malin

last: Östensson

first: Ogonna

last: Obudulu

first: Christopher

last: Agbajogu

first: Sara

last: Torkzadeh

first: Helder

last: Nakaya

first: Donata

last: Medaglini

first: Claire-Anne

last: Siegrist

first: Tom

middle: H

last: Ottenhoff

first: Ali

last: Harandi


title: Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish

first: Gaofei

last: Li

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South China University of Technology

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

overall_design: Refer to individual Series


title: PSIP1/LEDGF reduces R-loops at transcription sites and maintain genome integrity (HEK293T CUT&Tag-Seq)

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

summary: R-loops are transcriptional by-products that pose a persistent threat to genome integrity and are implicated in accelerated ageing and cancer. PSIP1/LEDGF is a multifunctional chromatin protein that associates with transcriptional elongation machinery. Here, we demonstrated that PSIP1 interacts with R-loops generated at the site of transcription and along with the factors involved in R-loop resolution, including PARP1.  Reduced PSIP1 levels in human and mouse cells lead to an increase in R-loop levels and DNA damage at the PSIP1 binding sites. This increased R-loops and DNA damage was specific at the RNA polymerase II transcription sites, causing local transcriptional arrest. In addition, we demonstrate that PSIP1 can be targeted for increasing the sensitivity of cancer cells to PARP1 inhibitors and transcription-coupled DNA damaging agents. These findings show the critical role of PSIP1 in reducing the R-loop burden and DNA damage at the transcriptionally active regions of the genome.

overall_design: Cleavage Under Targets and Tagmentation DNA-sequencing (CUT&Tag-Seq) for PSIP1, S9.6, gammaYH2AXX and IgG in HEK293T cells transduced with control shRNAs or PSIP1 sh RNAs. For each group, samples were processed in a minimum of two biological replicates.

first: Jayakumar

last: Sundarraj

first: Manthan

last: Patel

first: Madapura

last: Pradeepa


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (5029)

city: Amsterdam

first: Maarten

last: Slagter

email: m.slagter@nki.nl, hi@maartenslagter.nl

address: Plesmanlaan 108

institute: Netherlands Cancer Institute

summary: Tumors consist of a dynamic collection of interacting tumor cells, stromal cells and immune cells. In addition to the direct cell-cell interactions that are mediated by receptor-ligand interactions, cells in the tumor microenvironment (TME) influence each other through the secretion and sensing of soluble mediators, such as cytokines and chemokines. While signaling of the interferon γ (IFNγ) and tumor necrosis factor α (TNFα) cytokines has been shown to be critical in anti-tumor immune responses in a number of settings, our understanding of the spatiotemporal behavior of these cytokines in the TME is limited. Here, we describe a single cell transcriptome-based approach to infer which single or combined signals an individual cell has received and estimate the timing of such exposure. Using this technology, we demonstrate that, contrary to expectations, CD8+ T cell-derived IFNγ is the dominant modifier of the TME relative to TNFα. Furthermore, we demonstrate that cell pools that show abundant IFNγ sensing are characterized by decreased TGFβ signaling, consistent with IFNγ-mediated remodeling of the TME. Collectively, these data provide evidence that CD8+ T cell-secreted cytokines should be distinguished into local and more global modifiers of tumor tissue, and describe a broadly applicable approach to dissect cytokine and chemokine modulation of the tumor microenvironment.

overall_design: OVCAR5-cell exposed to various (combinations of) cytokines (TNFa, IFNy, tumor-cell T-cell co-culture supernatant) for 4 different durations (2, 6, 12, 24 hours of continuous stimulation)

first: Mirjam

last: Hoekstra


title: Infection of bone marrow-derived mast cells with Salmonella Typhimurium WT and S.Tm ∆invG

city: Uppsala

last: von Beek

address: Husargatan 3

department: IMBIM

country: Sweden

institute: Uppsala University

summary: Murine bone marrow-derived mast cells (BMMC) were infected for 4 h with Salmonella Typhimurium SL1344 wildtype (WT) and S.Tm ∆invG to explore BMMC mRNA expression levels upon infection and the role of type-3-secretion-system mediated invasion.

overall_design: mRNA from 0.5x10^6 mouse bone marrow-derived mast cells (BMMC) per group, infected with S.Tm WT or ∆invG, as well as uninfected, was analyzed by RNA seq. Every experimental group has 4 replicates. 2 replicates represent a repetition of the experiment on a different day but with the same BMMC culture. Within a day, both replicates were derived from independent S.Tm overnight cultures.

first: Gunnar

last: Pejler

first: Mikael

last: Sellin


title: PSIP1/LEDGF reduces R-loops at transcription sites and maintain genome integrity (TT-Seq)

overall_design: Transient transcriptome-sequencing (TT-Seq)  in RWPE-1 cells transduced with control shRNAs or PSIP1 sh RNAs. For each group, samples were processed in a minimum of two biological replicates.


title: PSIP1/LEDGF reduces R-loops at transcription sites and maintain genome integrity (RNA-Seq)

overall_design: RNAseq  in RWPE-1 cells transduced with control shRNAs or PSIP1 sh RNAs. For each group, samples were processed in three biological replicates.


title: Core promoterome of barley embryo

status: Public on Dec 07 2023

city: Olomouc

first: Šimon

last: Pavlů

address: Šlechtitelů 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

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


title: PSIP1/LEDGF reduces R-loops at transcription sites and maintain genome integrity


title: Core promoterome of barley embryo [ChIP-seq]

summary: We define the promotoreome sequence and epigenetic architecture in barley embryos to both put it into evolutionary perspective and to serve as a reference for agricultural and research biotechnology in cereals.

overall_design: ChIP-seq analysis conducted on isolated nuclei from three embryonic developmental stages: 8 days after pollination (8DAP), 24 days after pollination (24DAP) and 4 days after germination (4DAG)

first: Simon

last: Pavlu

first: Pavla

last: Navratilova

first: Sarvesh

last: Nikumbh

first: Boris

last: Lenhard

first: Hana

last: Simkova


title: Core promoterome of barley embryo [CAGE]

overall_design: Cap Analysis of Gene Expression conducted on total RNA isolated from three embryonic developmental stages: 8 days after pollination (8DAP), 24 days after pollination (24DAP) and 4 days after germination (4DAG) in two highly correlated replicates


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (7296)

address: Plesmanlaan 121

overall_design: Murine NRAS mutated melanoma-cells (NMM) exposed to the cytokines IFNy, TGFb in different orders. For 4 different prestimulations (2, 6, 12, 24 hours of continuous stimululation), followed up by a second stimulation (IFNg, TGFb, mix or control) for 24h.


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (6743)

overall_design: NMM tumors exposed to T-cells or PBS (control) in vivo in Rag-/- mice.


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (6601)

overall_design: intratumoral injection of IFNg, TNFa and combination in OVACR5 in vivo tumors


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (6489)

overall_design: OVCAR5-cell exposed to tumor-cell T-cell coculture supernatant at various dilutions and exposure durations in vitro


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (6369)

overall_design: OVCAR5-cell exposed to IFNy at various concentrations and exposure durations in vitro


title: Surplus Fatty Acid Synthesis Increases Oxidative Stress in Adipocytes and lnduces Lipodystrophy

city: Shanghai

first: Weng

address: No. 2005, Songhu Road, Yangpu District, Shanghai

institute: fudan university

summary: Adipocytes are the primary sites for fatty acid storage, but the synthesis rate of fatty acids is very low. The physiological significance of this phenomenon remains unclear. Here, we show that surplus fatty acid synthesis in adipocytes induces necroptosis and lipodystrophy. Transcriptional activation of FASN elevates fatty acid synthesis, but decreases NADPH level and increases ROS production, which ultimately leads to adipocyte necroptosis. We identify MED20, a subunit of the Mediator complex, as a negative regulator of FASN transcription. Adipocyte-specific male Med20 knockout mice progressively develop lipodystrophy, which is reversed by scavenging ROS. Further, in a murine model of HIV-associated lipodystrophy and a human patient with acquired lipodystrophy, ROS neutralization significantly improves metabolic disorders, indicating a causal role of ROS in disease onset. Our study well explains the low fatty acid synthesis rate in adipocytes, and sheds light on the management of acquired lipodystrophy.

overall_design: Total RNA was isolated on day 12 of differentiation from control and MED20-deficient adipocytes. RNAs from 3 samples were pooled and subjected to RNA-Seq analysis as previously described. Genes with a FPKM no less than 1 were included in the analysis.

first: Li

last: Weng

first: Wen-Shuai

last: Tang

first: Xu

last: Wang


title: PSIP1/LEDGF reduces R-loops at transcription sites and maintain genome integrity (CUT&Tag-Seq)

first: Pradeepa

last: Madapura

overall_design: Cleavage Under Targets and Tagmentation DNA-sequencing (CUT&Tag-Seq) for PSIP1, S9.6, gammaH2AX and IgG in RWPE-1 cells transduced with control shRNAs or PSIP1 sh RNAs. For each group, samples were processed in a minimum of two biological replicates.

first: Jayakumar

last: Sundarraj


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (6493)

overall_design: OVCAR5-cell exposed to T-cells or not in vivo at two different time points past T-cell injection


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (6600)

overall_design: Ex vivo tumor cells exposed to (combinations of) various dilutions of cytokines in vitro


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (5310)

overall_design: OVCAR5-cell exposed to TNFa, IFNy and their combination in vitro, as well as to T-cell exposure or not (PBS control) in NSG-B2m-/- mice in vivo


title: Death Induced by Survival gene Elimination (DISE) is correlated with neurotoxicity in Alzheimer's disease and aging

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: Analysis of RISC bound short (s)RNAs in various cell lines and mouse models of Alzheimer's disease and in human AD patients reveals a contribution of 6mer seed toxicity to the neurotoxicity associated with AD

overall_design: Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq

first: Elizabeth

last: Bartom


title: The Tumor Microenvironment of Laryngeal Squamous Cell Carcinoma Revealed by Single-Cell Transcriptomics

city: shenyang

first: sun

middle: yuan

last: yuan

address: 沈北新区蒲河路77号

institute: China Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a malignant tumor with a high possibility of metastasis. The tumor microenvironment (TME) is well known to play an important role in LSCC metastasis. To gain insights into the TME of LSCC, we performed single-cell RNA-seq (scRNA-seq) using LSCC with lymph node metastases.

overall_design: We collected 10 fresh tissues immediately after surgery, including carcinoma in situ (T), normal laryngeal mucosal epithelia (N), margins of cancer (R), and lymph nodes (L). Single-cell suspension was prepared immediately and then subjected to 3’ droplet- based single-cell sequencing (10×Genomics)

first: Yuanyuan

last: Sun

first: Weineng

last: Fu

first: Wei

last: Yan

first: Zhenming

last: Xu

first: Sheng

last: Chen

first: Yongping

last: Lu


title: Thrombocytes-derived Dickkopf1 promotes wound-healing macrophage polarization

status: Public on Dec 06 2023

city: Richmond

first: Eun-Ah

last: Sung

state: VA

address: 401 College Street

institute: Virginia Common Wealth University

summary: Immune responses are crucial to maintaining tissue homeostasis upon tissue injury. Upon various types of challenges, macrophages play a central role in regulating inflammation and tissue repair processes. While an immunomodulatory role of Wnt antagonist Dickkopf1 (DKK1) has been implicated, the role of Wnt antagonist DKK1 in regulating macrophage polarization in inflammation and the tissue repair process remains elusive. Here we found that DKK1 induces differential gene expression profiles from type 2-cytokine-activated macrophages to promote inflammation and tissue repair. Importantly, DKK1 induced pro-inflammatory and pro-resolving gene expressions via JNK (c-jun N-terminal kinase) in macrophages. Furthermore, DKK1 potentiated IL-13-mediated macrophage polarization and activation. Co-inhibition of JNK and STAT6 markedly decreased pro-inflammatory and pro-resolving gene expressions by DKK1 and IL-13. Interestingly, thrombocyte-specific deletion of DKK1 in mice reduced monocyte-derived macrophages in the acute sterile bleomycin (BLM)-induced lung injury model, suggesting that thrombocytes communicate with macrophages via DKK1 to orchestrate inflammation-induced injury repair process. Taken together, our study demonstrates DKK1’s role as a key regulatory role in macrophage polarization in the injury-induced inflammation and repair process.

overall_design:
Three biological replicates were analyzed for each of 4 conditions
BMDMs: untreated
BMDMs: IL-13 stimulation for 24 hr
BMDMs: DKK1 stimulation for 24 hr
BMDMs: IL-13+DKK1 stimulation for 24 hr

first: Wook-Jin

last: Chae

first: MinHee

last: Park

first: Jinze

last: Liu

first: Hasan

last: Alanya

first: E

middle: Z

last: Erson-Omay


title: A Non-invasive Mouse Model That Recapitulates Disuse-Induced Muscle Atrophy in Immobilized Patients

city: Taichung

first: Yu-Jung

last: Cheng

state: OTH

address: Road NaN-Tong, sec 1, 152-8, 8F

department: Physical Therapy

country: Taiwan

summary: Disuse muscle atrophy occurs consequent to prolonged limb immobility or bed rest, which represents an unmet medical need. As existing animal models of limb immobilization often cause skin erosion, edema, and other untoward effects, we here report an alternative method via thermoplastic immobilization of hindlimbs in mice. While significant decreases in the weight and fiber size were noted after 7 days of immobilization, no apparent skin erosion or edema was found. To shed light onto the molecular mechanism underlying this muscle wasting, we performed the next-generation sequencing analysis of gastrocnemius muscles from immobilized versus non-mobilized legs.  Among a total of 55,487 genes analyzed, 787 genes were differentially expressed (> 4-fold; 454 and 333 genes up- and down-regulated, respectively), which included genes associated with muscle tissue development, muscle system process, protein digestion and absorption, and inflammation-related signaling.  To the best our knowledge, this is the first study that used RNA-seq to reveal changes in the skeletal muscle transcriptome profiling in response to disuse atrophy without denervation.  From a clinical perspective, this model may help understand the molecular/cellular mechanism that drives muscle disuse and identify therapeutic strategies for this debilitating disease.

overall_design: Animals: C57Bl/6 male mice, eight -weeks old. Grouping: NC, muscle from naïve mice; Dis, muscle from immobilized leg; Con, muscle from immobilized leg. Treatment: right immobilize hindlimb for 7 days with thermoplastic bandage. Tissue: gastrocnemius.   Muscle. Analysis: next-generation sequencing


title: Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice

status: Public on Dec 05 2023

city: La Jolla

first: Hiutung

last: Chu

state: CA

address: 9500 Gilman

institute: UC San Diego

summary: Type I interferons (IFNs) exert a broad range of biological effects important in coordinating immune responses, which have classically been studied in the context of pathogen clearance. Yet, whether immunomodulatory bacteria operate through IFN pathways to support intestinal immune tolerance remains elusive. Here, we reveal that the commensal bacterium, Bacteroides fragilis, utilizes canonical antiviral pathways to modulate intestinal dendritic cells (DCs) and regulatory T cell (Treg) responses. Specifically, IFN signaling is required for commensal-induced tolerance, as IFNAR1-deficient DCs display blunted IL-10 and IL-27 production in response to B. fragilis. We further establish that IFN-driven IL-27 in DCs is critical in shaping the ensuing Foxp3+ Treg via IL27Ra signaling. Consistent with these findings, single cell RNA sequencing of gut Tregs demonstrated that colonization with B. fragilis promotes a distinct IFN gene signature in Foxp3+ Tregs during intestinal inflammation. Altogether, our findings demonstrate a critical role of commensal-mediated immune tolerance via tonic type I IFN signaling.

overall_design: Cells were isolated from mesenteric lymh nodes (MLNs) and enriched by Fluorescent-activated cell sorting (FACS) according to the presence of CD4+hCD2+ signal and analyzed using scRNAseq.


title: Pivotal role of mitochondria in development and treatment of severe phenotypes of desmin-mutated cardiomyocytes from a patient with myofibrillar myopathy

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

institute: INSERM

summary: Desmin-related myofibrillar myopathy, a severe muscle disease, is caused by mutations in the desmin-encoding gene, leading to skeletal myopathies and/or cardiomyopathy. Although previous studies suggested that desmin mutations alter the cellular structure and mitochondria function in myocyte, the pathophysiological mechanism by which mutated desmin impairs cardiac function has been poorly explored in physiologically relevant human disease models.  In this attempt, we generated cardiomyocytes from induced pluripotent stem cells (hiPSC) of a patient carrying the heterozygous DESE439K mutation together with an isogenic pair of mutant hiPSC harboring the same mutation. Using 2D and 3D models as well as cardiac biopsies, we demonstrated that in mutant cardiomyocytes this heterozygous desmin mutation leads to disorganization in their cytoarchitecture and to a perturbation of their mitochondrial architecture and function. Finally, we then demonstrated that transfer of exogenous healthy mitochondria rescues the phenotypic impairment of mitochondrial function in desmin-mutated cardiomyocytes leading to the reversion of the diseased phenotype. This work advances our understanding on the critical role of mitochondria in the development of cardiomyopathy related to desmin mutation and opens up new potential therapeutic perspectives for this debilitating and still incurable disease.

overall_design: We used PBMC of the patient CIII who was diagnosed with desmin-related myofibrillar myopathy (MFM1) with cardiac manifestation at the age of 36 years and carries the DESE439K (Desmine) variant present in his family. PBMC of CIII patient were reprogrammed into induced pluripotent stem cells (iPSCs) using a non-integrative method (Epi5™ Episomal iPSC Reprogramming Kit, Thermo Fisher Scientific). The clone c15 was isolated and used in transcriptome analysis.  Gibco Human Episomal iPSC clone (Control 1, Thermo Fisher Scientific) derived from healthy individuals without any cardiac pathology, was used as control. Frozen iPSC-CM (cardiomyocytes derived from induced pluripotent stem cells) from Clone c15 and Gibco Human Episomal iPSC clone (Control 1), Thermo Fisher Scientific) were thawed, centrifuged at 200xg to remove freezing medium and directly seeded on Matrigel-coated 12 well plates. They were then cultured 20 days in maturation medium, detached using TrypLE Select 1X, pelleted and flash frozen in liquid nitrogen. The cells were afterwards submitted to mRNA sequencing.

first: Onnik

last: Agbulut

first: Hakim

last: Hocini

first: Cécile

last: Lefebvre


title: Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity

status: Public on Dec 04 2023

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The co-infection of hepatitis B (HBV) patients with the hepatitis D virus (HDV) causes the most severe form of viral hepatitis and thus drastically worsens the course of the disease. Therapy options for HBV/HDV patients are still limited. Here, we investigated the potential of natural killer (NK) cells that are crucial drivers of the innate immune response against viruses to target HDV-infected hepatocytes. We established in vitro co-culture models using HDV-infected hepatoma cell lines and human peripheral blood NK cells. We determined NK cell activation by flow cytometry, transcriptome analysis, bead-based cytokine immunoassays, and NK cell-mediated effects on T cells by flow cytometry. We validated the mechanisms using CRISPR/Cas9-mediated gene deletions. Moreover, we assessed the frequencies and phenotype of NK cells in peripheral blood of HBV and HDV superinfected patients. Upon co-culture with HDV-infected hepatic cell lines, NK cells upregulated activation markers, interferon-stimulated genes (ISGs) including the death receptor ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), produced interferon (IFN)-gamma and eliminated HDV-infected cells via the TRAIL-TRAIL-R2 axis. We identified IFN-beta released by HDV-infected cells as an important enhancer of NK cell activity. In line with our in vitro data, we observed activation of peripheral blood NK cells from HBV/HDV co-infected, but not HBV mono-infected patients. Our data demonstrate NK cell activation in HDV infection and their potential to eliminate HDV-infected hepatoma cells via the TRAIL/TRAIL-R2 axis which implies a high relevance of NK cells for the design of novel anti-viral therapies.

overall_design:
Primary peripheral NK cells from healthy donors were co-cultured with HDV-infected or non-infected HepG2-hNTCP cells, isolated and analyzed using RNA-seq.

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Submitter states that missing raw data are being made available for controlled access in EGA.
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first: Seufert

last: Isabelle

first: Rippe

last: Karsten

first: Groth

last: Christopher

first: Cerwenka

last: Adelheid


title: Trellis Single-Cell Screening Reveals Stromal Regulation of Patient-Derived Organoid Drug Responses

first: James

last: Opzoomer

address: 72 Huntley Street

department: Department of Oncology

institute: University College London Cancer Institute

summary: Patient-derived organoids (PDOs) can model personalized therapy responses, however current screening technologies cannot reveal drug response mechanisms or how tumor microenvironment cells alter therapeutic performance. To address this, we developed a highly-multiplexed mass cytometry platform to measure post translational modification (PTM) signaling, DNA-damage, cell-cycle activity, and apoptosis in >2,500 colorectal cancer (CRC) PDOs and cancer associated fibroblasts (CAFs) in response to clinical therapies at single-cell resolution. To compare patient- and microenvironment specific drug responses in thousands of single-cell datasets, we developed Trellis — a highly-scalable, hierarchical tree-based treatment effect analysis method. Trellis single-cell screening revealed that on-target cell-cycle blockage and DNA-damage drug effects are common, even in chemorefractory PDOs. However, drug-induced apoptosis is rare, patient-specific, and aligns with cancer cell PTM signaling. We find that CAFs can regulate cancer cell plasticity — shifting proliferative stem cells to slow-cycling revival stem cells via YAP to protect cancer cells from chemotherapy.

overall_design: Single-cell RNA-seq was performed using the SPLiT-seq protocol on 2 human PDO (PDO21 and PDO27) 3D cell models in triplicate samples of PDO and CAF mono- and co-cultures. The sample preparation was performed in two batches, one for each PDO. For each batch, 9 samples were multiplexed, corresponding to each cell type's mono culture and co-cultures, all perfomed in triplicate (3x3). In total, 18 samples across the 2 SPLiT-seq experiments were analyzed.The dataset contains 4 sublibraries with 39852 cells, these correspond to the 2 sublibraries from each SPLiT-seq barcoding experiment. Further information on the SPLiT-seq barcoding layout can be found at : https://github.com/TAPE-Lab/Ramos-et-al-Trellis

first: M

last: Ramos Zapatero

first: A

last: Tong

first: J

middle: W

first: R

last: O'Sullivan

first: F

last: Cardoso Rodriguez

last: Sufi

first: P

last: Vlckova

first: C

last: Nattress

first: X

last: Qin

last: Claus

first: D

last: Hochhauser

first: S

last: Krishnaswamy

last: Tape


first: Marcus

last: Peter

overall_design: Refer to individual Series


title: Egr2 deletion in autoimmune-prone C57BL6/lpr mice suppresses the expression of methylation-sensitive Dlk1-Dio3 cluster microRNAs

city: Blacksburg

first: Zhuang

last: Wang

address: 1739 Autumn Splendor Way

institute: VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY

type: Methylation profiling by high throughput sequencing

summary: Our previous study demonstrated a significant upregulation of a large set of miRNAs at the genomic imprinted Dlk1-Dio3 locus in lymphocytes of diverse murine lupus-prone strains. The upregulation of Dlk1-Dio3 miRNAs in lupus-prone mice is correlated with the global DNA hypomethylation. In this study, by performing genome-wide DNA methylation analysis, we reported that Dlk1-Dio3 genomic region in CD4+ T cells of MRL/lpr mice was hypomethylated, further linking hypomethylation to the increased expression of Dlk1-Dio3 miRNAs in lupus. Then, we assessed the gene expression levels of enzymes that either write (DNA methyltransferases, DNMTs) or erase DNA methylation (Ten-eleven translation proteins, TETs) to understand the molecular contributor to the DNA hypomethylation in MRL/lpr CD4+ T cells. The expression levels of Dnmt1, Dnmt3b, Tet1, and Tet2 were significantly increased in CD4+ T cells of MRL/lpr mice, as well as in B6/lpr and B6.sle123 mice, compared to their respective control mice. These data indicate the significant involvement of the TETs-mediated active demethylation pathway rather than reduced DNMTs-mediated passive demethylation pathway in the hypomethylation of murine lupus CD4+ T cells. The transcription factor, early growth response 2 (EGR2) is critically involved in regulating T cell functions and autoimmunity. In this research, we found that Egr2 deletion in B6/lpr mice notably reduced methylation-sensitive Dlk1-Dio3 cluster miRNAs expression in CD4+ T cells. Surprisingly, even though EGR2 has been shown to induce DNA demethylation by recruiting TET2, we found that deleting Egr2 in B6/lpr mice induced a higher number of hypomethylated DMRs than hypermethylated DMRs at either whole genome or the Dlk1-Dio3 locus in CD4+ T cells of B6/lpr mice. These data are the first finding on the positive role of EGR2 on the expression of Dlk1-Dio3 cluster miRNAs in lupus mice. Given that Dlk1-Dio3 miRNAs target the major signaling pathways in autoimmunity, these data provide a new perspective in understanding the potential pathogenic role of upregulated EGR2 in lupus.

overall_design: Evaluate the methylation difference between CD4+ T cells of MRL/lpr and MRL mice as well as between EGR2-/-B6/lpr and EGR2 fl/fl B6/lpr mice

first: Rujuan

last: Dai

last: Ahmed


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment (5892)

first: Maarten

last: Slagter

overall_design: Murine NRAS mutated melanoma-cells (NMM) exposed to various (combinations of) cytokines (TNFa, IFNy, tumor-cell T-cell co-culture supernatant) for 4 different durations (2, 6, 12, 24 hours of continuous stimulation)

first: Mirjam

last: Hoekstra


title: The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation [ChIP-seq]

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

summary: Proper differentiation of corneal epithelial cells (CECs) from limbal stem/progenitor cells (LSCs) is required for maintaining ocular homeostasis and clear vision. Here, using a single-cell transcriptomic atlas, we delineate the comprehensive and refined molecular regulatory dynamics during human CEC development and differentiation. We find that RORA is a CEC-specific molecular switch that initiates and drives LSCs to differentiate into mature CECs by activating PITX1. RORA dictates CEC differentiation by establishing CEC-specific enhancers and chromatin interactions between CEC gene promoters and distal regulatory elements. Conversely, RORA silences LSC-specific promoters and disrupts promoter-anchored chromatin loops to turn off LSC genes. Collectively, our work provides detailed and comprehensive insights into the transcriptional dynamics and RORA-mediated epigenetic remodeling underlying human corneal epithelial differentiation.

overall_design: ChIP-seq for RORA-flag, H3K27ac, H3K27me3 and H3K4me3 in RORA-overexpressed LSCs. ChIP-seq for H3K27ac, H3K27me3 and H3K4me3 in control LSCs.


title: Effect of ROCK Inhibitor on myeloid cells during GvHD

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: GvHD mice (allo transplant) and treated mice with ROCK Inhibitor 8mg /kg or PBS (vehicle)

overall_design: 5x10^6 BM, 0,3x10^6 tcells from C57BL6/N to BALB/cAnN were injected i.v. after 2x irradiation with 5 Gy

first: Enrique

last: de Vega Gomez

first: Kristina

last: Maas-Bauer

first: Anna-Verena

last: Stell

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation [RNA-Seq]

overall_design: RNA-seq for control and RORA-overexpressed LSCs. RNA-seq for control and PITX1-overexpressed LSCs.


title: Single cell transcriptomic analysis of hematopoetic stem/progenitor cells (HSPCs) from bone marrow and spleen during hemolytic anemia

city: Houston

first: Jong

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: HSPCs possess multipotent differentiation potential and are responsive to extrinsic stress. In this study, we employed single-cell RNA sequencing (scRNA-seq) to investigate the response of HSPCs to acute blood loss.

overall_design: HSPCs (lineage-Sca-1+c-kit+ cells) were isolated from bone marrow and spleen treated with either phenylhydrazine (PHZ) or control PBS using fluorescence-activated cell sorting (FACS).

first: Daisuke

last: Nakada

first: Yu-Jung

last: Tseng

first: Yuki

last: Kageyama

first: James

last: Martin


title: Single-step deamination sequencing of 5-hydroxymethylcytosine in genomic DNA at single-base resolution

city: Beijing

first: Nengbin

last: Xie

address: whu

institute: whu

summary: 5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark that can regulate gene expression. While some methods were developed to detect 5hmC, direct genome-wide mapping of 5hmC at base resolution are still highly desirable. Herein, we proposed a single-step deamination sequencing (SSD-seq) method for the genome-wide mapping of 5hmC at single-base resolution. This method capitalizes on a screened engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein to produce differential deamination activity toward cytosine (C), 5-methylcytosine (5mC), and 5hmC. In SSD-seq, an engineered A3A protein (eA3A-v10) can adequately deaminate C and 5mC, but not 5hmC. The original C and 5mC in DNA are deaminated by eA3A-v10 to form uracil (U) and thymine (T), both of which are read as T during sequencing. However, 5hmC is resistant to the deamination by eA3A-v10 and is still read as C during sequencing. Therefore, the remaining C in the sequence reads manifests the original 5hmC. Applying SSD-seq to generate a base-resolution map of 5hmC in human lung tissue, we found that 5hmC was almost entirely confined to CpG dinucleotides. The base-resolution map of 5hmC from human lung tissue generated by SSD-seq correlated strongly with that generated by prior ACE-seq. Taken together, the SSD-seq method is single-step, bisulfite-free and does not require DNA glycosylation or chemical treatment, which offers a valuable tool for the direct and quantitative detection of 5hmC in genomes at single-base resolution.

overall_design:
Single-base resolution mapping of 5-hydroxymethylcytosine in human normal lung tissue by SSD-seq and ACE-seq.
DD-seq/SSD-seq (resolutionSingle-step deamination sequencing) mapping 5hmC at single-base.
ACE-seq (APOBEC-Coupled Epigenetic Sequencing): Schutsky, E. K et al. (Nat Biotechnol 2018, 36, 1083-1090).

There are two data columns in the 'P5_10X_P5M_10X_10kb_amf.txt':
the 5hmC signals from ACE-seq are provided in fileID_P5_10X.merged.hapinfo.txt column
the 5hmC signals from SSD-seq are provided in fileID_P5_M_10X.merged.hapinfo.txt column

first: Yuan

last: Liang

first: Bifeng

last: Yuan


title: The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation [Promoter capture Hi-C]

overall_design: Promoter capture Hi-C-seq in control and RORA-overexpressed LSCs.


title: Impact of proteasome inhibition on nascent transcription of APOBEC3 cytidine deaminases

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

summary: To assess the impact of the proteasome inhibitor MG132 on nascent transcription inMDA-MB-453 cells, csRNA-seq was conducted to compare transcript abundances between treated and DMSO control cells. Analysis of transcripts following MG132 treatment showed that APOBEC3A is one of the most differentially expressed genes. Comparison to other APOBEC family genes, revealed APOBEC3A is unique in its transcriptional upregulation by MG132. Analysis of transcription factor binding sites enriched in the promoter regions of genes changed greater than 2-fold in expression highlighted potential transcription factors driving increased APOBEC3A transcription.

overall_design: Harvested MDA-MB-453 cells treated with MG132 or DMSO were analyzed by csRNA-seq

first: Margo

last: Coxon

first: Marina

last: Savenkova

first: Steven

last: Roberts


title: Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment

city: Amsterdam

first: Maarten

last: Slagter

institute: Netherlands Cancer Institute

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


title: A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

summary: As a human tumor virus, EBV is present as a latent infection in its associated malignancies where genetic and epigenetic changes have been shown to impede cellular differentiation and viral reactivation. One such change is increased levels of the Wnt signaling effector, lymphoid enhancer binding factor 1 (LEF1) following EBV epithelial infection.  In silico analysis of EBV type 1 and 2 genomes identified over 20 Wnt-response elements suggesting that LEF1 may directly bind the EBV genome and regulate the viral life cycle. Using CUT&RUN-seq, LEF1 was shown to bind the latent EBV genome at various sites encoding viral lytic products that included the immediate early transactivator BZLF1 and viral primase BSLF1 genes. SiRNA depletion of specific LEF1 isoforms revealed that the alternative-promoter derived isoform with an N-terminal truncation (∆N LEF1) transcriptionally repressed lytic genes associated with LEF1 binding. Furthermore, forced expression of the ∆N LEF1 isoform antagonized EBV reactivation from latency. The LEF1 mediated repression requires histone deacetylase activity through either recruitment or a direct intrinsic histone deacetylase activity. SiRNA depletion of LEF1 resulted in increased histone 3 lysine 9 and lysine 27 acetylation at LEF1 binding sites and across the EBV genome. These results support a novel role for LEF1 in maintaining EBV latency and restriction viral reactivation via repressive chromatin remodeling of critical lytic cycle factors

overall_design: Cut-and-run analysis was used to evaluate the binding and occupancy of the transcription factor LEF1 acriss the Epstein-Barr virus genome in the latently infected Akata BL cell line and following reactivation.  The full-length LEF1 isoforms were specifically siRNA depleted to evaluate binding by the N-terminal truncated LEF1 isoforms to the EBV genome. LEF1 binding to the EBV genome was also evaluated in non-target controls and following depletion of all LEF1 isoforms (FL+DN) .  Histone acetylation across the EBV genome was also evaluated ifollowing siRNA depletion of LEF1 isoforms in EBV-infected normal oral keratinocyte (NOK) cell line.

first: B

last: Ward

first: Kanchanjunga

last: Praai

first: Danielle

last: Schaal

first: Jian

last: Wang

middle: S


title: Characterization of transcriptome in post-replicative mouse male germ cells [RNA-seq]

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary:
To investigate the complexity of RNA present in different stage germ cells from adult mice, we isolated cells via FACS
We then performed paired end RNA-Seq to characterize the expression state of each cell type

overall_design: De novo transcriptome assembly and expression analysis of cells in five developmental stages

first: Mark

last: Gill


title: Characterization of transcriptome in post-replicative mouse male germ cells


title: The effect of PHZ-induced hemolytic anemia on HSCs

first: Rebecca

last: Murdaugh

state: Texas


title: Characterization of transcriptome in post-replicative mouse male germ cells [ChIP-Seq]

summary:
To investigate transcriptional changes in developing mouse testicular germ cells, cells were isolated via FACS or centrifugal elutriation
Isolated cells were subjected to native ChIP-Seq with an antibody against H3K4me3

overall_design: Cells from 3 different stages were subjected to ChIP-Seq for H3K4me3


title: The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation

status: Public on Dec 02 2023

first: Mingsen

last: Li


title: The effect of PHZ-induced hemolytic anemia on HSCs [RNA-seq]

summary: Hematopoietic stem cells (HSCs) are capable of regenerating the blood system, but the instructive cues that direct HSCs to regenerate particular lineages lost to the injury remain elusive. Here, we show that iron is increasingly taken up by HSCs during anemia and induces erythroid gene expression and regeneration in a Tet2-dependent manner. Lineage tracing of HSCs revealed that HSCs respond to hemolytic anemia by increasing erythroid output. The number of HSCs in the spleen, but not bone marrow, increased upon anemia and these HSCs exhibited enhanced proliferation, erythroid differentiation, iron uptake, and TET2 protein expression. Increased iron in HSCs promoted DNA demethylation and expression of erythroid genes. Suppressing iron uptake or TET2 expression impaired erythroid genes expression and erythroid differentiation of HSCs; iron supplementation, however, augmented these processes. These results establish that the physiological level of iron taken up by HSCs has an instructive role in promoting erythroid-biased differentiation of HSCs.

overall_design: RNA-seq in control bone marrow HSCs and PHZ-treated bone marrow and splenic HSCs. Bone marrow HSC sample has 3 replicates, splenic HSC sample has two replicates.

first: Yu-Jung

last: Tseng

first: Kevin

last: Hoegenauer

first: Daisuke

last: Nakada


title: The effect of PHZ-induced hemolytic anemia on HSCs [bisulfite-seq]

overall_design: Bisulfite-seq in control bone marrow HSCs and PHZ-treated bone marrow and splenic HSCs. The WT and PHZ-treated bone marrow HSC samples have 3 replicates each, the WT splenic HSC samples have 2 replicates, and the PHZ-treated splenic HSC samples have 3 replicates.


title: COVID-19 and influenza infections mediate distinct pulmonary cellular and transcriptomic changes [scRNA-Seq]

city: New Orleans

first: Jay

last: Kolls

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: SARS-CoV-2 infection can cause persistent respiratory sequelae, as seen in long COVID. However, the underlying mechanisms remain unclear. To investigate pulmonary cellular and transcriptomic changes mediated by SARS-CoV-2 and influenza infection, we characterized the SARS-CoV-2-infected K18-hACE2 (K18) mice and compared their lung recovery with a mouse-adapted influenza model and verified the finding in SARS-CoV-2-infected nonhuman primates and in fatal human COVID-19 cases. K18-hACE2 mice infected with a sub-lethal dose of SARS-CoV-2 lost body weight from 1 - 8 days post-infection (DPI), and then gradually returned to baseline weight between 8 -13 DPI. Infected mice showed patchy pneumonia associated with histiocytic inflammation, collagen deposition, and increased pulmonary interferon and inflammatory response signature gene changes at 21 and 45 DPI. Transcriptomic analyses revealed that compared to influenza-infected mice, SARS-CoV-2-infected mice had reduced interferon-gamma/alpha responses at 4 DPI and failed to induce keratin 5 (Krt5) at 6 DPI in lung, a marker of nascent pulmonary progenitor cells. They also showed reduced activation of epithelial-to-mesenchymal transition and apical junction pathways compared to influenza (Flu)-infected mice. Histologically, influenza- but not SARS-CoV-2- infected mice showed extensive Krt5+ “pods” structure co-stained with stem cell markers Trp63/ NGFR proliferated in the pulmonary consolidation area at both 7 and 14 DPI, with regression at 21 DPI. These Krt5+ “pods” and proliferative stem cells were not observed in SARS-CoV-2 infection in the lungs of humans or nonhuman primates. These results suggest that SARS-CoV-2 infection fails to induce nascent Krt5+ cell proliferation in consolidated regions, leading to incomplete repair of the injured lung which may underlie the persistent clinical symptoms of long COVID.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for COVID mice at 4DPI, 6DPI and 21DPI and Influenza infected mice.
Third party re-analysis of GSM5352467 is the acession number of the sample in GSE175996 for COVID mice Day4, scRNAseq

first: Chenxiao

first: Mst

last: Shamima Khatun

first: Zhe

last: Zhang

first: Michaela

last: Allen

first: Zheng

last: Chen

first: Calder

middle: R

last: Ellsworth

first: Joshua

last: Currey

first: Guixiang

last: Dai

first: Di

last: Tian

first: Konrad

last: Bach

first: Xiao-Ming

last: Yin

first: Vicki

last: Traina-Dorge

last: Rappaport

first: Nicholas

last: Maness

first: Robert

middle: V

last: Blair

middle: K

first: Derek

last: Pociask

first: Xuebin

last: Qin


title: COVID-19 and influenza infections mediate distinct pulmonary cellular and transcriptomic changes [RNA-seq]

first: Jay

last: Kolls

overall_design: Comparative gene expression profiling analysis of RNA-seq data for COVID mice at 4DPI, 6DPI and 21DPI and Influenza infected mice.

last: Wang

middle: J


title: EcoToxChip 2016 LSARP RNASeq database

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

summary: As part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. Whole transcriptome analyses were conducted on these samples resulting in a rich RNA seq dataset covering various species, life stages and chemicals, which is one of the largest purposeful complications of RNA seq data within ecotoxicology. Recently, a unified bioinformatics platform of relevance to ecotoxicology, EcoOmicsAnalyst and ExpressAnalyst, was developed to facilitate RNA Seq analysis of non-model species lacking a reference transcriptome. The platform uses the Seq2Fun algorithm to map RNA-seq reads from eukaryotic species to an ortholog database comprised of protein sequences from >600 eukaryotic species (EcoOmicsDB) with a translated search. The availability of these tools presents a unique opportunity to examine the EcoToxChip RNA Seq dataset for cross species comparisons. This work shows the potential of the EcoOmicsAnalyst and Seq2Fun platform to facilitate fast and simple analysis of RNA Seq datasets from non-model organisms with unannotated genomes and conduct comparative transcriptomic analysis across various species and life stages for cross-species extrapolation.

sample_organism:
Oncorhynchus mykiss
Xenopus laevis
Lithobates pipiens
Phalacrocorax auritus
Pimephales promelas
Coturnix japonica

overall_design: Japanese quail, fathead minnow, African clawed frog, double crested cormorant, rainbow trout, and northern leopard frog adults and/or embryos were exposed to 8 chemicals of environmental concern at various concentrations.

first: Markus

last: Hecker

first: Natacha

last: Hogan

first: Jessica

last: Head

first: Doug

last: Crump

first: Jianguo

last: Xia

first: Krittika

last: Mittal


title: Embryos Assist Each Other’s Morphogenesis: calcium and ATP signaling mechanisms in collective resistance to teratogens (Stage 35)

city: Boston

first: Megan

middle: M

last: Sperry

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute at Harvard University

summary: We investigated whether normal embryonic developmental cues are only at the level of cells within the embryo or whether they exist in interactions between embryos. To explore this, we subjected groups of embryos with disruptors of normal development while varying group size. RNA-seq analysis revealed a small set of transcripts specific for teratogen response in large groups but not small ones.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for metamorphosing X. laevis tadpoles exposed to thioridazine. Control and exposed treatments in triplicate.

first: Angela

last: Tung

first: Michael

last: Levin


title: COVID-19 and influenza infections mediate distinct pulmonary cellular and transcriptomic changes

overall_design: Refer to individual Series


title: Embryos Assist Each Other’s Morphogenesis: calcium and ATP signaling mechanisms in collective resistance to teratogens


title: Analysis of gene expression changes in lipid droplet formation of human liver cancer cell HepG2

status: Public on Dec 01 2023

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

summary: Fatty liver is a condition of excessive triglyceride accumulation in hepatocytes. Additionally, hepatocytes showed a high degree of fat droplet accumulation during excessive alcohol consumption and metabolic syndrome. However, the molecular mechanisms involved in fat droplet formation remain unknown. This study used an in vitro fatty liver formation model of the human liver cancer cell line HepG2 to comprehensively search for fat droplet formation-related genes whose expression changes during fat droplet formation. Microarray analysis with extracted total RNA determined the genes that are involved in fat droplet formation and confirmed their expression by real-time polymerase chain reaction after culturing HepG2 cells in a culture medium containing 0, 50, 200, and 500 μM of oleic acid for 24 h. The results revealed 142 genes demonstrating increased expressions by >2.0 fold with oleic acid treatment and 426 genes demonstrating decreased expressions. Perilipin 2 (PLIN2) was estimated as the gene most closely associated with fatty liver. Lipid droplet formation in HepG2 upregulated PLIN2 in an oleic acid-treated concentration-dependent manner. These results indicate the involvement of genes in oleate treatment-induced lipid droplet formation in HepG2, particularly PLIN2 may play an important role.

overall_design: Gene expressions in the HepG2 cell line treated with 0, 50, 200, and 500 μM of oleic acid were examined by microarray analysis.

first: Kana

last: Matsumoto


title: Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù


title: miRNA expression profile in human medulloblastoma cell lines.

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

summary: We deep sequenced and analyzed miRNAs using small RNA sequencing in six medulloblastoma cell lines (SHH: DAOY and ONS-76, Group 3: D341 and D425, Group 4: CHLA-01-MED and CHLA-01R-MED).

overall_design: Medulloblastoma miRNA profiles were generated by deep sequencing, using Illumina NextSeq 550.

first: Menglang

last: Yuan

first: Kandarp

last: Joshi


title: Embryos Assist Each Other’s Morphogenesis: calcium and ATP signaling mechanisms in collective resistance to teratogens (Stage 25)


title: Small transcriptional differences among cell clones lead to distinct NF-κB dynamics

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

summary: Transcription factor dynamics is fundamental to determine the activation of accurate transcriptional programs and yet is heterogeneous at single-cell level, even between very similar cells. We asked how such heterogeneity emerges for the nuclear factor κB (NF-κB), whose dynamics have been reported to cover a wide spectrum of behaviors, including persistent, oscillatory and weak activation. We found that clonal populations of immortalized fibroblasts derived from a single mouse embryo display robustly distinct dynamics upon tumor necrosis factor α (TNF-α) stimulation, which give rise to differences in the transcription of NF-κB targets. Notably, standard transcriptomic analyses indicate that the clones differ mostly in transcriptional programs related with development, but not in TNF-α signaling. However, by combining transcriptomics data and simulations we show how the expression levels of genes coding for proteins of the signaling cascade determine the differences in early NF-κB activation; differences in the expression of IκBα determine differences in its persistence and oscillatory behavior. The same analysis predicts inter-clonal differences in the NF-κB response to IL-1β. We propose that small (less than twofold) differences at transcript level can lead to distinct transcription factor dynamics in cells within homogeneous cell populations, and all the more so among different cell types.

overall_design: To determine the mechanisms responsible for NF-kB transcriptional dynamical variations, we isolated several clones from the original cell population of GFP-MEFs and made RNA-Seq of the original populiation (pool) as control and three clonal populations sleected based on the NF-kB dynamics,  in five replicates.

first: Cise

last: Kizilirmak

first: Emanuele

last: Monteleone

first: Alessandra

last: Agresti

first: Marco

last: Bianchi

first: Samuel

last: Zambrano


title: Detection on the effect of TLR stimulation and NOS inhibition on human chondrocytes.

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To enlarge our understanding on the effect of TLR1/2 stimulation to human chondrocytes and how NOS inhibition blocks this stimulatory effects, we planned to apply RNAseq analysis to human chondrocytes that are treated with TLR1/2 agonists and NOS inhibitor.

overall_design: During human chondrocyte sphroid culture, TLR1/2 agonist PamCSK4 and NOS inhibitor L-NAME were added. After four days of culture under hypoxia condition, RNA were isolated from the spheroids and subjected to RNAseq analysis.

first: Ping

last: Shen

first: Gitta

middle: A

last: Heinz

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi

first: Max

last: Löhning


title: Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination [blood]

city: Cleveland

first: Richard

last: Silver

state: OH

address: 10900 Euclid Ave

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: Case Western Reserve University and the Louis Stokes Cleveland VA Medical Center

summary: RNA-Seq was utilized to provide an unbiased assessment of systemic and mucosal immunity using blood cells from LTBI subjects and recipients of ID and oral (PO) BCG.

overall_design: Blood CD4+ T cells were studied from groups of Mtb/BCG-naïve, BCG-vaccinated and LTBI subjects. We combined the pre-vaccination studies of individuals who subsequently received ID and/or PO BCG.  Blood was drawn into CPT tubes and PBMC isolated, aliquoted and frozen.  Following thawing, CD4+ T cells were isolated using Miltenyi positive selection kits.  Autologous monocyte-derived dendritic cells (MDDC) were prepared (Hoft et al, Mucosal immunology. 2018;11(2):486-95).  MDDC were cultured overnight with autologous CD4+ T cells (20:1, T cell:MDDC ratio), in presence of either Danish BCG (Statens Serum Institut, Copenhagen, MOI 20:1), or medium alone. Cell pellets were lysed for RNA extraction.

first: Daniel

last: Hoft

first: Chad

last: Storer

first: Rich

last: Head


title: Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (RNA-Seq)

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Translational regulation in in vivo tissue environments during viral pathogenesis has hardly been scrutinized due to the lack of tissue translatomes upon viral infection despite a number of the translatome studies on virus-infected cells cultured in vitro. We constructed the first temporal profile of lung translatomes during SARS-CoV-2 pathogenesis by applying ribosome profiling (Ribo-seq) to a severe COVID-19 mouse model. Unexpectedly, we observed gradual accumulations of non-canonical Ribo-seq reads representing hitherto-unidentified ribonucleoproteins (RNPs) that are likely involved in impeded translational elongation in the infected tissues. Contemporarily developing ribosome heterogeneity with prominently deviated 5S rRNP association supported the malfunction of elongating ribosomes. The analyses of canonical Riboseq reads (ribosome footprints) highlighted two obstructive characteristics to host gene expression: attenuated translation for transcriptionally up-regulated genes including immune response genes and ribosome stalling on codons within transmembrane domain-coding regions. Our study elucidates hidden molecular features of gene regulation in vivo underlying SARS-CoV-2 pathogenesis.

overall_design: RNA-seq for lung tissues of K18-hACE2 transgenic mice infected by SARS-CoV-2. For the library construction, we divided conditions as two groups, the early set (Control for the early set, 1 day post-infection, 2 days post-infection) and late set (Control for the late set, 5 days post-infection, 7 days post-infection). For each condition, we prepared quadruplets.

first: Junsoo

last: Kim

first: Daehwa

last: Youn

first: Seunghoon

last: Choi

first: Youn

last: Lee

first: Dulguun

last: Sumberzul

first: Jeongeun

last: Yoon

first: Hanju

first: Hyuna

last: Noh

first: Dain

last: On

first: Seung-Min

last: Hong

first: Se-Hee

last: An

first: Hui

last: Jang

first: Sang-Hyuk

last: Seok

first: Yu

first: Seo

middle: Y

first: Young

first: Ji-Yeon

last: Hwang

first: Hyo-Jung

first: Hong

first: Jun

last: Park

first: Jun-Won

last: Yun

first: Jeon-Soo

last: Shin

first: Jun-Young

last: Seo

first: Ki

middle: T

last: Nam

first: Kang-Seuk

first: Ho-Young

first: Je

last: Seong

last: Cho


title: Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology

first: Hyeshik

last: Chang


title: Dynamic interplay of BRD4 isoforms in embryonal rhabdomyosarcoma

city: Singapore

first: Reshma

last: Taneja

address: 10 Medical Dr

country: Singapore

institute: NUS

summary: In this study, we show that long and short isoform of the epigenetic regulator BRD4 is overexpressed in ERMS patient-derived cell lines and patient tumour specimens. Functionally, knockdown of long isoform of BRD4 reduced proliferation and promotes differentiation. Knockdown of the short isoform on the other hand promotes migration and invasion. The functional observations were confirmed in vitro and in vivo. Through RNA Sequencing analysis, we identified Myostatin (MSTN) and Integrins (ITGs) as important downstream target of long and short isoform of BRD4 respectively. We thus conclude from this study that long isoform functions as an oncogenic driver and can only promote metastasis only when the short isoform that functions as a blocker of tumor spread is removed. The interplay of the isoform identifies the long form as a therapeutic target and the short form as a predictive biomarker for metastasis in ERMS.

overall_design: RD cells were treated with control siRNA (BRD4WT), BRD4 Long siRNA (siBRD4L) or BRD4 Short siRNA (siBRD4S) for 48 hours, after which total RNA was collected with TRIzol reagent. RNA was purified and quality of purified RNA was checked using Nanodrop and gel electrophoresis. Three samples of each were used for sequencing analysis, done by Novogene.

first: Das

last: Dipanwita

first: Taneja

last: Reshma


title: Transcriptomics revealed sex differences in human pulmonary microvascular endothelial cells in normoxia and hypoxia

city: Dublin

first: Paul

last: McLoughlin

address: Belfield, Dublin 4

country: Ireland

institute: University College Dublin

summary: To investigate sex differences at the transcriptome level in human pulmonary microvascular endothelial cells (HPMECs) from healthy male and female donors basally (in normoxia) and in hypoxic conditions. RNA-seq was performed on male (n=3) and female (n=4) HPMECs that were cultured in conditions of physiological shear stress (PMID: 36730645) in normoxia (21% O2) or in hypoxia (1% O2) for either 24 or 48 hours.

overall_design: RNAseq of normoxic and hypoxic (for 24 or 48 hours) male and female HPMECs

first: Daria

last: Kostyunina


title: Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination

first: Richard

last: Silver

country: USA

overall_design: BAL cell gene expression was evaluated after overnight culture in medium alone (baseline conditions), or with virulent Mtb strain H37Rv in patients with latent tuberculosis infection (LTBI) and in BCG-vaccinated (ID and PO groups) and Mtb/BCG-naive patients.

first: Daniel

last: Hoft

first: Chad

last: Storer

last: Head